[gmx-users] Ligand coming out while trying Drug-enzyme tutorial

[vivek sharma]

Hi Tsjerk,
Thanks for your response,
I am finding problem in using original coordinates with the PRODRG topology
because of mismatch in number of Hydrogen atoms in original coordinate file
and PRODRG topology.
Can you tell me how can I try 2nd option you suggested i.e. Fit the
structure obtained from PRODRG to original structure?

Thanks & Regards,
Vivek

On 27 January 2010 10:35, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Vivek,
>
> Either
>
> 1. Use the original ligand coordinates with the PRODRG topology
>
> or
>
> 2. Fit the structure obtained from PRODRG to the original structure
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma
> <viveksharma.iitb at gmail.com> wrote:
> > Hi Dallas,
> > I am trying to run MD simulation over a docked complex (protein+ligand),
> to
> > confirm their dynamic stability in water media.
> > For the same I am using PRODRG server to generate topologies for ligand
> > molecule as gromacs can generate topology for 20 standard residues. As
> > mentioned in tutorial for drug-enzyme complex, I am editing the .top and
> > .gro files to include the PRODRG generated files (DRGGMX.ITP in .top and
> > DRGAPH.GRO in .gro file).
> > I observe that their are changes in co-ordinate of ligand after
> processing
> > them through PRODRG server. So these new co-ordinates for ligand are
> placing
> > ligand away from the protein while the ligand molecule was in protein
> pocket
> > in original docked complex.
> >
> > I hope it gives what I am trying to do, and where I am getting stuck.
> >
> > I am looking for some suggestions and more insight of the problem to
> solve
> > it.
> > Earlier I have done same procedure successfully for a different docked
> > complex.
> >
> > Regards,
> > Vivek
> >
> > 2010/1/27 Dallas B. Warren <Dallas.Warren at pharm.monash.edu.au>
> >>
> >> So, what EXACTLY are you doing?
> >>
> >>
> >>
> >> Catch ya,
> >>
> >> Dr. Dallas Warren
> >> Drug Delivery, Disposition and Dynamics
> >> Monash Institute of Pharmaceutical Sciences, Monash University
> >> 381 Royal Parade, Parkville VIC 3010
> >> dallas.warren at pharm.monash.edu.au
> >> +61 3 9903 9167
> >> ---------------------------------
> >> When the only tool you own is a hammer, every problem begins to resemble
> a
> >> nail.
> >>
> >>
> >>
> >> From: gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org]
> >> On Behalf Of vivek sharma
> >> Sent: Monday, 25 January 2010 7:38 PM
> >> To: Discussion list for GROMACS users
> >> Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme
> >> tutorial
> >>
> >>
> >>
> >> HI Tsjerk,
> >>
> >> Thanks for your reply. But, I can't see if it is going suddenly or
> >> gradually.
> >> What i can see is the ligand is away from the molecule after editing the
> >> gro file with PRODRG output.
> >>
> >> It seems liek PRODRG has modified the co-ordinates that places ligand
> away
> >> from the protein.
> >>
> >> ~Vivek
> >>
> >> 2010/1/25 Tsjerk Wassenaar <tsjerkw at gmail.com>
> >>
> >> Hi Vivek,
> >>
> >> > Now when I am processing the modified .gro file to generate box, the
> >> > ligand
> >> > and cofactor are going away from the protein molecule and I am not
> able
> >> > to
> >> > analyze the complex.
> >>
> >> Gradually going away, or suddenly jumping?
> >>
> >> In the latter case, read up on periodic boundary conditions.
> >>
> >> Tsjerk
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> Computational Chemist
> >> Medicinal Chemist
> >> Neuropharmacologist
> >> --
> >>
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
> gmx-users mailing list    gmx-users at gromacs.org
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