[gmx-users] zinc force field parameters

[w.j.schravendijk at students.pharm.uu.nl]

>
> PS: Can You recomend me some linux program for easy manual(by eyes) puting
> of ligand to protein. Thanks

Maybe Swisspdb viewer will help, you could merge a pdb file containg Zn
and a file with your protein and try to fit it in the right place using a
graphical interface ('drag and drop').
It may be that the pdb output should be a bit modified before gromacs can
handle it, but at least it gives you an idea what the coordinates should
be.

http://www.expasy.ch/spdbv/

Regrettably, the linux version is a port of the mac version, and is not as
nice as the windows or mac version.

Greetings, Pim