Hello, I'm trying to use an implementation of the CHARMM force fields in Gromacs and I'm still a little bit confused about how Gromacs retrieves the bonded/non-bonded parameters when the .top file is created. Concretely, I have : 1. a ffcharmmnb.itp where I have defined specific 1-4 LJ parameters in the [pairtypes] section
2. a ffcharmmbon.itp where I have defined bonded parameters 3. a ffcharmm.rtp where I have defined the topology of amimo acids, etc. Since the [bonds], [angles], [dihedral] sections are optional in the .rtp file, I haven't defined them. How all these parameters are taken into account when I generate the .top file with pdb2gmx? When I look in the .top file, I see an [atoms] section but no [bonds] or [pairs] etc. and the charmm ff doesn't seem to be included with an #include command. So, are all my specific 1-4 parameters really taken into account in this case? In fact, I have tried to add somd bonds and improper but that generates a chunk of warnings when I use grompp. Sorry for this basic question but I'm still new in Gromacs... Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
