[gmx-users] splitting of chains

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 30 15:48:13 CEST 2007

The relevant question is whether there are inter-chain SS bonds.


On 3/30/07, özge kül <ozgekul8233 at yahoo.com> wrote:
> After making Md simulation and getting the rmsd,gyration.. analyzing
> graphics I looked at the VMD.Then I saw  that the 2 chains are getting
> splitting at a time.And then got together.So I could understand why the
> graphics are so bad.Then I read the manual.It says I should use -merge in
> pdb2gmx line if you have disulphite bridges.My molecule has 2 chains that
> has disulfite bonds..Anything else that you know about this except -merge?
> Thank you
> özge
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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