[gmx-users] Formating PDB Files

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 10 14:11:49 CET 2009

Jack Shultz wrote:
> Hello,
> I am experimenting with formatting pdb files using pdb2gmx. Currently
> I am downloading ligand files from RCSB.ORG. These are non-protein pdb
> files. When I look at their residues, instead of having a standard
> residue, they use their pdb id as the residue id. pdb2gmx does not
> like this because these are not standard residues. Is there a setting
> I can use to make pdb2gmx to ignore this? Otherwise I can use a sed
> command to replace all instances of a given residue name. However,
> when I try replacing with a standard residue name, I still run into
> errors.

Even if you could make pdb2gmx ignore the given residue name, it has to know 
what molecule you have in order to construct the topology.  Usually such a 
procedure does not work for ligands.

> Here is an example ligand pdb file
> http://www.rcsb.org/pdb/files/ligand/002_ideal.pdb
> Notice instead of having a standard residue it uses 002
> ATOM      1  C1  002 A   1      -1.036   0.293   0.447  1.00 10.00           C
> ATOM      2  C2  002 A   1      -1.041   1.804   0.685  1.00 10.00           C
> ATOM      3  C3  002 A   1      -2.288   2.191   1.482  1.00 10.00           C
> ....
> Any advice?  Does GROMACS only support the standard 20 amino acids?

Check the .rtp file for the force field you're trying to use.  You can only use 
pdb2gmx if the appropriate building block is present (primarily amino acids and 

You can build a topology using the PRODRG (beta) server, but do note that the 
charges and charge groups will require manual adjustment and validation.  Hence 
why parameterization is difficult!



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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