Hi Neha, I guess you're referring to John Kerrigans tutorial, but it would usually help if you specified the one you're using. I think the tutorial should have a sentence stating that the ligand mayb be seen away from the protein during the simulations, but that that is due to the periodic boundary conditions. On another note, protein-ligand interactions is one step further than 'performing simulations' and I think you'd be better of first taking a tutorial on plain protein simulations. The one I linked on the gromacs wiki (http://nmr.chem.uu.nl/~tsjerk/course/molmod/) specifically addresses issues such as PBC jumps, and some other basic stuff, which may help you to get a feel for the things you may encounter when doing simulations.
Cheers, Tsjerk On Sun, Mar 29, 2009 at 3:30 AM, Neha Gandhi <[email protected]> wrote: > Many thanks Justin, > > It worked! > > 2009/3/29 Justin A. Lemkul <[email protected]>: >> >> >> Neha Gandhi wrote: >>> >>> Hi List, >>> >>> 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated >>> annealing followed by production runs of 5ns usng NPT and PBC and >>> PME.. After 5ns, the protein moves far away from the ligand. I >>> checked the 4ns gro files, the ligand and protein are bound together, >>> but its only that 5ns gives issues. >>> >>> 2) I ran another similar but smaller system and the complex is stable >>> even after 8ns. >>> >>> What went wrong with the simulations in case 1? Is there a way to fix >>> this problem? >> >> Did the protein and/or ligand cross a periodic boundary? If so, trjconv can >> "fix" this visualization artifact. >> >> -Justin >> >>> Your help is much appreciated. >>> >>> >>> Regards, >>> Neha Gandhi, >>> School of Biomedical Sciences, >>> Curtin University of Technology, >>> GPO Box U1987 Perth, >>> Western Australia 6845 >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://www.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 >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.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 >> > > > > -- > Regards, > Neha Gandhi, > School of Biomedical Sciences, > Curtin University of Technology, > GPO Box U1987 Perth, > Western Australia 6845 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.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
