[gmx-users] Formating PDB Files

Jack Shultz jackygrahamez at gmail.com
Tue Feb 10 14:04:57 CET 2009


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

Here is an example ligand pdb file
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?


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