TANI-C8(EB).png)
Friday, March 27, 2015
Sunday, March 15, 2015
Alkil Tetraaniline, HT (n=6) : Text Drawing
c-c=c-n-c=c-c-n-c-c=c-n-c=c-c-n-c=c-c-n-c-c-c-c-c-c " | | " " | | " | " " c-c=c c=c-c c-c=c c=c-c c=c-c o
Wednesday, March 11, 2015
Toluene Prodgr
The PDB file (all hydrogens)
The PDB file (polar/aromatic hydrogens)
The PDB file (polar hydrogens)
The PDB file (no hydrogens)
The GROMACS topology
REMARK REMARK REMARK This file was generated by PRODRG version AA100323.0717 REMARK PRODRG written/copyrighted by Daan van Aalten REMARK and Alexander Schuettelkopf REMARK REMARK Questions/comments to dava@davapc1.bioch.dundee.ac.uk REMARK REMARK When using this software in a publication, cite: REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004). REMARK PRODRG - a tool for high-throughput crystallography REMARK of protein-ligand complexes. REMARK Acta Crystallogr. D60, 1355--1363. REMARK REMARK HETATM 1 CAG DRG 1 -7.620 3.400 8.770 1.00 20.00 C HETATM 2 HAG DRG 1 -6.729 2.808 8.977 1.00 20.00 H HETATM 3 HAH DRG 1 -7.326 4.380 8.395 1.00 20.00 H HETATM 4 HAI DRG 1 -8.244 3.492 9.659 1.00 20.00 H HETATM 5 CAC DRG 1 -8.400 2.750 7.810 1.00 20.00 C HETATM 6 CAB DRG 1 -7.960 1.520 7.260 1.00 20.00 C HETATM 7 HAB DRG 1 -7.030 1.060 7.600 1.00 20.00 H HETATM 8 CAA DRG 1 -8.740 0.870 6.280 1.00 20.00 C HETATM 9 HAA DRG 1 -8.410 -0.070 5.850 1.00 20.00 H HETATM 10 CAD DRG 1 -9.950 1.460 5.860 1.00 20.00 C HETATM 11 HAD DRG 1 -10.550 0.960 5.100 1.00 20.00 H HETATM 12 CAE DRG 1 -10.400 2.690 6.400 1.00 20.00 C HETATM 13 HAE DRG 1 -11.340 3.130 6.070 1.00 20.00 H HETATM 14 CAF DRG 1 -9.620 3.340 7.380 1.00 20.00 C HETATM 15 HAF DRG 1 -9.960 4.280 7.800 1.00 20.00 H CONECT 1 2 3 4 5 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 6 14 CONECT 6 5 7 8 CONECT 7 6 CONECT 8 6 9 10 CONECT 9 8 CONECT 10 8 11 12 CONECT 11 10 CONECT 12 10 13 14 CONECT 13 12 CONECT 14 5 12 15 CONECT 15 14 END
The PDB file (polar/aromatic hydrogens)
REMARK REMARK REMARK This file was generated by PRODRG version AA100323.0717 REMARK PRODRG written/copyrighted by Daan van Aalten REMARK and Alexander Schuettelkopf REMARK REMARK Questions/comments to dava@davapc1.bioch.dundee.ac.uk REMARK REMARK When using this software in a publication, cite: REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004). REMARK PRODRG - a tool for high-throughput crystallography REMARK of protein-ligand complexes. REMARK Acta Crystallogr. D60, 1355--1363. REMARK REMARK HETATM 1 CAG DRG 1 -7.620 3.400 8.770 1.00 20.00 C HETATM 2 CAC DRG 1 -8.400 2.750 7.810 1.00 20.00 C HETATM 3 CAB DRG 1 -7.960 1.520 7.260 1.00 20.00 C HETATM 4 HAB DRG 1 -7.030 1.060 7.600 1.00 20.00 H HETATM 5 CAA DRG 1 -8.740 0.870 6.280 1.00 20.00 C HETATM 6 HAA DRG 1 -8.410 -0.070 5.850 1.00 20.00 H HETATM 7 CAD DRG 1 -9.950 1.460 5.860 1.00 20.00 C HETATM 8 HAD DRG 1 -10.550 0.960 5.100 1.00 20.00 H HETATM 9 CAE DRG 1 -10.400 2.690 6.400 1.00 20.00 C HETATM 10 HAE DRG 1 -11.340 3.130 6.070 1.00 20.00 H HETATM 11 CAF DRG 1 -9.620 3.340 7.380 1.00 20.00 C HETATM 12 HAF DRG 1 -9.960 4.280 7.800 1.00 20.00 H CONECT 1 2 CONECT 2 1 3 11 CONECT 3 2 4 5 CONECT 4 3 CONECT 5 3 6 7 CONECT 6 5 CONECT 7 5 8 9 CONECT 8 7 CONECT 9 7 10 11 CONECT 10 9 CONECT 11 2 9 12 CONECT 12 11 END
The PDB file (polar hydrogens)
REMARK REMARK REMARK This file was generated by PRODRG version AA100323.0717 REMARK PRODRG written/copyrighted by Daan van Aalten REMARK and Alexander Schuettelkopf REMARK REMARK Questions/comments to dava@davapc1.bioch.dundee.ac.uk REMARK REMARK When using this software in a publication, cite: REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004). REMARK PRODRG - a tool for high-throughput crystallography REMARK of protein-ligand complexes. REMARK Acta Crystallogr. D60, 1355--1363. REMARK REMARK HETATM 1 CAG DRG 1 -7.620 3.400 8.770 1.00 20.00 C HETATM 2 CAC DRG 1 -8.400 2.750 7.810 1.00 20.00 C HETATM 3 CAB DRG 1 -7.960 1.520 7.260 1.00 20.00 C HETATM 4 CAA DRG 1 -8.740 0.870 6.280 1.00 20.00 C HETATM 5 CAD DRG 1 -9.950 1.460 5.860 1.00 20.00 C HETATM 6 CAE DRG 1 -10.400 2.690 6.400 1.00 20.00 C HETATM 7 CAF DRG 1 -9.620 3.340 7.380 1.00 20.00 C CONECT 1 2 CONECT 2 1 3 7 CONECT 3 2 4 CONECT 4 3 5 CONECT 5 4 6 CONECT 6 5 7 CONECT 7 2 6 END
The PDB file (no hydrogens)
REMARK REMARK REMARK This file was generated by PRODRG version AA100323.0717 REMARK PRODRG written/copyrighted by Daan van Aalten REMARK and Alexander Schuettelkopf REMARK REMARK Questions/comments to dava@davapc1.bioch.dundee.ac.uk REMARK REMARK When using this software in a publication, cite: REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004). REMARK PRODRG - a tool for high-throughput crystallography REMARK of protein-ligand complexes. REMARK Acta Crystallogr. D60, 1355--1363. REMARK REMARK HETATM 1 CAG DRG 1 -7.620 3.400 8.770 1.00 20.00 C HETATM 2 CAC DRG 1 -8.400 2.750 7.810 1.00 20.00 C HETATM 3 CAB DRG 1 -7.960 1.520 7.260 1.00 20.00 C HETATM 4 CAA DRG 1 -8.740 0.870 6.280 1.00 20.00 C HETATM 5 CAD DRG 1 -9.950 1.460 5.860 1.00 20.00 C HETATM 6 CAE DRG 1 -10.400 2.690 6.400 1.00 20.00 C HETATM 7 CAF DRG 1 -9.620 3.340 7.380 1.00 20.00 C CONECT 1 2 CONECT 2 1 3 7 CONECT 3 2 4 CONECT 4 3 5 CONECT 5 4 6 CONECT 6 5 7 CONECT 7 2 6 END
The GROMACS topology
;
;
; This file was generated by PRODRG version AA100323.0717
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to dava@davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAG 1 0.040 15.0350
2 C 1 DRG CAC 1 -0.020 12.0110
3 CR1 1 DRG CAB 1 -0.012 12.0110
4 HC 1 DRG HAB 1 0.008 1.0080
5 CR1 1 DRG CAA 1 -0.012 12.0110
6 HC 1 DRG HAA 1 0.008 1.0080
7 CR1 1 DRG CAD 1 -0.012 12.0110
8 HC 1 DRG HAD 1 0.008 1.0080
9 CR1 1 DRG CAE 1 -0.012 12.0110
10 HC 1 DRG HAE 1 0.008 1.0080
11 CR1 1 DRG CAF 1 -0.012 12.0110
12 HC 1 DRG HAF 1 0.008 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.139 8660000.0 0.139 8660000.0 ; CAC CAG
2 3 2 0.139 10800000.0 0.139 10800000.0 ; CAC CAB
2 11 2 0.139 10800000.0 0.139 10800000.0 ; CAC CAF
3 4 2 0.109 12300000.0 0.109 12300000.0 ; CAB HAB
3 5 2 0.139 10800000.0 0.139 10800000.0 ; CAB CAA
5 6 2 0.109 12300000.0 0.109 12300000.0 ; CAA HAA
5 7 2 0.139 10800000.0 0.139 10800000.0 ; CAA CAD
7 8 2 0.109 12300000.0 0.109 12300000.0 ; CAD HAD
7 9 2 0.139 10800000.0 0.139 10800000.0 ; CAD CAE
9 10 2 0.109 12300000.0 0.109 12300000.0 ; CAE HAE
9 11 2 0.139 10800000.0 0.139 10800000.0 ; CAE CAF
11 12 2 0.109 12300000.0 0.109 12300000.0 ; CAF HAF
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CAG HAB
1 5 1 ; CAG CAA
1 9 1 ; CAG CAE
1 12 1 ; CAG HAF
2 6 1 ; CAC HAA
2 7 1 ; CAC CAD
2 10 1 ; CAC HAE
3 8 1 ; CAB HAD
3 9 1 ; CAB CAE
3 12 1 ; CAB HAF
4 6 1 ; HAB HAA
4 7 1 ; HAB CAD
4 11 1 ; HAB CAF
5 10 1 ; CAA HAE
5 11 1 ; CAA CAF
6 8 1 ; HAA HAD
6 9 1 ; HAA CAE
7 12 1 ; CAD HAF
8 10 1 ; HAD HAE
8 11 1 ; HAD CAF
10 12 1 ; HAE HAF
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 120.0 560.0 120.0 560.0 ; CAG CAC CAB
1 2 11 2 120.0 560.0 120.0 560.0 ; CAG CAC CAF
3 2 11 2 120.0 560.0 120.0 560.0 ; CAB CAC CAF
2 3 4 2 120.0 505.0 120.0 505.0 ; CAC CAB HAB
2 3 5 2 120.0 505.0 120.0 505.0 ; CAC CAB CAA
4 3 5 2 120.0 505.0 120.0 505.0 ; HAB CAB CAA
3 5 6 2 120.0 505.0 120.0 505.0 ; CAB CAA HAA
3 5 7 2 120.0 505.0 120.0 505.0 ; CAB CAA CAD
6 5 7 2 120.0 505.0 120.0 505.0 ; HAA CAA CAD
5 7 8 2 120.0 505.0 120.0 505.0 ; CAA CAD HAD
5 7 9 2 120.0 505.0 120.0 505.0 ; CAA CAD CAE
8 7 9 2 120.0 505.0 120.0 505.0 ; HAD CAD CAE
7 9 10 2 120.0 505.0 120.0 505.0 ; CAD CAE HAE
7 9 11 2 120.0 505.0 120.0 505.0 ; CAD CAE CAF
10 9 11 2 120.0 505.0 120.0 505.0 ; HAE CAE CAF
2 11 9 2 120.0 505.0 120.0 505.0 ; CAC CAF CAE
2 11 12 2 120.0 505.0 120.0 505.0 ; CAC CAF HAF
9 11 12 2 120.0 505.0 120.0 505.0 ; CAE CAF HAF
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 11 3 2 0.0 167.4 0.0 167.4 ; imp CAC CAG CAF CAB
3 2 5 4 2 0.0 167.4 0.0 167.4 ; imp CAB CAC CAA HAB
5 3 7 6 2 0.0 167.4 0.0 167.4 ; imp CAA CAB CAD HAA
7 5 9 8 2 0.0 167.4 0.0 167.4 ; imp CAD CAA CAE HAD
9 7 11 10 2 0.0 167.4 0.0 167.4 ; imp CAE CAD CAF HAE
11 2 9 12 2 0.0 167.4 0.0 167.4 ; imp CAF CAC CAE HAF
2 3 5 7 2 0.0 209.3 0.0 209.3 ; imp CAC CAB CAA CAD
3 5 7 9 2 0.0 209.3 0.0 209.3 ; imp CAB CAA CAD CAE
5 7 9 11 2 0.0 209.3 0.0 209.3 ; imp CAA CAD CAE CAF
7 9 11 2 2 0.0 209.3 0.0 209.3 ; imp CAD CAE CAF CAC
9 11 2 3 2 0.0 209.3 0.0 209.3 ; imp CAE CAF CAC CAB
11 2 3 5 2 0.0 209.3 0.0 209.3 ; imp CAF CAC CAB CAA
Friday, March 06, 2015
Steps to Perform a Simulation
Below is presented a generalised procedure for performing a simulation. The exact steps and processes involved will vary depending on exactly what is being attempted. Use as a general guide only!
