[gmx-users] question about pdb2gmx

[Justin Lemkul]

On 7/19/12 6:28 AM, reisingere at 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

-- 
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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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