Quoting [EMAIL PROTECTED]: > > > Hi all, > I have been try to put up MD simulation of guanidium chloride simulation > in SPC water model.I have been facing problem regarding *.rtp, *.itp > file generation for new entry for guanidium ion.If any one is aware > about how to create above mentioned file please let me give some insight > about file corresponding guanidium ion. > I tried to make it with argenine side chain but i have been facing > problem while generating above mentioned file.
http://wiki.gromacs.org/index.php/Parameterization You could use PRODRG to generate the topology, but you will have to validate the parameters (see the above link), especially the charges that PRODRG assigns. They are often unsatisfactory. -Justin > > > kinshuk raj srivastava > IIT-Bombay > Mumbai, India > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users@gromacs.org 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
