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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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 <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
-- 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