- Clearly identify the property / phenomena of interest to be studied by performing the simulation. Do not continue further until you are clear on this!
- Select the appropriate tools to be able to perform the simulation and observe the property / phenomena of interest. It is important to read and familiarise yourself with publications by other researchers on similar systems. Tools include:
- software to perform the simulation with, consideration of force field may influence this decision.
- force field which describes how the atoms / particles within the system interact with each other. Select one that is appropriate for the system being studied and the property / phenomena of interest. Very important and non-trivial step! Consider now how you will analyze your simulation data to make your observations. - Obtain / generate the initial coordinate file for each molecule to be placed within the system. The page linked there has some software suggestions.
- Generate the raw starting structure for the system by placing the molecules within the coordinate file as appropriate. Molecules may be specifically placed or arranged randomly.
- Obtain / generate the topology file for the system, using (for example)
- pdb2gmx,
- SwissParam (for CHARMM forcefield),
- PRODRG (for ffgmx/GROMOS96 43A1),
- Automated Topology Builder (for GROMOS96 53A6),
- MKTOP (for OPLS/AA) or
- your favourite text editor in concert with chapter 5 of theGROMACS Manual.
- For the AMBER force fields, antechamber or acpype might be appropriate. - Describe a simulation box (e.g. using editconf) whose size is appropriate for the eventual density you would like, fill it with solvent (e.g. using genbox), and add any counter-ions needed to neutralize the system (e.g. using grompp and genion). In these steps you may need to edit your topology file to stay current with your coordinate file.
- Run an energy minimization on the system (using grompp and mdrun). This is required to sort out any bad starting structures caused during generation of the system, which may cause the production simulation to crash. It may be necessary also to minimize your solute structure in vacuo before introducing solvent molecules (or your lipid bilayer or whatever else). You should consider using flexible water models and not using bond constraints or frozen groups. The use of position restraints and/or distance restraints should be evaluated carefully.
- Select the appropriate simulation parameters for the equilibration simulation (defined in .mdp file). You need to choose simulation parameters that are consistent with how force field was derived. You may need to simulate at NVT with position restraints on your solvent and/or solute to get the temperature almost right, then relax to NPT to fix the density (which should be done with Berendsen until after the density is stabilized, before a further switch to a barostat that produces the correct ensemble), then move further (if needed) to reach your production simulation ensemble (e.g. NVT, NVE). If you have problems here with the system blowing up, consider using the suggestions on that page, e.g. position restraints on solutes, or not using bond constraints, or using smaller integration timesteps, or several gentler heating stage(s).
- Run the equilibration simulation for sufficient time so that the system relaxes sufficiently in the target ensemble to allow the production run to be commenced (using grompp and mdrun, then g_energy and trajectory visualization tools).
- Select the appropriate simulation parameters for the production simulation (defined in .mdp file). In particular, be careful not to re-generate the velocities. You still need to be consistent with how the force field was derived and how to measure the property / phenomena of interest.
- Run the production simulation for sufficient time so that property / phenomena of interest can be observed in required detail (using grompp / tpbconv and mdrun).
- Analyse / visualise the resulting trajectory and data files to obtain information on the property / phenomena of interest.
Thursday, March 05, 2015
Fatal error: Atomtype SDMSO not found
Fatal error:
Atomtype SDMSO not found
Error was deleted by changing SDMSO into SDmso in the itp file, obtained from the site of topology calculation PRODRG.
Atomtype SDMSO not found
Error was deleted by changing SDMSO into SDmso in the itp file, obtained from the site of topology calculation PRODRG.
25 SDMSO 1 AMO SAB 6 1.652 32.0600
topol.top
; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Wed Mar 04 23:33:55 2015 ; ; This is your topology file ; "Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp Fiction) ; ; Include forcefield parameters #include "ffG43a1.itp" #include "AMO.ITP" [ system ] AMO 4 [ molecules ] AMO 4
AMO.itp
;
;
; This file was generated by PRODRG version AA100323.0717
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to dava@davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
AMO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 AMO CBE 1 -0.011 15.0350
2 CH2 1 AMO CBD 1 0.011 14.0270
3 CH2 1 AMO CBC 2 0.000 14.0270
4 CH2 1 AMO CBB 2 0.000 14.0270
5 CH2 1 AMO CBA 2 0.001 14.0270
6 CH2 1 AMO CAZ 2 -0.001 14.0270
7 CH2 1 AMO CAY 3 0.000 14.0270
8 CH2 1 AMO CAX 3 0.002 14.0270
9 CH2 1 AMO CAW 3 0.000 14.0270
10 CH2 1 AMO CAV 3 0.000 14.0270
11 CH2 1 AMO CAU 3 0.000 14.0270
12 CH2 1 AMO CAT 3 -0.001 14.0270
13 CH2 1 AMO CAS 3 -0.001 14.0270
14 CH2 1 AMO CAR 4 0.037 14.0270
15 CH2 1 AMO CAQ 4 0.038 14.0270
16 CH2 1 AMO CAP 4 0.038 14.0270
17 CH2 1 AMO CAO 4 0.036 14.0270
18 CH2 1 AMO CAN 4 0.038 14.0270
19 C 1 AMO CAL 4 0.219 12.0110
20 O 1 AMO OAM 4 -0.406 15.9994
21 C 1 AMO CAJ 5 -0.002 12.0110
22 CR1 1 AMO CAK 5 -0.002 12.0110
23 HC 1 AMO HAK 5 0.006 1.0080
24 C 1 AMO CAE 5 -0.002 12.0110
25 SDMSO 1 AMO SAB 6 1.652 32.0600
26 OM 1 AMO OAC 6 -0.569 15.9994
27 OM 1 AMO OAD 6 -0.569 15.9994
28 OM 1 AMO OAA 6 -0.569 15.9994
29 CR1 1 AMO CAI 6 -0.015 12.0110
30 HC 1 AMO HAI 6 0.001 1.0080
31 CR1 1 AMO CAG 6 -0.016 12.0110
32 HC 1 AMO HAG 6 0.001 1.0080
33 C 1 AMO CAF 6 0.084 12.0110
34 N 1 AMO NAH 7 0.032 14.0067
35 H 1 AMO HAH 7 -0.027 1.0080
36 C 1 AMO CBF 7 0.032 12.0110
37 CR1 1 AMO CBJ 7 -0.037 12.0110
38 HC 1 AMO HBQ 7 0.000 1.0080
39 CR1 1 AMO CBK 8 -0.021 12.0110
40 HC 1 AMO HBR 8 0.001 1.0080
41 CR1 1 AMO CBG 8 -0.020 12.0110
42 HC 1 AMO HBO 8 0.000 1.0080
43 CR1 1 AMO CBH 8 -0.021 12.0110
44 HC 1 AMO HBP 8 0.001 1.0080
