[gmx-users] splitting of chains

andrea spitaleri spitaleri.andrea at hsr.it
Fri Mar 30 15:51:41 CEST 2007

if I understand well your question, you are dealing with SS bond, are you? in vmd you may not see
the bond since vmd is guessing the SS bond based on the distance and not on your topology (actually
the new version 1.8.5 should work better). What I think it should be important for your simulation
is to check whether the SS bond is present in your topology in order to be used as it is during the
gromacs simulation. Check for the specbond.dat file

I hope that it helps



özge kül 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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Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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