[gmx-users] FF & LIGANDS's topology

David spoel at xray.bmc.uu.se
Thu Aug 19 17:04:37 CEST 2004

On Thu, 2004-08-19 at 15:50, Arturas wrote:
> Hello , gmx-users,
> I do modeling on protein-ligand complex and got error that my iginad's
> atoms "has mass 0".
> Similar error was found in mailing list. I have checked the thread
> "GROMOS96 and protein-ligand complex" posted almost a year ago in the
> gmx mailing list. However i didn't found the summurising answers how
> to treat prepared ligand topology with PRODRG applying to FF43a1
> model.
> In the mailing list, some (David van der Spoel) advised to add mass
> column to ligand's topology file, but some (Anton Feenstra) said that
> it is a bad way as "It sounds as if you're mixing (parts of)
> forcefields ...".
You should not mix force fields, but convert the ligand topology to
ffG43 by adding masses, checking atom types and charges. Look for
similar fragments in the ffG43a1.rtp file.
> I'd like to hear how peaple treat that situation now and what manual
> changes are acceptable preparing ligand's topology for GROMOS96 FF ???
> With respect
> Arturas
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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