[gmx-users] SS bond

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 30 08:46:06 CET 2007

correafe at iq.usp.br wrote:
> Dear gmx users,
> We are trying to make an intermolecular cystine bond between two 
> residues in a dimeric protein (S:S - dist.: 0.203). The initial pdb file 
> should contain the SS bond. Therefore, we used the pdb2gmx -ss -merge to 
> generate the disulfide bond. Apparently it did not form the cystine and 
> added hydrogen atoms (HG). We have increased the cutoff in specbond.dat 
> (directory: /share/top/specbond.dat) from 0.2 to 0.4 and repeated the 
> commands above. We still did not observe the bond formation.
> Someone could help us ?
>                                    Thanks in advance,
The distance in the specbond file is not a cutoff but a bondlength. Your 
atoms should be within 10% of the target bondlength for the bond to be 
made. If pdb2gmx -merge does not work I'm not sure what the problem 
could be. Have you tried without -ss as well?
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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