[gmx-users] Ligand Topologies

MUSYOKA THOMMAS mutemibiochemistry at gmail.com
Mon Sep 9 09:46:17 CEST 2013

Dear Users,
I am trying to do Protein-Ligand MD simulations using GROMACS. I have tried
to build topology files of my ligands using external tools like PRODRG
server. I tried to correct the charges in line with Dr. Justin's paper
Considerations for Building GROMOS-Compatible Small-Molecule Topologies, *but
seems i cannot find the way, as the system crashes down during the
solvating stage
with an error message;* the net charge of my structure is not an integer
 value. *

I will be glad to get any assistance.

Thank you.

Mob nos **+27844846540**
B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*
*PhD Student-Bioinformatics (Rhodes University)
Alternative email - thommas at sia.co.ke

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