[gmx-users] breaking S-S bond using pdb2gmx

[Sahithya S Iyer]

Deal all,
I need to break 1 out of 4 S-S bonds in a protein. While using the pdb2gmx
command, i used -ss whereby i was asked which S-S bonds i would what to
keep intact and which i'd break. Since i wanted the S-S bond between CYS
6-CYS 127 to be broken, i gave he following command -
Link CYS-6 SG-48 and CYS-127 SG-981 (y/n) ?n
Link CYS-30 SG-238 and CYS-115 SG-889 (y/n) ?y
Link CYS-64 SG-513 and CYS-80 SG-630 (y/n) ?y
Link CYS-76 SG-601 and CYS-94 SG-724 (y/n) ?y
The .gro file generated , visualised using vmd, shows 4 S-S bonds instead
of 3. Where have i gone wrong. Is there any other method the break the S-S
bonds present in the pdb file ?
Thanks in advance.

-- 
Sahithya S Iyer