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