On 3/18/13 10:49 PM, shahid nayeem wrote:
I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid
My apologies. For some reason I always think there is a -cys option, when in
fact it is -ss. In any case, if you're trying to treat some strange form of
cysteine, some force fields have special names for different forms (CYM for
thiolate, etc) so naming and proper force field choice may be the only viable
mechanism here.
-Justin
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
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========================================
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
========================================
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