Re: [gmx-users] angle between helices
On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. cheers, marc ___ 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] angle between helices
Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it cheers, marc ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] angle between helices
On Mon, Oct 29, 2007 at 09:54:08AM +0100, David van der Spoel wrote: Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it yes, i should perhaps mention that my program calculates the helix axes, using some rotational fit. but for TM helices, that stay helix anyway, this is not such a relevant feature. cheers, marc ___ 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] angle between helices
HI David there are options like g_helix, g_angle and as you said g_bundle, but none of them gives the angle between helix pairs. anupam Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it cheers, marc ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- 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
Re: [gmx-users] angle between helices
g_bundle does give the angle between helix pairs...? Not directly, admittedly, but it gives you the tilt from the main axes, which you can use with some basic math to work out the angle between helices. - Original Message From: Anupam Nath Jha [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, October 29, 2007 10:37:13 AM Subject: Re: [gmx-users] angle between helices HI David there are options like g_helix, g_angle and as you said g_bundle, but none of them gives the angle between helix pairs. anupam Marc F. Lensink wrote: On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote: Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. i wrote a program for that. contact me off-list. as soon as i find a free moment, i'll upload it to the contrib page. otherwise g_bundle might do it cheers, marc ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] angle between helices
Anupam Nath Jha wrote: Dear all can i calculate the angle between trans-membrane alpha-helices by using gromacs? Probably. Check out section 7.4 of the manual. Mark ___ 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
