On 7/19/12 6:28 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
There is only one Cystein:
ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00
ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00
ATOM 1799 CB CYS A 211 12.968 1.606 4.452 1.00 1.00
ATOM 1800 SG CYS A 211 14.599 1.282 5.172 1.00 1.00
ATOM 1801 C CYS A 211 12.106 1.904 6.723 1.00 1.00
ATOM 1802 O CYS A 211 12.427 1.169 7.655 1.00 1.00
As I said before, -ss allows you to choose whether cysteine is free or involved
in a disulfide. With only one cysteine, there's nothing that -ss will do; there
is no possibility for a disulfide. If you need an anionic cysteine, you need to
use a force field that supports such a residue (Amber03 should) and name the
residue accordingly (CYM). Otherwise, CYS will be a free cysteine with the
normal protonated thiol.
-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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