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 <tsje...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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