45 C 1 AMO CBI 8 0.060 12.0110
46 N 1 AMO NBL 9 0.044 14.0067
47 H 1 AMO HBZ 9 -0.020 1.0080
48 C 1 AMO CBM 9 0.044 12.0110
49 CR1 1 AMO CBO 9 -0.028 12.0110
50 HC 1 AMO HBT 9 0.000 1.0080
51 C 1 AMO CBP 9 -0.040 12.0110
52 SDMSO 1 AMO SCA 10 1.652 32.0600
53 OM 1 AMO OCC 10 -0.569 15.9994
54 OM 1 AMO OCD 10 -0.569 15.9994
55 OM 1 AMO OCB 10 -0.569 15.9994
56 CR1 1 AMO CBN 10 -0.015 12.0110
57 HC 1 AMO HBS 10 0.001 1.0080
58 CR1 1 AMO CBR 10 -0.016 12.0110
59 HC 1 AMO HBU 10 0.001 1.0080
60 C 1 AMO CBQ 10 0.084 12.0110
61 N 1 AMO NBS 11 0.032 14.0067
62 H 1 AMO HB0 11 -0.027 1.0080
63 C 1 AMO CBT 11 0.032 12.0110
64 CR1 1 AMO CBU 11 -0.037 12.0110
65 HC 1 AMO HBV 11 0.000 1.0080
66 CR1 1 AMO CBV 12 -0.019 12.0110
67 HC 1 AMO HBW 12 0.001 1.0080
68 C 1 AMO CBW 12 0.064 12.0110
69 NT 1 AMO NBZ 12 0.019 14.0067
70 H 1 AMO HB2 12 -0.014 1.0080
71 H 1 AMO HB1 12 -0.014 1.0080
72 CR1 1 AMO CBY 12 -0.020 12.0110
73 HC 1 AMO HBY 12 0.001 1.0080
74 CR1 1 AMO CBX 12 -0.019 12.0110
75 HC 1 AMO HBX 12 0.001 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.153 7150000.0 0.153 7150000.0 ; CBD CBE
2 3 2 0.153 7150000.0 0.153 7150000.0 ; CBD CBC
3 4 2 0.153 7150000.0 0.153 7150000.0 ; CBC CBB
4 5 2 0.153 7150000.0 0.153 7150000.0 ; CBB CBA
5 6 2 0.153 7150000.0 0.153 7150000.0 ; CBA CAZ
6 7 2 0.153 7150000.0 0.153 7150000.0 ; CAZ CAY
7 8 2 0.153 7150000.0 0.153 7150000.0 ; CAY CAX
8 9 2 0.153 7150000.0 0.153 7150000.0 ; CAX CAW
9 10 2 0.153 7150000.0 0.153 7150000.0 ; CAW CAV
10 11 2 0.153 7150000.0 0.153 7150000.0 ; CAV CAU
11 12 2 0.153 7150000.0 0.153 7150000.0 ; CAU CAT
12 13 2 0.153 7150000.0 0.153 7150000.0 ; CAT CAS
13 14 2 0.153 7150000.0 0.153 7150000.0 ; CAS CAR
14 15 2 0.153 7150000.0 0.153 7150000.0 ; CAR CAQ
15 16 2 0.153 7150000.0 0.153 7150000.0 ; CAQ CAP
16 17 2 0.153 7150000.0 0.153 7150000.0 ; CAP CAO
17 18 2 0.153 7150000.0 0.153 7150000.0 ; CAO CAN
19 18 2 0.153 7150000.0 0.153 7150000.0 ; CAL CAN
19 20 2 0.123 16600000.0 0.123 16600000.0 ; CAL OAM
21 19 2 0.139 10800000.0 0.139 10800000.0 ; CAJ CAL
21 22 2 0.139 10800000.0 0.139 10800000.0 ; CAJ CAK
21 29 2 0.139 10800000.0 0.139 10800000.0 ; CAJ CAI
22 23 2 0.109 12300000.0 0.109 12300000.0 ; CAK HAK
24 22 2 0.139 10800000.0 0.139 10800000.0 ; CAE CAK
24 25 2 0.175 2619184.0 0.175 2619184.0 ; CAE SAB
24 33 2 0.139 10800000.0 0.139 10800000.0 ; CAE CAF
25 26 2 0.153 8040000.0 0.153 8040000.0 ; SAB OAC
25 27 2 0.153 8040000.0 0.153 8040000.0 ; SAB OAD
25 28 2 0.153 8040000.0 0.153 8040000.0 ; SAB OAA
29 30 2 0.109 12300000.0 0.109 12300000.0 ; CAI HAI
29 31 2 0.139 10800000.0 0.139 10800000.0 ; CAI CAG
31 32 2 0.109 12300000.0 0.109 12300000.0 ; CAG HAG
33 31 2 0.139 10800000.0 0.139 10800000.0 ; CAF CAG
33 34 2 0.133 10600000.0 0.133 10600000.0 ; CAF NAH
34 35 2 0.100 18700000.0 0.100 18700000.0 ; NAH HAH
36 34 2 0.133 10600000.0 0.133 10600000.0 ; CBF NAH
36 37 2 0.139 10800000.0 0.139 10800000.0 ; CBF CBJ
36 41 2 0.139 10800000.0 0.139 10800000.0 ; CBF CBG
37 38 2 0.109 12300000.0 0.109 12300000.0 ; CBJ HBQ
37 39 2 0.139 10800000.0 0.139 10800000.0 ; CBJ CBK
39 40 2 0.109 12300000.0 0.109 12300000.0 ; CBK HBR
45 39 2 0.139 10800000.0 0.139 10800000.0 ; CBI CBK
41 42 2 0.109 12300000.0 0.109 12300000.0 ; CBG HBO
41 43 2 0.139 10800000.0 0.139 10800000.0 ; CBG CBH
43 44 2 0.109 12300000.0 0.109 12300000.0 ; CBH HBP
45 43 2 0.139 10800000.0 0.139 10800000.0 ; CBI CBH
45 46 2 0.133 10600000.0 0.133 10600000.0 ; CBI NBL
46 47 2 0.100 18700000.0 0.100 18700000.0 ; NBL HBZ
48 46 2 0.133 10600000.0 0.133 10600000.0 ; CBM NBL
48 49 2 0.139 10800000.0 0.139 10800000.0 ; CBM CBO
48 56 2 0.139 10800000.0 0.139 10800000.0 ; CBM CBN
49 50 2 0.109 12300000.0 0.109 12300000.0 ; CBO HBT
51 49 2 0.139 10800000.0 0.139 10800000.0 ; CBP CBO
51 52 2 0.175 2619184.0 0.175 2619184.0 ; CBP SCA
51 60 2 0.139 10800000.0 0.139 10800000.0 ; CBP CBQ
52 53 2 0.153 8040000.0 0.153 8040000.0 ; SCA OCC
52 54 2 0.153 8040000.0 0.153 8040000.0 ; SCA OCD
52 55 2 0.153 8040000.0 0.153 8040000.0 ; SCA OCB
56 57 2 0.109 12300000.0 0.109 12300000.0 ; CBN HBS
56 58 2 0.139 10800000.0 0.139 10800000.0 ; CBN CBR
58 59 2 0.109 12300000.0 0.109 12300000.0 ; CBR HBU
60 58 2 0.139 10800000.0 0.139 10800000.0 ; CBQ CBR
60 61 2 0.133 10600000.0 0.133 10600000.0 ; CBQ NBS
61 62 2 0.100 18700000.0 0.100 18700000.0 ; NBS HB0
63 61 2 0.133 10600000.0 0.133 10600000.0 ; CBT NBS
63 64 2 0.139 10800000.0 0.139 10800000.0 ; CBT CBU
63 74 2 0.139 10800000.0 0.139 10800000.0 ; CBT CBX
64 65 2 0.109 12300000.0 0.109 12300000.0 ; CBU HBV
64 66 2 0.139 10800000.0 0.139 10800000.0 ; CBU CBV
66 67 2 0.109 12300000.0 0.109 12300000.0 ; CBV HBW
68 66 2 0.139 10800000.0 0.139 10800000.0 ; CBW CBV
68 69 2 0.133 10600000.0 0.133 10600000.0 ; CBW NBZ
68 72 2 0.139 10800000.0 0.139 10800000.0 ; CBW CBY
69 70 2 0.100 18700000.0 0.100 18700000.0 ; NBZ HB2
69 71 2 0.100 18700000.0 0.100 18700000.0 ; NBZ HB1
72 73 2 0.109 12300000.0 0.109 12300000.0 ; CBY HBY
72 74 2 0.139 10800000.0 0.139 10800000.0 ; CBY CBX
74 75 2 0.109 12300000.0 0.109 12300000.0 ; CBX HBX
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CBE CBB
2 5 1 ; CBD CBA
3 6 1 ; CBC CAZ
4 7 1 ; CBB CAY
5 8 1 ; CBA CAX
6 9 1 ; CAZ CAW
7 10 1 ; CAY CAV
8 11 1 ; CAX CAU
9 12 1 ; CAW CAT
10 13 1 ; CAV CAS
11 14 1 ; CAU CAR
12 15 1 ; CAT CAQ
13 16 1 ; CAS CAP
14 17 1 ; CAR CAO
15 18 1 ; CAQ CAN
16 19 1 ; CAP CAL
17 20 1 ; CAO OAM
17 21 1 ; CAO CAJ
18 22 1 ; CAN CAK
18 29 1 ; CAN CAI
19 23 1 ; CAL HAK
19 24 1 ; CAL CAE
19 30 1 ; CAL HAI
19 31 1 ; CAL CAG
20 22 1 ; OAM CAK
20 29 1 ; OAM CAI
21 25 1 ; CAJ SAB
21 32 1 ; CAJ HAG
21 33 1 ; CAJ CAF
22 26 1 ; CAK OAC
22 27 1 ; CAK OAD
22 28 1 ; CAK OAA
22 30 1 ; CAK HAI
22 31 1 ; CAK CAG
22 34 1 ; CAK NAH
23 25 1 ; HAK SAB
23 29 1 ; HAK CAI
23 33 1 ; HAK CAF
24 29 1 ; CAE CAI
24 32 1 ; CAE HAG
24 35 1 ; CAE HAH
24 36 1 ; CAE CBF
25 31 1 ; SAB CAG
25 34 1 ; SAB NAH
26 33 1 ; OAC CAF
27 33 1 ; OAD CAF
28 33 1 ; OAA CAF
29 34 1 ; CAI NAH
30 32 1 ; HAI HAG
30 33 1 ; HAI CAF
31 35 1 ; CAG HAH
31 36 1 ; CAG CBF
32 34 1 ; HAG NAH
33 37 1 ; CAF CBJ
33 41 1 ; CAF CBG
34 38 1 ; NAH HBQ
34 39 1 ; NAH CBK
34 42 1 ; NAH HBO
34 43 1 ; NAH CBH
35 37 1 ; HAH CBJ
35 41 1 ; HAH CBG
36 40 1 ; CBF HBR
36 44 1 ; CBF HBP
36 45 1 ; CBF CBI
37 42 1 ; CBJ HBO
37 43 1 ; CBJ CBH
37 46 1 ; CBJ NBL
38 40 1 ; HBQ HBR
38 41 1 ; HBQ CBG
38 45 1 ; HBQ CBI
39 41 1 ; CBK CBG
39 44 1 ; CBK HBP
39 47 1 ; CBK HBZ
39 48 1 ; CBK CBM
40 43 1 ; HBR CBH
40 46 1 ; HBR NBL
41 46 1 ; CBG NBL
