[gmx-users] Re :Using FFTK generated parameter file for Protein-Ligand simulations

[Soumya Lipsa Rath]

Dear Justin,
 I have used CGenFF for CHARMM. However, I am not able to understand how to
include the topology of inhibitor to start a simulation. The metal ions
which I had talked about are FL and BR and I have got their parameters
already from CHARMM. I am relatively new to gromacs, I just wanted to know
how to start a protein-ligand simulation andd how to incorporate the ligand
parameters.

Thanks,
Soumya


On 3/17/16 8:04 PM, Soumya Lipsa Rath wrote:
> > 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?
> >
>
> Yes, you should use CGenFF when using the CHARMM force field.  They're
> compatible by design.
>
> But I can't guarantee that you'll even be able to create a topology;
> CGenFF is
> for organic molecules.  Any metal parameters would have to come from CHARMM
> itself, but you still haven't told me what that metal is so I don't know if
> CHARMM will cover it...
>
> -Justin
>
> > 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
> >>
> >> ==================================================
> >>
> >>
> >>
> >>
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
>