[gmx-users] Building Topology with all hydrogens

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 21 14:17:08 CET 2008

Quoting Subhrangshu Supakar <ssupakar at gmail.com>:

> Hi All !
> I want to do a MD study of a few molecules in a box of sodium cetyl
> sulphate.
> I want the the topology Sod-cetyl-sulphate with all its hydrogens as without
> that there would occur a mismatch
> in the number of atoms in the system and the number of atoms in the topology
> file. I tried the the dundee server, but I got the topology of the molecule
> with no H.
> Can any one suggest a possible way for building the topology for the
> Sod-cetyl-sulphate with all its hydrogens.

You will have to derive the parameters yourself.  See relevant discussions about
ligands, drugs, etc. in the list archive (this sort of thing has been asked
dozens of times in recent memory).  Also have a look at:




> Subhrangshu Supakar
> Dept. of Bioinformatics
> WestBengal University of Technology
> Kolkkata, India


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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