Residue 'XXX' not found in residue topology database

Residue 'XXX' not found in residue topology database

This means that the force field you have selected while running pdb2gmx does not have an entry in the residue database for XXX. The residue database entry is necessary both for stand-alone molecules (e.g. formaldehyde) or a peptide (standard or non-standard). This entry defines the atom types, connectivity, bonded and non-bonded interaction types for the residue and is necessary to use pdb2gmx to build a .top file. A residue database entry may be missing simply because the database does not contain the residue at all, or because the name is different.

For new users, this error appears because they are running pdb2gmx blindly on a PDB file they have without consideration of the contents of the file. A force field is not something that is magical, it can only deal with molecules or residues (building blocks) that are provided in the residue database or included otherwise.

If you want to use pdb2gmx to automatically generate your topology, you have to ensure that the appropriate .rtp entry is present within the desired force field and has the same name as the building block you are trying to use. If you call your molecule "HIS," then pdb2gmx will not magically build a random molecule; it will try to build histidine, based on the [ HIS ] entry in the .rtp file, so it will look for the exact atomic entries for histidine, no more no less.

If you want a topology for an arbitrary molecule, you cannot use pdb2gmx (unless you build the .rtp entry yourself). You will have to build it by hand, or use another program (such as x2top or one of the scripts contributed by users) to build the .top file.

If there is not an entry for this residue in the database, then the options for obtaining the force field parameters are:

• see if there is a different name being used for the residue in the residue database and rename as appropriate,
• parameterize the residue / molecule yourself (lots of work, even for an expert),
• find a topology file for the molecule, convert it to an .itp file and include it in your .top file,
• use another force field which has parameters available for this,
• search the primary literature for publications for parameters for the residue that are consistent with the force field that is being used.

Once you have determined the parameters and topology for your residue, see adding a residue to a force field for instructions on how to proceed.