Quoting "E.M." <[EMAIL PROTECTED]>: > Greetings. > > I was wondering if any of you have a library file for oxaloacetate > compatible with > the atp files of any force field?. Your quick input would be greatly > appreciated, > also I was wondering, how to include these not standard molecules so I can > create an initial system?.
Parameters for ATP have already been derived and are included in the Gromos96 force fields. Check the .rtp files, and you will find ATP. As for oxaloacetate, you will likely have to derive parameters for them yourself, which is an advanced topic and should not be taken lightly. You would have to derive these parameters in a manner consistent with the derivation of the original force field. See here: http://wiki.gromacs.org/index.php/Parameterization As for including these parameters, search the manual for information about topologies, especially .itp files. -Justin > > > Thanks for the help > > Eduard > > _______________________________________________ > 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