42 44 1 ; HBO HBP
42 45 1 ; HBO CBI
43 47 1 ; CBH HBZ
43 48 1 ; CBH CBM
44 46 1 ; HBP NBL
45 49 1 ; CBI CBO
45 56 1 ; CBI CBN
46 50 1 ; NBL HBT
46 51 1 ; NBL CBP
46 57 1 ; NBL HBS
46 58 1 ; NBL CBR
47 49 1 ; HBZ CBO
47 56 1 ; HBZ CBN
48 52 1 ; CBM SCA
48 59 1 ; CBM HBU
48 60 1 ; CBM CBQ
49 53 1 ; CBO OCC
49 54 1 ; CBO OCD
49 55 1 ; CBO OCB
49 57 1 ; CBO HBS
49 58 1 ; CBO CBR
49 61 1 ; CBO NBS
50 52 1 ; HBT SCA
50 56 1 ; HBT CBN
50 60 1 ; HBT CBQ
51 56 1 ; CBP CBN
51 59 1 ; CBP HBU
51 62 1 ; CBP HB0
51 63 1 ; CBP CBT
52 58 1 ; SCA CBR
52 61 1 ; SCA NBS
53 60 1 ; OCC CBQ
54 60 1 ; OCD CBQ
55 60 1 ; OCB CBQ
56 61 1 ; CBN NBS
57 59 1 ; HBS HBU
57 60 1 ; HBS CBQ
58 62 1 ; CBR HB0
58 63 1 ; CBR CBT
59 61 1 ; HBU NBS
60 64 1 ; CBQ CBU
60 74 1 ; CBQ CBX
61 65 1 ; NBS HBV
61 66 1 ; NBS CBV
61 72 1 ; NBS CBY
61 75 1 ; NBS HBX
62 64 1 ; HB0 CBU
62 74 1 ; HB0 CBX
63 67 1 ; CBT HBW
63 68 1 ; CBT CBW
63 73 1 ; CBT HBY
64 69 1 ; CBU NBZ
64 72 1 ; CBU CBY
64 75 1 ; CBU HBX
65 67 1 ; HBV HBW
65 68 1 ; HBV CBW
65 74 1 ; HBV CBX
66 70 1 ; CBV HB2
66 71 1 ; CBV HB1
66 73 1 ; CBV HBY
66 74 1 ; CBV CBX
67 69 1 ; HBW NBZ
67 72 1 ; HBW CBY
68 75 1 ; CBW HBX
69 73 1 ; NBZ HBY
69 74 1 ; NBZ CBX
70 72 1 ; HB2 CBY
71 72 1 ; HB1 CBY
73 75 1 ; HBY HBX
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 520.0 109.5 520.0 ; CBE CBD CBC
2 3 4 2 109.5 520.0 109.5 520.0 ; CBD CBC CBB
3 4 5 2 109.5 520.0 109.5 520.0 ; CBC CBB CBA
4 5 6 2 109.5 520.0 109.5 520.0 ; CBB CBA CAZ
5 6 7 2 109.5 520.0 109.5 520.0 ; CBA CAZ CAY
6 7 8 2 109.5 520.0 109.5 520.0 ; CAZ CAY CAX
7 8 9 2 109.5 520.0 109.5 520.0 ; CAY CAX CAW
8 9 10 2 109.5 520.0 109.5 520.0 ; CAX CAW CAV
9 10 11 2 109.5 520.0 109.5 520.0 ; CAW CAV CAU
10 11 12 2 109.5 520.0 109.5 520.0 ; CAV CAU CAT
11 12 13 2 109.5 520.0 109.5 520.0 ; CAU CAT CAS
12 13 14 2 109.5 520.0 109.5 520.0 ; CAT CAS CAR
13 14 15 2 109.5 520.0 109.5 520.0 ; CAS CAR CAQ
14 15 16 2 109.5 520.0 109.5 520.0 ; CAR CAQ CAP
15 16 17 2 109.5 520.0 109.5 520.0 ; CAQ CAP CAO
16 17 18 2 109.5 520.0 109.5 520.0 ; CAP CAO CAN
17 18 19 2 109.5 520.0 109.5 520.0 ; CAO CAN CAL
18 19 20 2 121.0 685.0 121.0 685.0 ; CAN CAL OAM
18 19 21 2 115.0 610.0 115.0 610.0 ; CAN CAL CAJ
20 19 21 2 121.0 685.0 121.0 685.0 ; OAM CAL CAJ
19 21 22 2 120.0 560.0 120.0 560.0 ; CAL CAJ CAK
19 21 29 2 120.0 560.0 120.0 560.0 ; CAL CAJ CAI
22 21 29 2 120.0 560.0 120.0 560.0 ; CAK CAJ CAI
21 22 23 2 120.0 505.0 120.0 505.0 ; CAJ CAK HAK
21 22 24 2 120.0 505.0 120.0 505.0 ; CAJ CAK CAE
23 22 24 2 120.0 505.0 120.0 505.0 ; HAK CAK CAE
22 24 25 2 120.0 560.0 120.0 560.0 ; CAK CAE SAB
22 24 33 2 120.0 560.0 120.0 560.0 ; CAK CAE CAF
25 24 33 2 120.0 560.0 120.0 560.0 ; SAB CAE CAF
24 25 26 2 109.5 518.0 109.5 518.0 ; CAE SAB OAC
24 25 27 2 109.5 518.0 109.5 518.0 ; CAE SAB OAD
24 25 28 2 109.5 518.0 109.5 518.0 ; CAE SAB OAA
26 25 27 2 109.5 518.0 109.5 518.0 ; OAC SAB OAD
26 25 28 2 109.5 518.0 109.5 518.0 ; OAC SAB OAA
27 25 28 2 109.5 518.0 109.5 518.0 ; OAD SAB OAA
21 29 30 2 120.0 505.0 120.0 505.0 ; CAJ CAI HAI
21 29 31 2 120.0 505.0 120.0 505.0 ; CAJ CAI CAG
30 29 31 2 120.0 505.0 120.0 505.0 ; HAI CAI CAG
29 31 32 2 120.0 505.0 120.0 505.0 ; CAI CAG HAG
29 31 33 2 120.0 505.0 120.0 505.0 ; CAI CAG CAF
32 31 33 2 120.0 505.0 120.0 505.0 ; HAG CAG CAF
24 33 31 2 120.0 560.0 120.0 560.0 ; CAE CAF CAG
24 33 34 2 115.0 610.0 115.0 610.0 ; CAE CAF NAH
31 33 34 2 120.0 560.0 120.0 560.0 ; CAG CAF NAH
33 34 35 2 123.0 415.0 123.0 415.0 ; CAF NAH HAH
33 34 36 2 117.0 635.0 117.0 635.0 ; CAF NAH CBF
35 34 36 2 123.0 415.0 123.0 415.0 ; HAH NAH CBF
34 36 37 2 120.0 560.0 120.0 560.0 ; NAH CBF CBJ
34 36 41 2 120.0 560.0 120.0 560.0 ; NAH CBF CBG
37 36 41 2 120.0 560.0 120.0 560.0 ; CBJ CBF CBG
36 37 38 2 120.0 505.0 120.0 505.0 ; CBF CBJ HBQ
36 37 39 2 120.0 505.0 120.0 505.0 ; CBF CBJ CBK
38 37 39 2 120.0 505.0 120.0 505.0 ; HBQ CBJ CBK
37 39 40 2 120.0 505.0 120.0 505.0 ; CBJ CBK HBR
37 39 45 2 120.0 505.0 120.0 505.0 ; CBJ CBK CBI
40 39 45 2 120.0 505.0 120.0 505.0 ; HBR CBK CBI
36 41 42 2 120.0 505.0 120.0 505.0 ; CBF CBG HBO
36 41 43 2 120.0 505.0 120.0 505.0 ; CBF CBG CBH
42 41 43 2 120.0 505.0 120.0 505.0 ; HBO CBG CBH
41 43 44 2 120.0 505.0 120.0 505.0 ; CBG CBH HBP
41 43 45 2 120.0 505.0 120.0 505.0 ; CBG CBH CBI
44 43 45 2 120.0 505.0 120.0 505.0 ; HBP CBH CBI
39 45 43 2 120.0 560.0 120.0 560.0 ; CBK CBI CBH
39 45 46 2 120.0 560.0 120.0 560.0 ; CBK CBI NBL
43 45 46 2 120.0 560.0 120.0 560.0 ; CBH CBI NBL
45 46 47 2 123.0 415.0 123.0 415.0 ; CBI NBL HBZ
45 46 48 2 117.0 635.0 117.0 635.0 ; CBI NBL CBM
47 46 48 2 123.0 415.0 123.0 415.0 ; HBZ NBL CBM
46 48 49 2 120.0 560.0 120.0 560.0 ; NBL CBM CBO
46 48 56 2 120.0 560.0 120.0 560.0 ; NBL CBM CBN
49 48 56 2 120.0 560.0 120.0 560.0 ; CBO CBM CBN
48 49 50 2 120.0 505.0 120.0 505.0 ; CBM CBO HBT
48 49 51 2 120.0 505.0 120.0 505.0 ; CBM CBO CBP
50 49 51 2 120.0 505.0 120.0 505.0 ; HBT CBO CBP
49 51 52 2 120.0 560.0 120.0 560.0 ; CBO CBP SCA
49 51 60 2 120.0 560.0 120.0 560.0 ; CBO CBP CBQ
52 51 60 2 120.0 560.0 120.0 560.0 ; SCA CBP CBQ
51 52 53 2 109.5 518.0 109.5 518.0 ; CBP SCA OCC
51 52 54 2 109.5 518.0 109.5 518.0 ; CBP SCA OCD
51 52 55 2 109.5 518.0 109.5 518.0 ; CBP SCA OCB
53 52 54 2 109.5 518.0 109.5 518.0 ; OCC SCA OCD
53 52 55 2 109.5 518.0 109.5 518.0 ; OCC SCA OCB
54 52 55 2 109.5 518.0 109.5 518.0 ; OCD SCA OCB
48 56 57 2 120.0 505.0 120.0 505.0 ; CBM CBN HBS
48 56 58 2 120.0 505.0 120.0 505.0 ; CBM CBN CBR
57 56 58 2 120.0 505.0 120.0 505.0 ; HBS CBN CBR
56 58 59 2 120.0 505.0 120.0 505.0 ; CBN CBR HBU
56 58 60 2 120.0 505.0 120.0 505.0 ; CBN CBR CBQ
59 58 60 2 120.0 505.0 120.0 505.0 ; HBU CBR CBQ
51 60 58 2 120.0 560.0 120.0 560.0 ; CBP CBQ CBR
51 60 61 2 115.0 610.0 115.0 610.0 ; CBP CBQ NBS
58 60 61 2 120.0 560.0 120.0 560.0 ; CBR CBQ NBS
60 61 62 2 123.0 415.0 123.0 415.0 ; CBQ NBS HB0
60 61 63 2 117.0 635.0 117.0 635.0 ; CBQ NBS CBT
62 61 63 2 123.0 415.0 123.0 415.0 ; HB0 NBS CBT
61 63 64 2 120.0 560.0 120.0 560.0 ; NBS CBT CBU
61 63 74 2 120.0 560.0 120.0 560.0 ; NBS CBT CBX
64 63 74 2 120.0 560.0 120.0 560.0 ; CBU CBT CBX
63 64 65 2 120.0 505.0 120.0 505.0 ; CBT CBU HBV
63 64 66 2 120.0 505.0 120.0 505.0 ; CBT CBU CBV
65 64 66 2 120.0 505.0 120.0 505.0 ; HBV CBU CBV
64 66 67 2 120.0 505.0 120.0 505.0 ; CBU CBV HBW
64 66 68 2 120.0 505.0 120.0 505.0 ; CBU CBV CBW
67 66 68 2 120.0 505.0 120.0 505.0 ; HBW CBV CBW
66 68 69 2 120.0 560.0 120.0 560.0 ; CBV CBW NBZ
66 68 72 2 120.0 560.0 120.0 560.0 ; CBV CBW CBY
