Russell Green wrote:
Hello,
I just changed the disulfide max bond length in the specbond.dat file to
various numbers (0.4, 0.5, 1.2, 8.0, ...) and pdb2gmx only assigns some
of the disulfides in my protein but not all. If I use 0.4, it finds 22
of the 52 CYS residues to be in disulfide bonds when all 52 should be in
disulfide bonds. And, if I use higher bond lengths the number of
disulfide CYS found decreases. Where should I look next to sort out this
problem?
pdb2gmx will only make the bonds if they are within 10% of the
equilibrium length (0.2 nm).
Thanks,
Russell Green
On 7/1/07, *Mark Abraham* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Did you use specbond.dat correctly?
http://wiki.gromacs.org/index.php/specbond.dat
Mark
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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