Hi Stephan, With 'collide in a specific way based on Docking', do you mean to pull them together? I'm not certain that will be protocollized easily. And your ligands, are they protein/peptide too, or do you have topologies for them? If not, it is likely to become more dirty than quick.
Interesting mismatch between your signature and the name from the mail address, btw :p Cheers, Tsjerk On Mon, Mar 29, 2010 at 3:20 PM, lloyd riggs <[email protected]> wrote: > > Dear Folks, > > I am new to posting here. In any case, I wanted to set initial trajectories > for two large macromolecules. Basically I am using gromacs for several > things, on would be simple energy calculations. For this I wanted to take to > proteins, or protein and larger ligands and set an initial trajactory for > these in the solvent so that they collide in a specific way based on Docking, > other things etc...as a quick and dirty type run. > > Does anyone have a really simple protocol, > > such as a) input output > b) input output, etc... > > I have read several things in the manual that state this is possible, but I > wanted to avoid a day of trying to get it to work, and just get it to work > quickly. > > Grüsse > > Stephan Watkins > -- > GMX DSL: Internet, Telefon und Entertainment für nur 19,99 EUR/mtl.! > http://portal.gmx.net/de/go/dsl02 > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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
