[gmx-users] Dismantling the methyl group

[Erik Marklund]

2 jul 2007 kl. 14.32 skrev David van der Spoel:

> Jussi Lehtola wrote:
>> Hi again,
>> thanks to Tsjerk and Erik for a quick reply. Would anyone happen  
>> to have
>> a .gro file (& al) for methanol using OPLS or another all-hydrogen  
>> force
>> field? I tried running pdb2gmx on the tutorial .pdb files, but it  
>> failed
>> with the error
>> Fatal error:
>> Atom Me1 in residue MET 1 not found in rtp entry with 17 atoms
>>              while sorting atoms
> chapter 5.
>
> pdb2gmx only works on proteins.
>

(And nucleic acids)
/Erik

> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala  
> University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys