[gmx-users] How to break a disulfide bond ???

[Mark Abraham]

----- Original Message -----
From: Venkat Reddy <venkat4bt at gmail.com>
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 <gmx-users at gromacs.org>

> 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