[gmx-users] S-S Bonds

Roberto Marchese 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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