Quoting Robert Fenwick <[EMAIL PROTECTED]>: > > > Hi, > > I would like to make some unrestrained simulations of ATP and GTP > binding proteins and wondered if there were any topology files > floating about for OPLSAA or the GROMOS96.1 forcefields for these two > ligands?
ATP is present in ffG43a1 (have a look at the .rtp file), and GTP has been discussed across this list within the last few days (check out the archives). -Justin > > I understand that the gmx forcefields have been deprecated and that I > should use one of the newer ones, however there are not that many > ligand topology files about. > > I am just starting out, so any suggestions would be welcome. The > systems are approximately 300 residues in size and I am interested in > the stability and rms fluctuations of the systems. > > A secondary question is that of the AMBER forcefields, I am using the > 3.3.2 version, however the amber files state specifically to use the > port for the relevant version, one of which is missing for 3.3.2. Is > it safe to use the 3.3.1 amber ff port with version 3.3.2 of GROMACS? > > Finally, if anyone can point me in the direction of a small test > project that does some simple replica exchange, with some > instructions as to how to get it to run, I would be very grateful. > > > Bryn > > > > > > > > > _______________________________________________ > 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 Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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
