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 <[email protected]> > 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 > [email protected] > +61 3 9903 9167 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > *From:* [email protected] [mailto: > [email protected]] *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 <[email protected]> > > 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 > -- > > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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