[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position

[neeru sharma]

Dear Justin,

Thanks for the reply. It worked absolutely fine. I was minimizing the
ligand with PRODRG, which was causing this issue.

--Neeru



> Message: 1
> Date: Thu, 19 Jun 2014 09:05:58 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem in running protein-ligand (Heteroatom
>         type) system: Ligand position not in correct position
> Message-ID: <53A2E036.2020303 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 6/19/14, 5:03 AM, neeru sharma wrote:
> > Dear gromacs Users,
> >
> > I am running a simulation of Protein-Ligand complex. In this case, the
> > ligand consists of a GTP molecule, whose parameters I am deriving from
> > PRODRG server.
> > When I try to generate the complex using coordinates obtained from PRODRG
> > for GTP and from pdb2gmx for Protein, the position of ligand is not the
> > same.
> >
> > I am following these steps in building this protein-ligand complex.
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
> >
> > I have followed the same set-up previously, for the same system and it
> > worked fine then but now it is not.
> >
> > Can anyone help me out and let me know where I am wrong. Any suggestion
> > would be welcome.
> >
>
> You're manipulating the coordinates somehow, either by allowing PRODRG to
> minimize your ligand or by altering the box dimensions of the protein (and
> thereby changing its position) before adding the ligand back in.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
>