[gmx-users] abbreviations in pdb files

[jtomlins at purdue.edu]

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