[gmx-users] pdb2gmx for small molecules?

Warren Gallin wgallin at ualberta.ca
Thu Apr 18 21:32:41 CEST 2013


	I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability.  My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input.

	I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows:

	pdb2gmx -f BrMT_mono_nores.pdb -water tip4

	I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid):

Program pdb2gmx, VERSION 4.5.4
Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581

Fatal error:
Residue '' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

 and just above that message there is also a Warning in the message saying:

Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules?


Warren Gallin

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