Hi Rick, I found this thread which is of immediate interest to me, so I hope you and preeti do not mind if I barge in with two questions of my own.
I am working with a coiled-coil parallel dimer. I am generating my .psf .crd and .pdb files for the dimer by GENErating each chain separately from a pdb xtal structure and appending the two chains before minimization. The published structure shows a disulfide bond, although at the published resolution (2.3angstroms), the author admits that it is not completely clear that the structure is cross-linked. This molecule is known to be experimentally oxidized though it is not known if the cross-link is functionally relevant.
After generating, appending and minimizing my structure for MD, the charmm generated structure that is produced is cross-linked (ie. -S-S- bond is present) like the original pdb structure file. Given your comment here, do I still need to include a PATCh DISU ... command when appending the chains eventhough the generated structure is actually disulfide cross-linked?
In order to remove the cross-link, I am assuming that I have to manually rotate about the C-S bond and re-minimimize the structure. If there a simpler way to do this, could you point me to it?