Hello, Thank you for your response.
The topology file was propared using pdb2gmx. I changed one of the improper dihedral angles (CG-CD-CB-O) for HYP to (CG-CD-O-CB) and CG of HYP stopped inverting. There seems to be much less of proper dihedrals in the topology file on using pdb2gmx for GROMOS force fields compared to OPLS-AA or AMBER. For example, for the OPLS-AA there are 3 dihedrals in the topology around the N-CA bond: C(i-1) - N - Ca - Ha C(i-1) - N - Ca - C C(i-1) - N - Ca - Cb Following the same logic, there should be two dihedrals in the GROMOS topology file, but there is only one (C(i-1) - N - Ca - C). Any special reason for this? Abil ---------------------------------------- > Date: Sun, 19 Oct 2008 10:52:13 +0200 > From: [EMAIL PROTECTED] > To: [email protected] > Subject: Re: [gmx-users] HYP GROMOS > > Abil Aliev wrote: >> Hello, >> >> I have done calculations using standard GROMOS 43a1 and 53a6 parameters >> (GROMACS 3.3.3) for a 4-hydroxy-L-proline derivative (HYP), where the >> gamma-OH and the alpha-CO groups are trans to each other in the starting >> structure. However, over the course of MD the trans-configuration of >> these two substituents changes into a cis-configuration, which was not >> supposed to happen. Is there any way to avoid such isomerisation? >> > Dihedral potentials, maybe you need to add an improper... >> Abil >> >> >> >> Get the best wallpapers on the Web - FREE. Click here! >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > > > -- > David van der Spoel, Ph.D., Professor of Biology > 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 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 _________________________________________________________________ Catch up on all the latest celebrity gossip http://clk.atdmt.com/GBL/go/115454061/direct/01/_______________________________________________ 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
