[gmx-users] Charge on drug

[Mark Abraham]

Hi,

Your energy minimization literally cannot create bonds because those are
already defined by your topology. See
http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds
for what's probably going on.

Mark

On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausar12 at gmail.com> wrote:

> Dear All
>
>
> I am using Acpype server to generate topology file of drug molecule to
> perform protein drug MD simulation. Acpype have generated the itp file and
> other necessary for MD simulations. I am doing MD on gromacs 5.1.4 software
> using amber99sb force field. When I have done energy minimization some
> unwanted bonds are formed in drug molecule. So the position restraint is
> not able to execute. The problem is due to the unusual bond in drug atom.
> When I used the itp file of PRODRG server position restraint goes
> successfully. I have used the gromos54a7 ff. But there is problem with the
> charge present on the atom that comes from PRODRG.
>
> Please tell me how charge on the atom can be corrected in itp file of
> PRODRG.  How the problem in energy minimization with the Acpype itp will be
> resolved.
>
> Thanks in Advance
> With Regards
> Tasneem
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