Hi Victor, Assigning the right parameters for a molecule is a difficult task, and a single run of PRODRG is usually just the beginning. Search the archives and maybe also the wiki for more information, and read a few papers where simulations of proteins were done with hetero-molecule if you haven't done so already.
It's not a good idea to have a residual charge. You can obviously scale this, but I would start by verifying that the PRODRG charges make sense in any case. Ran Victor Manuel Rosas-Garcia wrote: > Hello everybody, > > I'm trying to use gromacs to model an aza-type macrocycle (17 atoms around > the ring). The structure does not include any aminoacids or sugars so, I'm > building the itp file by hand. I started with a base topology from the > PRODRG server and then added all the missing hydrogens (I want to use > OPLS/AA). The problem is that, after assigning all the atom types as best as > I could, I end up with a residual charge = -0.034. The macrocycle itself > should be neutral. Does this mean I need to develop new parameters? Is there > any way to fix this without reparametrizing? > > Thanx > > > Victor M. Rosas García > > > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > _______________________________________________ > 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 > > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ 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
