[gmx-users] FF & LIGANDS's topology

Arturas a3arzi at vaidila.vdu.lt
Thu Aug 19 15:50:23 CEST 2004

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

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 ...".

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

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