[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 80

[Soumya Lipsa Rath]

Dear Justin,

Thanks for your reply. I meant, that the PRODRG server gave error in giving
the topology file since my inhibitor contains a metal which the server
doesn't process. If PRODRG is meant for GROMOS, should I use CGENFF for
CHARMM? In that case, how do we include the topology of the inhibitor
during the protein-ligand simulation?

Thanks,
Soumya

>
>
> On 3/16/16 10:18 PM, Soumya Lipsa Rath wrote:
> > Dear Gromacs Users,
> >
> > I have to run a protein-ligand system. I am using CHARMM36 ff for the
> > simulation. For generating the parameters for the ligand molecule I used
> > the forcefield development toolkit of vmd, which gives CHARMM compatible
> > parameters.
> >
> > But, I am unable to understand how should I include the parameters I had
> > obtained. I went through the tutorial files which shows an example of
> > PRODRG server for generating the itp file, but my ligand contains metal
> > atoms. I would appreciate if somebody could suggest me how to solve this.
> >
>
> What are the ligands?  What metal?
>
> Don't use PRODRG; it's only intended for GROMOS force fields (and even
> then, the
> topologies need a lot of work).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
>
>