[gmx-users] Disulphide bonds

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 1 16:05:20 CEST 2006

Cesar Araujo wrote:
> Cesar Araujo wrote:
>> Hi,
>> Anybody knows if there is some way to tell pdb2gmx to
>> recognize automatically S-S bonds and not through the modification of
>> specbond.dat file and -ss option???
> it does if they are within the normal distance. are your pdb files ok?
> I want to force some disulphide bond and simulate the structure to 
> compare both (with and without the S-S bond). I was wondering if GROMACS 
> can use SSBOND in pdb files directly. I'm writing some scripts using 
> Expect language but at the moment I'm stucked with some TCL stuff.

gromacs does not take such things into account. Doesn't the -ss option work?

> Regards,
> César.-
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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

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