> I did try changing the bond length but it wouldn't catch all the > disulfides. I do have multiple chains but I don't believe they should be > merged. My current work around is to just leave the disulfide residues > named > CYX according to the amber format and then change them to CYS2 in the .itp > files for the corresponding .top file. This way pdb2gmx doesn't protonate > the disulfide residues and the charges for CYS2 are maintained. If anyone > thinks this is not a good idea, please tell me.
You still won't get them bonded with this procedure... you need a .top file with S-S bonds, and you get that by producing one by hand or using pdb2gmx. If you want pdb2gmx to recognise your S-S bonds, and for some reason which isn't clear to me, some of thse bonded sulfurs are more than 2A apart, then you should do a preliminary minimization with constraints on these S-S pairs to bring them closer together so that pdb2gmx can recognise them. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
