[gmx-users] abbreviations in pdb files

[David Mobley]

pdb2gmx only knows how to convert pdb files containing proteins with
standard residues into GROMACS format, not (typically) small molecules
like methane, methanol and so on. You will either need to obtain
GROMACS topologies for these molecules from some other source, or
generate them yourself.

The strategy for generating them for yourself varies somewhat
depending on the force field you are using. Prodrg generates itp
(topology, basically) files for some small  molecules that are
appropriate for the GROMOS ff, if I remember correctly. There is some
utility available for automatically generating OPLS parameters for
small molecules, although I don't know that this would generate
GROMACS topologies, so if you wanted to use OPLS, you might have to
figure out how to convert these into GROMACS topologies. In AMBER, the
Antechamber module can generate GAFF parameters for various small
molecules, which can be converted from AMBER format into GROMACS
format. It simply isn't as simple as running through pdb2gmx. Small
molecule parameterization is a nontrivial thing.

David


On 8/24/06, jtomlins at purdue.edu <jtomlins at purdue.edu> wrote:
> Hi,
> I'm new to gromacs and have been having trouble with my .pdb file conversions.
> I've read the online help information and paper manual.  I'm trying to do
> assorted small molecules in water.  To create the .pdb file I'm using PRODRG or
> HIC-up then editing it to further fit the gromacs requirements.
>
> For example methanol:
> I have looked over the data online
> (www.gromacs.org/gromacs/topologies/gromacs-building-blocks.html) and found that
> in the pdb the abbreviation for methanol is MTH.  However when I try and do
> pdb2gmx to create my .top and .gro files I get this error:
> Fatal error:
> Residue 'MTH' not found in residue topology database
>
> In the tutorial there is a methanol.pdb and the abbreviation is MeO.  However,
> when I use this I abbreviation I get this error:
> Fatal error:
> There were 14 missing atoms in molecule Protein, if you want to use this
> incomplete topology anyhow, use the option -missing
>
> If I do -missing command then it will create the .top and .gro files, but it
> removes 3 hydrogens and just puts C, O, and 1 H into the .top file.
>
> For some of the other molecules that I want to do I'm unsure of the
> abbreviation, is there any standard thing to use for small molecules?
> Any hints or suggestions would be greatly appreciated.
> Thanks,
> Jill
>
> jtomlins at purdue.edu
> Purdue Univeristy
> Department of Chemistry
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