69 68 72 2 120.0 560.0 120.0 560.0 ; NBZ CBW CBY
68 69 70 2 120.0 390.0 120.0 390.0 ; CBW NBZ HB2
68 69 71 2 120.0 390.0 120.0 390.0 ; CBW NBZ HB1
70 69 71 2 120.0 445.0 120.0 445.0 ; HB2 NBZ HB1
68 72 73 2 120.0 505.0 120.0 505.0 ; CBW CBY HBY
68 72 74 2 120.0 505.0 120.0 505.0 ; CBW CBY CBX
73 72 74 2 120.0 505.0 120.0 505.0 ; HBY CBY CBX
63 74 72 2 120.0 505.0 120.0 505.0 ; CBT CBX CBY
63 74 75 2 120.0 505.0 120.0 505.0 ; CBT CBX HBX
72 74 75 2 120.0 505.0 120.0 505.0 ; CBY CBX HBX
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
19 18 20 21 2 0.0 167.4 0.0 167.4 ; imp CAL CAN OAM CAJ
21 19 29 22 2 0.0 167.4 0.0 167.4 ; imp CAJ CAL CAI CAK
22 21 24 23 2 0.0 167.4 0.0 167.4 ; imp CAK CAJ CAE HAK
24 22 25 33 2 0.0 167.4 0.0 167.4 ; imp CAE CAK SAB CAF
25 24 27 26 2 35.3 334.8 35.3 334.8 ; imp SAB CAE OAD OAC
29 21 31 30 2 0.0 167.4 0.0 167.4 ; imp CAI CAJ CAG HAI
31 29 33 32 2 0.0 167.4 0.0 167.4 ; imp CAG CAI CAF HAG
33 34 31 24 2 0.0 167.4 0.0 167.4 ; imp CAF NAH CAG CAE
34 33 35 36 2 0.0 167.4 0.0 167.4 ; imp NAH CAF HAH CBF
36 34 41 37 2 0.0 167.4 0.0 167.4 ; imp CBF NAH CBG CBJ
37 36 39 38 2 0.0 167.4 0.0 167.4 ; imp CBJ CBF CBK HBQ
39 37 45 40 2 0.0 167.4 0.0 167.4 ; imp CBK CBJ CBI HBR
41 36 43 42 2 0.0 167.4 0.0 167.4 ; imp CBG CBF CBH HBO
43 41 45 44 2 0.0 167.4 0.0 167.4 ; imp CBH CBG CBI HBP
45 46 43 39 2 0.0 167.4 0.0 167.4 ; imp CBI NBL CBH CBK
46 45 47 48 2 0.0 167.4 0.0 167.4 ; imp NBL CBI HBZ CBM
48 46 56 49 2 0.0 167.4 0.0 167.4 ; imp CBM NBL CBN CBO
49 48 51 50 2 0.0 167.4 0.0 167.4 ; imp CBO CBM CBP HBT
51 49 52 60 2 0.0 167.4 0.0 167.4 ; imp CBP CBO SCA CBQ
52 51 54 53 2 35.3 334.8 35.3 334.8 ; imp SCA CBP OCD OCC
56 48 58 57 2 0.0 167.4 0.0 167.4 ; imp CBN CBM CBR HBS
58 56 60 59 2 0.0 167.4 0.0 167.4 ; imp CBR CBN CBQ HBU
60 61 58 51 2 0.0 167.4 0.0 167.4 ; imp CBQ NBS CBR CBP
61 60 62 63 2 0.0 167.4 0.0 167.4 ; imp NBS CBQ HB0 CBT
63 61 74 64 2 0.0 167.4 0.0 167.4 ; imp CBT NBS CBX CBU
64 63 66 65 2 0.0 167.4 0.0 167.4 ; imp CBU CBT CBV HBV
66 64 68 67 2 0.0 167.4 0.0 167.4 ; imp CBV CBU CBW HBW
68 72 69 66 2 0.0 167.4 0.0 167.4 ; imp CBW CBY NBZ CBV
69 68 71 70 2 0.0 167.4 0.0 167.4 ; imp NBZ CBW HB1 HB2
72 68 74 73 2 0.0 167.4 0.0 167.4 ; imp CBY CBW CBX HBY
74 63 72 75 2 0.0 167.4 0.0 167.4 ; imp CBX CBT CBY HBX
63 64 66 68 2 0.0 209.3 0.0 209.3 ; imp CBT CBU CBV CBW
64 66 68 72 2 0.0 209.3 0.0 209.3 ; imp CBU CBV CBW CBY
66 68 72 74 2 0.0 209.3 0.0 209.3 ; imp CBV CBW CBY CBX
68 72 74 63 2 0.0 209.3 0.0 209.3 ; imp CBW CBY CBX CBT
72 74 63 64 2 0.0 209.3 0.0 209.3 ; imp CBY CBX CBT CBU
74 63 64 66 2 0.0 209.3 0.0 209.3 ; imp CBX CBT CBU CBV
48 49 51 60 2 0.0 209.3 0.0 209.3 ; imp CBM CBO CBP CBQ
49 51 60 58 2 0.0 209.3 0.0 209.3 ; imp CBO CBP CBQ CBR
51 60 58 56 2 0.0 209.3 0.0 209.3 ; imp CBP CBQ CBR CBN
60 58 56 48 2 0.0 209.3 0.0 209.3 ; imp CBQ CBR CBN CBM
58 56 48 49 2 0.0 209.3 0.0 209.3 ; imp CBR CBN CBM CBO
56 48 49 51 2 0.0 209.3 0.0 209.3 ; imp CBN CBM CBO CBP
36 37 39 45 2 0.0 209.3 0.0 209.3 ; imp CBF CBJ CBK CBI
37 39 45 43 2 0.0 209.3 0.0 209.3 ; imp CBJ CBK CBI CBH
39 45 43 41 2 0.0 209.3 0.0 209.3 ; imp CBK CBI CBH CBG
45 43 41 36 2 0.0 209.3 0.0 209.3 ; imp CBI CBH CBG CBF
43 41 36 37 2 0.0 209.3 0.0 209.3 ; imp CBH CBG CBF CBJ
41 36 37 39 2 0.0 209.3 0.0 209.3 ; imp CBG CBF CBJ CBK
21 22 24 33 2 0.0 209.3 0.0 209.3 ; imp CAJ CAK CAE CAF
22 24 33 31 2 0.0 209.3 0.0 209.3 ; imp CAK CAE CAF CAG
24 33 31 29 2 0.0 209.3 0.0 209.3 ; imp CAE CAF CAG CAI
33 31 29 21 2 0.0 209.3 0.0 209.3 ; imp CAF CAG CAI CAJ
31 29 21 22 2 0.0 209.3 0.0 209.3 ; imp CAG CAI CAJ CAK
29 21 22 24 2 0.0 209.3 0.0 209.3 ; imp CAI CAJ CAK CAE
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CBB CBC CBD CBE
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CBA CBB CBC CBD
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAZ CBA CBB CBC
7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAY CAZ CBA CBB
8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih CAX CAY CAZ CBA
9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAW CAX CAY CAZ
10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih CAV CAW CAX CAY
11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih CAU CAV CAW CAX
12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih CAT CAU CAV CAW
13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih CAS CAT CAU CAV
14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih CAR CAS CAT CAU
15 14 13 12 1 0.0 5.9 3 0.0 5.9 3 ; dih CAQ CAR CAS CAT
16 15 14 13 1 0.0 5.9 3 0.0 5.9 3 ; dih CAP CAQ CAR CAS
17 16 15 14 1 0.0 5.9 3 0.0 5.9 3 ; dih CAO CAP CAQ CAR
18 17 16 15 1 0.0 5.9 3 0.0 5.9 3 ; dih CAN CAO CAP CAQ
19 18 17 16 1 0.0 5.9 3 0.0 5.9 3 ; dih CAL CAN CAO CAP
17 18 19 21 1 0.0 1.0 6 0.0 1.0 6 ; dih CAO CAN CAL CAJ
29 21 19 18 1 180.0 5.9 2 180.0 5.9 2 ; dih CAI CAJ CAL CAN
22 24 25 28 1 0.0 4.2 3 0.0 4.2 3 ; dih CAK CAE SAB OAA
24 33 34 36 1 180.0 33.5 2 180.0 33.5 2 ; dih CAE CAF NAH CBF
41 36 34 33 1 180.0 33.5 2 180.0 33.5 2 ; dih CBG CBF NAH CAF
39 45 46 48 1 180.0 33.5 2 180.0 33.5 2 ; dih CBK CBI NBL CBM
56 48 46 45 1 180.0 33.5 2 180.0 33.5 2 ; dih CBN CBM NBL CBI
49 51 52 55 1 0.0 4.2 3 0.0 4.2 3 ; dih CBO CBP SCA OCB
51 60 61 63 1 180.0 33.5 2 180.0 33.5 2 ; dih CBP CBQ NBS CBT
74 63 61 60 1 180.0 33.5 2 180.0 33.5 2 ; dih CBX CBT NBS CBQ
66 68 69 71 1 180.0 33.5 2 180.0 33.5 2 ; dih CBV CBW NBZ HB1
AMOx4.mdp
; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 250.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no)
AMOx4conf.pdb
HEADER Glycine aRginine prOline Methionine Alanine Cystine Serine REMARK THIS IS A SIMULATION BOX CRYST1 95.137 95.137 95.137 90.00 90.00 90.00 P 1 1 MODEL ATOM 1 CBE AMO S 1 40.976 55.387 19.931 1.00 0.00 ATOM 2 CBD AMO S 1 42.076 55.277 20.981 1.00 0.00 ATOM 3 CBC AMO S 1 41.466 54.917 22.331 1.00 0.00 ATOM 4 CBB AMO S 1 42.576 54.807 23.381 1.00 0.00 ATOM 5 CBA AMO S 1 41.976 54.437 24.731 1.00 0.00 ATOM 6 CAZ AMO S 1 43.106 54.287 25.751 1.00 0.00 ATOM 7 CAY AMO S 1 42.536 53.877 27.111 1.00 0.00 ATOM 8 CAX AMO S 1 43.696 53.677 28.091 1.00 0.00 ATOM 9 CAW AMO S 1 43.166 53.217 29.451 1.00 0.00 ATOM 10 CAV AMO S 1 44.366 52.947 30.361 1.00 0.00 ATOM 11 CAU AMO S 1 43.896 52.427 31.721 1.00 0.00 ATOM 12 CAT AMO S 1 45.136 52.077 32.541 1.00 0.00 ATOM 13 CAS AMO S 1 44.736 51.507 33.911 1.00 0.00 ATOM 14 CAR AMO S 1 46.006 51.097 34.641 1.00 0.00 ATOM 15 CAQ AMO S 1 45.666 50.507 36.011 1.00 0.00 ATOM 16 CAP AMO S 1 46.966 50.047 36.671 1.00 0.00 ATOM 17 CAO AMO S 1 