[gmx-users] SS bridges

Xavier Periole x.periole at chem.rug.nl
Mon Jul 12 15:38:10 CEST 2004

Dmitry Kovalsky wrote:

>However there are Cys-Cys bonds within one chain that are not processed 
>properly also. 
>Any way I tried -merge and this does not result in merging SS bonds.
>Any ideas?
>If I manually substitute in top file all CYSH entries with CYS2? Is it a walk 
Don't forget to modify your topology file where the atom numbers are 
going to be
changed and consequently all the topology.
Did you try to define it as CYS2 in the pdb before running pdb2gmx ???
Try another version of gromacs to generate the topology, I did the 
cys-cys intra through
the -ss and it worked. That was 3.0 version.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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