The relevant question is whether there are inter-chain SS bonds.
Tsjerk On 3/30/07, özge kül <[EMAIL PROTECTED]> wrote:
After making Md simulation and getting the rmsd,gyration.. analyzing graphics I looked at the VMD.Then I saw that the 2 chains are getting splitting at a time.And then got together.So I could understand why the graphics are so bad.Then I read the manual.It says I should use -merge in pdb2gmx line if you have disulphite bridges.My molecule has 2 chains that has disulfite bonds..Anything else that you know about this except -merge? Thank you özge ________________________________ Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. _______________________________________________ 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
-- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
