Re: [gmx-users] GTP topology generation in OPLS-AA force field
Bear in mind that parameterising a new molecule is an advanced topic. Maybe an easier solution would be to use another forcefield which already has a GTP topology. For example the amber forcefields I know to have GTP parameters available, all you would have to do is to convert them into GROMACS format. Tom --On Wednesday, April 30, 2008 06:49:35 -0400 "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Quoting Shankar Prasad Kanaujia <[EMAIL PROTECTED]>: Dear gmx-users, I want to run MD for my protein with GTP compound. I am using OPLS-AA force field. How can I generate the topology file for GTP in OPLS-AA force field ? Derive parameters consistent with the methods used to generate the original force field. http://wiki.gromacs.org/index.php/Parameterization -Justin Thanking you all for your kind support and suggestions. --- Yours Sincerely, Shankar Prasad Kanaujia Research Student C/O - Dr. K. Sekar Bioinformatics Center, Department of SERC IISc, Bangalore - 12, INDIA. Office Phone: 2469, 3059 Mobile: 9845631581 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-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 listgmx-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 -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-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
Re: [gmx-users] GTP topology generation in OPLS-AA force field
Quoting Shankar Prasad Kanaujia <[EMAIL PROTECTED]>: > Dear gmx-users, > I want to run MD for my protein with GTP compound. > I am using OPLS-AA force field. How can I generate > the topology file for GTP in OPLS-AA force field ? Derive parameters consistent with the methods used to generate the original force field. http://wiki.gromacs.org/index.php/Parameterization -Justin > > Thanking you all for your kind support and suggestions. > > --- > Yours Sincerely, > Shankar Prasad Kanaujia > Research Student > C/O - Dr. K. Sekar > Bioinformatics Center, Department of SERC > IISc, Bangalore - 12, INDIA. > Office Phone: 2469, 3059 > Mobile: 9845631581 > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > ___ > gmx-users mailing listgmx-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 listgmx-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
[gmx-users] GTP topology generation in OPLS-AA force field
Dear gmx-users, I want to run MD for my protein with GTP compound. I am using OPLS-AA force field. How can I generate the topology file for GTP in OPLS-AA force field ? Thanking you all for your kind support and suggestions. --- Yours Sincerely, Shankar Prasad Kanaujia Research Student C/O - Dr. K. Sekar Bioinformatics Center, Department of SERC IISc, Bangalore - 12, INDIA. Office Phone: 2469, 3059 Mobile: 9845631581 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-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
