I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx. shahid
On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul <[email protected]> wrote: > > > On 3/18/13 10:39 AM, shahid nayeem wrote: >> >> Hi All >> How can I get a topology file using pdb2gmx from a single chain >> polypeptide with one of the CYS, SH in the form of SG as if it is >> involved in disulfide linkage, while the other chain with which I >> expect it to form disulfide link is not in the input pdb file. or can >> I use pdb2gmx command and get the separate .top and .gro file for each >> chain using index file. >> > > You may be able to use the -cys option to fool pdb2gmx, but I don't know if > that will cause problems. Having half a disulfide present is odd, though > some force fields support thiolate or neutral (i.e. radical) forms of > cysteine. You'll have to look into the force field files to see what's > available. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
