Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Hi all, > > I am trying to use AMBER96 ff under GROMACS package. I read the suggestions > that were given at http://chemistry.csulb.edu/ffamber/. > It has been stated that if any ion-related GROMACS tools will be used, then > the AMBER ion definition to the ions.itp file should be added. > So, does it mean that, I will copy the ions definitions that were given in > the ffamber96.rtp file to the ions.itp file? > I am a little bit confused because the definition of ions in AMBER is > completely different from those of OPLS and GROMOS ff.
I don't see how these definitions are "completely different." Use either of these sections (OPLS or GROMOS) in ions.itp as a guide and add the appropriate sections for AMBER96. Using the OPLS definitions will be most directly analogous in terms of how the atom types are defined. -Justin > > Thanks in advance > Ozge Engin > ================================= > Computational Science & Engineering > Koc University > _______________________________________________ > 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
