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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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