[gmx-users] pdb2gmx for small molecules?

[Justin Lemkul]

On 4/18/13 3:32 PM, Warren Gallin wrote:
> Hi,
>
> 	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?
>

pdb2gmx only knows how to handle what it knows about.  There is no generic 
support for arbitrary compounds.

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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