[gmx-users] pdb2gmx for small molecules?

[David van der Spoel]

On 2013-04-18 21:35, Justin Lemkul wrote:
>
>
> 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
>
Try GAFF using the Ambertools and acpype.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se