[gmx-users] Charge on drug

[tasneem kausar]

Thanks for reply

I have visualized solvate.gro and em.gro. Some bonds that are not present
in box.gro is seen in em.gro.
I am giving you the link of the file to visualize.
https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
I addition to that I have done energy minimization multiple times with
steepest decent and conjugate gradient method. Potential energy value is
negative in every minimization. When I am trying position restrain core
dump with multiple lincs warning occurs.
Please tell me how this problem would be resolved

On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>