----- Original Message ----- From: Venkat Reddy <[email protected]> Date: Saturday, March 7, 2009 17:09 Subject: Re: Re: Re: [gmx-users] How to break a disulfide bond ??? To: Discussion list for GROMACS users <[email protected]>
> Thanks Sharada madam n justin sir for ur kind attention.I followed ur command > "pdb2gmx -ss".its asking like > > Link CYS-37 SG-306 and CYS-59 SG-453 (y/n) ?n > Link CYS-44 SG-358 and CYS-50 SG-390 (y/n) ?y > Link CYS-72 SG-560 and CYS-101 SG-764 (y/n) ?y > Link CYS-82 SG-628 and CYS-93 SG-707 (y/n) ?y > Link CYS-150 SG-1137 and CYS-156 SG-1173 (y/n) ?y > Link CYS-203 SG-1546 and CYS-258 SG-1984 (y/n) ?y > Link CYS-210 SG-1603 and CYS-231 SG-1767 (y/n) ?y > > actually i want to break the s-s bond between CYS37 n CYS59 . so i've given > the options like as shown above. When i again visualized the pdb in pymol,its > showing the disulfides as it is (no break between CYS37 n CYS59). Can u > suggest me wat to do ???? See the bottom of this page http://wiki.gromacs.org/index.php/Trajectory_Visualisation Mark _______________________________________________ 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