46.686 49.457 38.051 1.00 0.00 ATOM 18 CAN AMO S 1 47.976 48.897 38.681 1.00 0.00 ATOM 19 CAL AMO S 1 48.406 47.577 38.041 1.00 0.00 ATOM 20 OAM AMO S 1 48.906 47.527 36.911 1.00 0.00 ATOM 21 CAJ AMO S 1 48.236 46.407 38.791 1.00 0.00 ATOM 22 CAK AMO S 1 49.346 45.827 39.431 1.00 0.00 ATOM 23 HAK AMO S 1 50.346 46.267 39.301 1.00 0.00 ATOM 24 CAE AMO S 1 49.166 44.697 40.241 1.00 0.00 ATOM 25 SAB AMO S 1 50.616 43.767 40.651 1.00 0.00 ATOM 26 OAC AMO S 1 50.256 42.377 41.181 1.00 0.00 ATOM 27 OAD AMO S 1 51.466 43.597 39.401 1.00 0.00 ATOM 28 OAA AMO S 1 51.406 44.547 41.701 1.00 0.00 ATOM 29 CAI AMO S 1 46.946 45.847 38.951 1.00 0.00 ATOM 30 HAI AMO S 1 46.096 46.267 38.421 1.00 0.00 ATOM 31 CAG AMO S 1 46.766 44.727 39.781 1.00 0.00 ATOM 32 HAG AMO S 1 45.766 44.307 39.891 1.00 0.00 ATOM 33 CAF AMO S 1 47.876 44.167 40.471 1.00 0.00 ATOM 34 NAH AMO S 1 47.686 43.787 41.751 1.00 0.00 ATOM 35 HAH AMO S 1 48.326 44.177 42.421 1.00 0.00 ATOM 36 CBF AMO S 1 46.766 42.927 42.231 1.00 0.00 ATOM 37 CBJ AMO S 1 46.456 43.107 43.591 1.00 0.00 ATOM 38 HBQ AMO S 1 47.056 43.767 44.221 1.00 0.00 ATOM 39 CBK AMO S 1 45.366 42.417 44.161 1.00 0.00 ATOM 40 HBR AMO S 1 45.146 42.547 45.221 1.00 0.00 ATOM 41 CBG AMO S 1 46.006 42.027 41.441 1.00 0.00 ATOM 42 HBO AMO S 1 46.276 41.837 40.401 1.00 0.00 ATOM 43 CBH AMO S 1 44.916 41.337 42.011 1.00 0.00 ATOM 44 HBP AMO S 1 44.326 40.657 41.391 1.00 0.00 ATOM 45 CBI AMO S 1 44.586 41.537 43.381 1.00 0.00 ATOM 46 NBL AMO S 1 43.336 41.337 43.831 1.00 0.00 ATOM 47 HBZ AMO S 1 42.986 41.997 44.501 1.00 0.00 ATOM 48 CBM AMO S 1 42.506 40.337 43.481 1.00 0.00 ATOM 49 CBO AMO S 1 42.946 39.007 43.301 1.00 0.00 ATOM 50 HBT AMO S 1 43.996 38.797 43.121 1.00 0.00 ATOM 51 CBP AMO S 1 42.026 37.937 43.411 1.00 0.00 ATOM 52 SCA AMO S 1 42.566 36.357 42.831 1.00 0.00 ATOM 53 OCC AMO S 1 43.466 35.727 43.891 1.00 0.00 ATOM 54 OCD AMO S 1 41.386 35.427 42.551 1.00 0.00 ATOM 55 OCB AMO S 1 43.336 36.547 41.531 1.00 0.00 ATOM 56 CBN AMO S 1 41.146 40.577 43.761 1.00 0.00 ATOM 57 HBS AMO S 1 40.786 41.597 43.861 1.00 0.00 ATOM 58 CBR AMO S 1 40.226 39.517 43.891 1.00 0.00 ATOM 59 HBU AMO S 1 39.186 39.737 44.121 1.00 0.00 ATOM 60 CBQ AMO S 1 40.676 38.187 43.751 1.00 0.00 ATOM 61 NBS AMO S 1 40.136 37.247 44.551 1.00 0.00 ATOM 62 HB0 AMO S 1 40.786 36.717 45.111 1.00 0.00 ATOM 63 CBT AMO S 1 38.826 36.927 44.691 1.00 0.00 ATOM 64 CBU AMO S 1 38.516 36.187 45.851 1.00 0.00 ATOM 65 HBV AMO S 1 39.296 35.857 46.531 1.00 0.00 ATOM 66 CBV AMO S 1 37.176 35.857 46.131 1.00 0.00 ATOM 67 HBW AMO S 1 36.926 35.287 47.021 1.00 0.00 ATOM 68 CBW AMO S 1 36.156 36.287 45.241 1.00 0.00 ATOM 69 NBZ AMO S 1 34.886 35.987 45.511 1.00 0.00 ATOM 70 HB2 AMO S 1 34.166 36.277 44.891 1.00 0.00 ATOM 71 HB1 AMO S 1 34.666 35.467 46.331 1.00 0.00 ATOM 72 CBY AMO S 1 36.456 37.027 44.081 1.00 0.00 ATOM 73 HBY AMO S 1 35.666 37.347 43.401 1.00 0.00 ATOM 74 CBX AMO S 1 37.796 37.347 43.801 1.00 0.00 ATOM 75 HBX AMO S 1 38.046 37.877 42.881 1.00 0.00 ATOM 76 CBE AMO S 2 55.680 60.867 46.291 1.00 0.00 ATOM 77 CBD AMO S 2 55.699 59.349 46.154 1.00 0.00 ATOM 78 CBC AMO S 2 55.189 58.709 47.441 1.00 0.00 ATOM 79 CBB AMO S 2 55.209 57.184 47.297 1.00 0.00 ATOM 80 CBA AMO S 2 54.690 56.537 48.574 1.00 0.00 ATOM 81 CAZ AMO S 2 54.676 55.019 48.390 1.00 0.00 ATOM 82 CAY AMO S 2 54.121 54.342 49.646 1.00 0.00 ATOM 83 CAX AMO S 2 54.064 52.830 49.405 1.00 0.00 ATOM 84 CAW AMO S 2 53.467 52.123 50.624 1.00 0.00 ATOM 85 CAV AMO S 2 53.350 50.633 50.298 1.00 0.00 ATOM 86 CAU AMO S 2 52.703 49.882 51.464 1.00 0.00 ATOM 87 CAT AMO S 2 52.518 48.428 51.037 1.00 0.00 ATOM 88 CAS AMO S 2 51.832 47.620 52.151 1.00 0.00 ATOM 89 CAR AMO S 2 51.596 46.209 51.634 1.00 0.00 ATOM 90 CAQ AMO S 2 50.900 45.361 52.700 1.00 0.00 ATOM 91 CAP AMO S 2 50.622 43.979 52.108 1.00 0.00 ATOM 92 CAO AMO S 2 49.936 43.084 53.136 1.00 0.00 ATOM 93 CAN AMO S 2 49.559 41.724 52.516 1.00 0.00 ATOM 94 CAL AMO S 2 48.353 41.828 51.583 1.00 0.00 ATOM 95 OAM AMO S 2 48.432 42.346 50.463 1.00 0.00 ATOM 96 CAJ AMO S 2 47.139 41.293 52.030 1.00 0.00 ATOM 97 CAK AMO S 2 46.714 40.042 51.547 1.00 0.00 ATOM 98 HAK AMO S 2 47.312 39.515 50.788 1.00 0.00 ATOM 99 CAE AMO S 2 45.535 39.471 52.046 1.00 0.00 ATOM 100 SAB AMO S 2 44.829 38.145 51.109 1.00 0.00 ATOM 101 OAC AMO S 2 43.377 37.884 51.519 1.00 0.00 ATOM 102 OAD AMO S 2 44.850 38.514 49.634 1.00 0.00 ATOM 103 OAA AMO S 2 45.677 36.894 51.333 1.00 0.00 ATOM 104 CAI AMO S 2 46.376 41.979 53.005 1.00 0.00 ATOM 105 HAI AMO S 2 46.679 42.965 53.345 1.00 0.00 ATOM 106 CAG AMO S 2 45.206 41.393 53.519 1.00 0.00 ATOM 107 HAG AMO S 2 44.629 41.937 54.267 1.00 0.00 ATOM 108 CAF AMO S 2 44.799 40.107 53.072 1.00 0.00 ATOM 109 NAH AMO S 2 44.337 39.243 53.999 1.00 0.00 ATOM 110 HAH AMO S 2 44.794 38.347 54.025 1.00 0.00 ATOM 111 CBF AMO S 2 43.323 39.424 54.867 1.00 0.00 ATOM 112 CBJ AMO S 2 43.392 38.619 56.018 1.00 0.00 ATOM 113 HBQ AMO S 2 44.110 37.799 56.087 1.00 0.00 ATOM 114 CBK AMO S 2 42.514 38.856 57.096 1.00 0.00 ATOM 115 HBR AMO S 2 42.561 38.214 57.976 1.00 0.00 ATOM 116 CBG AMO S 2 42.350 40.452 54.775 1.00 0.00 ATOM 117 HBO AMO S 2 42.251 41.042 53.863 1.00 0.00 ATOM 118 CBH AMO S 2 41.472 40.689 55.853 1.00 0.00 ATOM 119 HBP AMO S 2 40.735 41.494 55.780 1.00 0.00 ATOM 120 CBI AMO S 2 41.557 39.891 57.028 1.00 0.00 ATOM 121 NBL AMO S 2 41.142 40.359 58.218 1.00 0.00 ATOM 122 HBZ AMO S 2 41.709 40.132 59.014 1.00 0.00 ATOM 123 CBM AMO S 2 40.040 41.095 58.452 1.00 0.00 ATOM 124 CBO AMO S 2 38.806 40.846 57.813 1.00 0.00 ATOM 125 HBT AMO S 2 38.772 40.278 56.888 1.00 0.00 ATOM 126 CBP AMO S 2 37.600 41.291 58.406 1.00 0.00 ATOM 127 SCA AMO S 2 36.152 41.259 57.393 1.00 0.00 ATOM 128 OCC AMO S 2 35.626 39.827 57.334 1.00 0.00 ATOM 129 OCD AMO S 2 35.061 42.177 57.942 1.00 0.00 ATOM 130 OCB AMO S 2 36.518 41.744 55.997 1.00 0.00 ATOM 131 CBN AMO S 2 40.050 41.794 59.676 1.00 0.00 ATOM 132 HBS AMO S 2 40.995 42.028 60.157 1.00 0.00 ATOM 133 CBR AMO S 2 38.853 42.224 60.284 1.00 0.00 ATOM 134 HBU AMO S 2 38.896 42.750 61.235 1.00 0.00 ATOM 135 CBQ AMO S 2 37.619 41.939 59.663 1.00 0.00 ATOM 136 NBS AMO S 2 36.571 41.625 60.450 1.00 0.00 ATOM 137 HB0 AMO S 2 36.126 40.740 60.261 1.00 0.00 ATOM 138 CBT AMO S 2 36.042 42.357 61.462 1.00 0.00 ATOM 139 CBU AMO S 2 35.212 41.636 62.346 1.00 0.00 ATOM 140 HBV AMO S 2 34.980 40.589 62.169 1.00 0.00 ATOM 141 CBV AMO S 2 34.663 42.281 63.470 1.00 0.00 ATOM 142 HBW AMO S 2 34.022 41.736 64.157 1.00 0.00 ATOM 143 CBW