[gmx-users] S-S Bonds
roberto.marchese at gmail.com
Mon Jul 2 13:11:30 CEST 2007
Dear GROMACS Users,
I want to do MD of insulin monomer (first two chain of 4ins.pdb).
When I convert with pdb2gmx, the software find only one ss bond (the
only inside the same chain). I have resolved this problem doing a
first conversion pdb->gro, then gro->pdb end in the final conversion
pdb->gro the software find the all three ss bond, and number the
residues of the two chain like one.
But now there is the big problem, when I do a two step minimization
(for bad contacts) the two chain go away, like no ss bonds exist.
Whit VMD I can see that all the S atoms is on one chain (the first,
whit have the internal SS bond). Then there are two CYS with two S
atoms and two (on the other chain) with no S atom.
I have cecked the topology file, and the bond between CB and S, and S-
S are all correct.
I think that the problem is inside the two chain configuration, but I
haven't explanation for the CYS without S.
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