[gmx-users] Ligand Topologies

[Mark Abraham]

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

Mark

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