[gmx-users] protonated cys -S

[David van der Spoel]

Giacomo Bastianelli wrote:
> Hi Tsjerk,
> 
> the distance of the "not formed" S-S is 0.202
> while the two "formed" S-S are 0.204 and 0.203.
> Therefore, gromacs should recognize all three and
> create the SS bonds.
> 
> CYS    SG    1    CYS    SG    1    0.2    CYS2    CYS2
> 
> this is the second line of my specbond.dat
> 

please check the output of pdb2gmx, in particular the distance matrix, 
and report it back to the list (completely) if there are problems.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++