CHARMM Topology Files

CHARMM Topology Files

The CHARMM topology files used in PDB Reader are list below. The residues in the PDB file that users want to read must be defined in these topology files. Otherwise, CHARMM will be terminated abnormally.Please use the following website to obtain the official CHARMM additive FFs: http://mackerell.umaryland.edu/charmm_ff.shtml

• Protein topologies and parameters
  top_all36_prot.rtf
  par_all36_prot.prm
• Nucleic acids topologies and parameters
  top_all36_na.rtf
  par_all36_na.prm
• Carbohydrates topologies and parameters
  top_all36_carb.rtf
  par_all36_carb.prm
• Lipids topologies and parameters
  top_all36_lipid.rtf
  par_all36_lipid.prm
• CGENFF topologies and parameters
  top_all36_cgenff.rtf
  par_all36_cgenff.prm
• Glycopeptide topologies and parameters
  toppar_all36_carb_glycopeptide.str
• Additional topologies and parameters for phosphorylation
  toppar_all36_prot_fluoro_alkanes.str
  toppar_all36_prot_na_combined.str
• Additional topologies and parameters for nitroxide spin labels
  toppar_all36_spin_label.str
  toppar_all36_spin_label_dummy.str
• Additional topologies and parameters for MTS chemical modifier
  toppar_all36_mts.str
• Additional topologies and parameters for unnatural amino acid substitution
  toppar_unna_amin_acid_cgenff.str
  toppar_unna_amin_acid_para_cgenff.str
  toppar_unna_amin_acid_gaff.str
  toppar_unna_amin_acid_para_gaff.str
• Additional topologies and parameters for water and ions
  toppar_water_ions.str
  toppar_dum_noble_gases.str
• Additional topologies and parameters
  toppar_all36_na_nad_ppi.str 

Additional CHARMM topologies and parameters used in Membrane Builder are list below.

• Additional lipid topologies and parameters
  toppar_all36_lipid_bacterial.str 
  toppar_all36_lipid_cardiolipin.str 
  toppar_all36_lipid_cholesterol.str 
  toppar_all36_lipid_glycolipid.str 
  toppar_all36_lipid_inositol.str 
  toppar_all36_lipid_miscellaneous.str 
  toppar_all36_lipid_sphingo.str 
  toppar_all36_lipid_yeast.str
• Detergent topologies and parameters
  toppar_all36_detergent.str
• HMMM topologies and parameters
  toppar_all36_lipid_hmmm.str

Additional CHARMM topologies and parameters used in Implicit Solvent Modeler are list below.

• Additional topologies and parameters for ACE and FACTS_P19 model
  ace2parpx.inp
  acepar19.inp
  toph19.inp
  param19.inp
• Additional topologies and parameters for EEF1 and SASA model
  toph19_eef1.inp
  param19_eef1.inp
  solvpar.inp
• Additional topologies and parameters for GBSW and FACTS_P22 model
  top_all27_prot_na.rtf
  par_all27_prot_na_gbsw.prm
  radii_prot_na.str
  radius_gbsw.str
• Additional topologies and parameters for GBWV model
  radii_prot_na.str
• Additional topologies and parameters for SCPISM model
  scpism.inp
• Additional topologies and parameters for EEF1/IMM1 model
  toph19_eef1.1.inp
  param19_eef1.1.inp
  solvpar.inp
• Additional topologies and parameters for GBSWmemb model
  radii_prot_na.str
• Additional topologies and parameters for GBMVmemb model
  radii_prot_na.str
  radii_prot_na.str
• Additional topologies and parameters for PHMD model
  top_all27_prot_na_gbsw_phmd.rtf
  par_all27_prot_na_gbsw_phmd.prm
  par_phmd.inp
  radii_prot_na.str
  radius_gbsw.str