AMO S 2 34.965 43.649 63.700 1.00 0.00 ATOM 144 NBZ AMO S 2 34.457 44.258 64.771 1.00 0.00 ATOM 145 HB2 AMO S 2 34.657 45.217 64.937 1.00 0.00 ATOM 146 HB1 AMO S 2 33.873 43.750 65.397 1.00 0.00 ATOM 147 CBY AMO S 2 35.794 44.377 62.824 1.00 0.00 ATOM 148 HBY AMO S 2 36.015 45.429 63.006 1.00 0.00 ATOM 149 CBX AMO S 2 36.333 43.731 61.698 1.00 0.00 ATOM 150 HBX AMO S 2 36.936 44.296 60.986 1.00 0.00 ATOM 151 CBE AMO S 3 53.853 69.094 73.884 1.00 0.00 ATOM 152 CBD AMO S 3 54.067 69.162 72.376 1.00 0.00 ATOM 153 CBC AMO S 3 53.581 67.871 71.728 1.00 0.00 ATOM 154 CBB AMO S 3 53.797 67.947 70.213 1.00 0.00 ATOM 155 CBA AMO S 3 53.304 66.665 69.555 1.00 0.00 ATOM 156 CAZ AMO S 3 53.487 66.782 68.041 1.00 0.00 ATOM 157 CAY AMO S 3 52.964 65.522 67.349 1.00 0.00 ATOM 158 CAX AMO S 3 53.106 65.697 65.834 1.00 0.00 ATOM 159 CAW AMO S 3 52.545 64.474 65.105 1.00 0.00 ATOM 160 CAV AMO S 3 52.630 64.739 63.600 1.00 0.00 ATOM 161 CAU AMO S 3 52.028 63.568 62.820 1.00 0.00 ATOM 162 CAT AMO S 3 52.044 63.938 61.338 1.00 0.00 ATOM 163 CAS AMO S 3 51.414 62.819 60.494 1.00 0.00 ATOM 164 CAR AMO S 3 51.379 63.282 59.045 1.00 0.00 ATOM 165 CAQ AMO S 3 50.745 62.209 58.158 1.00 0.00 ATOM 166 CAP AMO S 3 50.669 62.751 56.730 1.00 0.00 ATOM 167 CAO AMO S 3 50.052 61.714 55.796 1.00 0.00 ATOM 168 CAN AMO S 3 49.877 62.288 54.377 1.00 0.00 ATOM 169 CAL AMO S 3 48.711 63.273 54.292 1.00 0.00 ATOM 170 OAM AMO S 3 48.777 64.412 54.772 1.00 0.00 ATOM 171 CAJ AMO S 3 47.554 62.854 53.625 1.00 0.00 ATOM 172 CAK AMO S 3 47.310 63.298 52.314 1.00 0.00 ATOM 173 HAK AMO S 3 48.003 64.008 51.837 1.00 0.00 ATOM 174 CAE AMO S 3 46.190 62.823 51.618 1.00 0.00 ATOM 175 SAB AMO S 3 45.698 63.729 50.178 1.00 0.00 ATOM 176 OAC AMO S 3 44.273 63.368 49.752 1.00 0.00 ATOM 177 OAD AMO S 3 45.741 65.217 50.490 1.00 0.00 ATOM 178 OAA AMO S 3 46.683 63.416 49.053 1.00 0.00 ATOM 179 CAI AMO S 3 46.667 61.942 54.247 1.00 0.00 ATOM 180 HAI AMO S 3 46.830 61.634 55.276 1.00 0.00 ATOM 181 CAG AMO S 3 45.557 61.451 53.539 1.00 0.00 ATOM 182 HAG AMO S 3 44.883 60.752 54.034 1.00 0.00 ATOM 183 CAF AMO S 3 45.333 61.858 52.195 1.00 0.00 ATOM 184 NAH AMO S 3 44.941 60.913 51.316 1.00 0.00 ATOM 185 HAH AMO S 3 45.503 60.828 50.487 1.00 0.00 ATOM 186 CBF AMO S 3 43.872 60.096 51.401 1.00 0.00 ATOM 187 CBJ AMO S 3 43.988 58.909 50.656 1.00 0.00 ATOM 188 HBQ AMO S 3 44.798 58.774 49.937 1.00 0.00 ATOM 189 CBK AMO S 3 43.038 57.879 50.822 1.00 0.00 ATOM 190 HBR AMO S 3 43.124 56.971 50.225 1.00 0.00 ATOM 191 CBG AMO S 3 42.784 60.273 52.294 1.00 0.00 ATOM 192 HBO AMO S 3 42.655 61.214 52.832 1.00 0.00 ATOM 193 CBH AMO S 3 41.835 59.244 52.460 1.00 0.00 ATOM 194 HBP AMO S 3 41.008 59.382 53.162 1.00 0.00 ATOM 195 CBI AMO S 3 41.964 58.032 51.725 1.00 0.00 ATOM 196 NBL AMO S 3 41.440 56.882 52.182 1.00 0.00 ATOM 197 HBZ AMO S 3 41.993 56.054 52.060 1.00 0.00 ATOM 198 CBM AMO S 3 40.246 56.726 52.782 1.00 0.00 ATOM 199 CBO AMO S 3 39.082 57.404 52.355 1.00 0.00 ATOM 200 HBT AMO S 3 39.162 58.303 51.752 1.00 0.00 ATOM 201 CBP AMO S 3 37.805 56.880 52.667 1.00 0.00 ATOM 202 SCA AMO S 3 36.420 57.950 52.414 1.00 0.00 ATOM 203 OCC AMO S 3 36.080 57.967 50.926 1.00 0.00 ATOM 204 OCD AMO S 3 35.199 57.487 53.207 1.00 0.00 ATOM 205 OCB AMO S 3 36.787 59.350 52.887 1.00 0.00 ATOM 206 CBN AMO S 3 40.112 55.535 53.523 1.00 0.00 ATOM 207 HBS AMO S 3 40.997 55.026 53.893 1.00 0.00 ATOM 208 CBR AMO S 3 38.844 54.996 53.822 1.00 0.00 ATOM 209 HBU AMO S 3 38.777 54.068 54.385 1.00 0.00 ATOM 210 CBQ AMO S 3 37.684 55.654 53.360 1.00 0.00 ATOM 211 NBS AMO S 3 36.648 54.897 52.947 1.00 0.00 ATOM 212 HB0 AMO S 3 36.326 55.065 52.006 1.00 0.00 ATOM 213 CBT AMO S 3 35.987 53.941 53.645 1.00 0.00 ATOM 214 CBU AMO S 3 35.213 53.062 52.859 1.00 0.00 ATOM 215 HBV AMO S 3 35.121 53.201 51.786 1.00 0.00 ATOM 216 CBV AMO S 3 34.536 51.990 53.473 1.00 0.00 ATOM 217 HBW AMO S 3 33.937 51.307 52.878 1.00 0.00 ATOM 218 CBW AMO S 3 34.655 51.809 54.877 1.00 0.00 ATOM 219 NBZ AMO S 3 34.026 50.787 55.458 1.00 0.00 ATOM 220 HB2 AMO S 3 34.097 50.656 56.440 1.00 0.00 ATOM 221 HB1 AMO S 3 33.482 50.164 54.904 1.00 0.00 ATOM 222 CBY AMO S 3 35.426 52.681 55.669 1.00 0.00 ATOM 223 HBY AMO S 3 35.506 52.536 56.746 1.00 0.00 ATOM 224 CBX AMO S 3 36.093 53.755 55.053 1.00 0.00 ATOM 225 HBX AMO S 3 36.653 54.466 55.661 1.00 0.00 ATOM 226 CBE AMO S 4 55.617 66.293 39.703 1.00 0.00 ATOM 227 CBD AMO S 4 56.173 65.293 40.711 1.00 0.00 ATOM 228 CBC AMO S 4 55.593 63.910 40.439 1.00 0.00 ATOM 229 CBB AMO S 4 56.156 62.911 41.455 1.00 0.00 ATOM 230 CBA AMO S 4 55.590 61.523 41.183 1.00 0.00 ATOM 231 CAZ AMO S 4 56.201 60.535 42.178 1.00 0.00 ATOM 232 CAY AMO S 4 55.679 59.123 41.905 1.00 0.00 ATOM 233 CAX AMO S 4 56.355 58.151 42.877 1.00 0.00 ATOM 234 CAW AMO S 4 55.894 56.719 42.600 1.00 0.00 ATOM 235 CAV AMO S 4 56.663 55.783 43.535 1.00 0.00 ATOM 236 CAU AMO S 4 56.283 54.327 43.261 1.00 0.00 ATOM 237 CAT AMO S 4 57.158 53.441 44.146 1.00 0.00 ATOM 238 CAS AMO S 4 56.857 51.956 43.892 1.00 0.00 ATOM 239 CAR AMO S 4 57.818 51.129 44.733 1.00 0.00 ATOM 240 CAQ AMO S 4 57.572 49.636 44.508 1.00 0.00 ATOM 241 CAP AMO S 4 58.606 48.853 45.318 1.00 0.00 ATOM 242 CAO AMO S 4 58.400 47.351 45.139 1.00 0.00 ATOM 243 CAN AMO S 4 59.500 46.555 45.868 1.00 0.00 ATOM 244 CAL AMO S 4 60.838 46.609 45.131 1.00 0.00 ATOM 245 OAM AMO S 4 61.543 47.625 45.124 1.00 0.00 ATOM 246 CAJ AMO S 4 61.263 45.450 44.471 1.00 0.00 ATOM 247 CAK AMO S 4 62.245 44.636 45.064 1.00 0.00 ATOM 248 HAK AMO S 4 62.706 44.937 46.016 1.00 0.00 ATOM 249 CAE AMO S 4 62.619 43.437 44.440 1.00 0.00 ATOM 250 SAB AMO S 4 64.134 42.694 44.979 1.00 0.00 ATOM 251 OAC AMO S 4 64.628 41.646 43.979 1.00 0.00 ATOM 252 OAD AMO S 4 65.198 43.773 45.106 1.00 0.00 ATOM 253 OAA AMO S 4 63.894 42.052 46.345 1.00 0.00 ATOM 254 CAI AMO S 4 60.665 45.071 43.246 1.00 0.00 ATOM 255 HAI AMO S 4 59.940 45.721 42.765 1.00 0.00 ATOM 256 CAG AMO S 4 61.027 43.858 42.634 1.00 0.00 ATOM 257 HAG AMO S 4 60.559 43.583 41.689 1.00 0.00 ATOM 258 CAF AMO S 4 61.982 43.006 43.254 1.00 0.00 ATOM 259 NAH AMO S 4 61.733 41.681 43.245 1.00 0.00 ATOM 260 HAH AMO S 4 61.746 41.229 44.143 1.00 0.00 ATOM 261 CBF AMO S 4 61.501 40.890 42.179 1.00 0.00 ATOM 262 CBJ AMO S 4 60.782 39.717 42.471 1.00 0.00 ATOM 263 HBQ AMO S 4 60.604 39.410 43.503 1.00 0.00 ATOM 264 CBK AMO S 4 60.295 38.911 41.421 1.00 0.00 ATOM 265 HBR AMO S 4 59.757 37.993 41.657 1.00 0.00 ATOM 266 CBG AMO S 4 61.767 41.245 40.831 1.00 0.00 ATOM 267 HBO AMO S 4 62.374 