VMD-L Mailing List

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Tue Oct 13 2009 - 01:02:30 CDT

Dear VMD users:

I am studing conformations of a protein that has three disulfide bonds in its native state, I equilibrate the system (protein plus explicit water) at 1000 K during 10 ns using molecular dynamic simulation with NAMD. Now I want to analyse structures that were produced during the simulation. I need to identify if disulfide bonds have been broken o not. Does anybody know how can I do that? Are there any script to do it?

Thanks for your suggestion

Andres
                                               
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