[gmx-users] Ligand Topologies

Mark Abraham mark.j.abraham at gmail.com
Mon Sep 9 11:08:20 CEST 2013

Find out why your charge is not integral! Read all the output of
whatever tool built the .itp file and reconsider your choices.


On Mon, Sep 9, 2013 at 9:46 AM, MUSYOKA THOMMAS
<mutemibiochemistry at gmail.com> wrote:
> 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
>  *Practical
> 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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