42.121 40.597 1.00 0.00 ATOM 268 CBH AMO S 4 61.279 40.440 39.781 1.00 0.00 ATOM 269 HBP AMO S 4 61.475 40.729 38.746 1.00 0.00 ATOM 270 CBI AMO S 4 60.530 39.265 40.075 1.00 0.00 ATOM 271 NBL AMO S 4 59.646 38.767 39.195 1.00 0.00 ATOM 272 HBZ AMO S 4 58.783 38.418 39.569 1.00 0.00 ATOM 273 CBM AMO S 4 59.803 38.679 37.861 1.00 0.00 ATOM 274 CBO AMO S 4 61.025 38.309 37.258 1.00 0.00 ATOM 275 HBT AMO S 4 61.956 38.394 37.810 1.00 0.00 ATOM 276 CBP AMO S 4 61.033 37.771 35.949 1.00 0.00 ATOM 277 SCA AMO S 4 62.601 37.666 35.138 1.00 0.00 ATOM 278 OCC AMO S 4 63.348 36.447 35.672 1.00 0.00 ATOM 279 OCD AMO S 4 62.444 37.541 33.623 1.00 0.00 ATOM 280 OCB AMO S 4 63.390 38.936 35.428 1.00 0.00 ATOM 281 CBN AMO S 4 58.604 38.513 37.139 1.00 0.00 ATOM 282 HBS AMO S 4 57.661 38.831 37.574 1.00 0.00 ATOM 283 CBR AMO S 4 58.600 37.961 35.841 1.00 0.00 ATOM 284 HBU AMO S 4 57.656 37.834 35.317 1.00 0.00 ATOM 285 CBQ AMO S 4 59.819 37.554 35.257 1.00 0.00 ATOM 286 NBS AMO S 4 59.818 36.440 34.500 1.00 0.00 ATOM 287 HB0 AMO S 4 60.464 35.717 34.777 1.00 0.00 ATOM 288 CBT AMO S 4 59.056 36.176 33.410 1.00 0.00 ATOM 289 CBU AMO S 4 58.988 34.814 33.048 1.00 0.00 ATOM 290 HBV AMO S 4 59.564 34.063 33.581 1.00 0.00 ATOM 291 CBV AMO S 4 58.173 34.418 31.971 1.00 0.00 ATOM 292 HBW AMO S 4 58.113 33.373 31.683 1.00 0.00 ATOM 293 CBW AMO S 4 57.422 35.401 31.272 1.00 0.00 ATOM 294 NBZ AMO S 4 56.639 35.026 30.261 1.00 0.00 ATOM 295 HB2 AMO S 4 56.115 35.707 29.762 1.00 0.00 ATOM 296 HB1 AMO S 4 56.588 34.065 30.007 1.00 0.00 ATOM 297 CBY AMO S 4 57.483 36.762 31.627 1.00 0.00 ATOM 298 HBY AMO S 4 56.907 37.510 31.080 1.00 0.00 ATOM 299 CBX AMO S 4 58.305 37.155 32.698 1.00 0.00 ATOM 300 HBX AMO S 4 58.399 38.212 32.950 1.00 0.00 TER ENDMDL
Sunday, March 01, 2015
Steps to Perform a Simulation
Below is presented a generalised procedure for performing a simulation. The exact steps and processes involved will vary depending on exactly what is being attempted. Use as a general guide only!
- Clearly identify the property / phenomena of interest to be studied by performing the simulation. Do not continue further until you are clear on this!
- Select the appropriate tools to be able to perform the simulation and observe the property / phenomena of interest. It is important to read and familiarise yourself with publications by other researchers on similar systems. Tools include:
- software to perform the simulation with, consideration of force field may influence this decision.
- force field which describes how the atoms / particles within the system interact with each other. Select one that is appropriate for the system being studied and the property / phenomena of interest. Very important and non-trivial step! Consider now how you will analyze your simulation data to make your observations. - Obtain / generate the initial coordinate file for each molecule to be placed within the system. The page linked there has some software suggestions.
- Generate the raw starting structure for the system by placing the molecules within the coordinate file as appropriate. Molecules may be specifically placed or arranged randomly.
- Obtain / generate the topology file for the system, using (for example)
- pdb2gmx,
- SwissParam (for CHARMM forcefield),
- PRODRG (for ffgmx/GROMOS96 43A1),
- Automated Topology Builder (for GROMOS96 53A6),
- MKTOP (for OPLS/AA) or
- your favourite text editor in concert with chapter 5 of theGROMACS Manual.
- For the AMBER force fields, antechamber or acpype might be appropriate. - Describe a simulation box (e.g. using editconf) whose size is appropriate for the eventual density you would like, fill it with solvent (e.g. using genbox), and add any counter-ions needed to neutralize the system (e.g. using grompp and genion). In these steps you may need to edit your topology file to stay current with your coordinate file.
- Run an energy minimization on the system (using grompp and mdrun). This is required to sort out any bad starting structures caused during generation of the system, which may cause the production simulation to crash. It may be necessary also to minimize your solute structure in vacuo before introducing solvent molecules (or your lipid bilayer or whatever else). You should consider using flexible water models and not using bond constraints or frozen groups. The use of position restraints and/or distance restraints should be evaluated carefully.
- Select the appropriate simulation parameters for the equilibration simulation (defined in .mdp file). You need to choose simulation parameters that are consistent with how force field was derived. You may need to simulate at NVT with position restraints on your solvent and/or solute to get the temperature almost right, then relax to NPT to fix the density (which should be done with Berendsen until after the density is stabilized, before a further switch to a barostat that produces the correct ensemble), then move further (if needed) to reach your production simulation ensemble (e.g. NVT, NVE). If you have problems here with the system blowing up, consider using the suggestions on that page, e.g. position restraints on solutes, or not using bond constraints, or using smaller integration timesteps, or several gentler heating stage(s).
- Run the equilibration simulation for sufficient time so that the system relaxes sufficiently in the target ensemble to allow the production run to be commenced (using grompp and mdrun, then g_energy and trajectory visualization tools).
- Select the appropriate simulation parameters for the production simulation (defined in .mdp file). In particular, be careful not to re-generate the velocities. You still need to be consistent with how the force field was derived and how to measure the property / phenomena of interest.
- Run the production simulation for sufficient time so that property / phenomena of interest can be observed in required detail (using grompp / tpbconv and mdrun).
- Analyse / visualise the resulting trajectory and data files to obtain information on the property / phenomena of interest.
Resources
- Flow Chart - simple flow chart of a typical GROMACS MD run of a protein in a box of water.
- GROMACS Flowsheet - flowsheet of the general procedure for performing a molecular dynamic simulation using GROMACS. Shows linkage between files required and generated in each step and general command lines used.
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