한상화 wrote: > Dear Mark, > Could you kindly tell me how it can be done?
The general procedure is to get a structure with the relevant S atoms close enough together, then use pdb2gmx -ss on that structure (possibly with -ignh too). You may need to copy specbond.dat from the library to your working directory and edit it to increase tolerance for SS bond or similar. You may need to do an MD simulation with a harmonic restraint to position the sulfur atoms close enough for the new structure to be vaguely realistic. > Or tell me where in the manual to look up? Unfortunately it isn't there. Searching the mailing lists from the gromacs webpage is a good start, though. > What I am trying to do is either generating a new residue CysS-SG (named > CYG, for example) or forming a disulfide between CysSH and GSH during > running Gromacs (I am not sure if there is a command or flag for this > purpose). You'll have to be prepared to get your hands dirty for the former, but the latter should be painless (not that I've ever done it). Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
