fix disulfide bond in coarse grain(CG) model for NAMD

From: Deng, Jinxia (Nancy) (jinxianancy.deng_at_zoetis.com)
Date: Mon Oct 24 2016 - 11:46:11 CDT

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Hi All,

I thought i fixed the disulfide bond for the CG model, and it shows in the psf file as:

 REMARKS patch DISU A:37 A:46
 REMARKS patch DISU A:33 A:50

But by vmd, i could not see the two cys connected, as in the atomic model.

And during the simulation, the MD shows the atom pairs felt apart, means dosn't seem that the bond is there.

What I did was to follow the tutorial so called: residue-based coarse graining using Martini Force Field in NAMD.

And I patch the disulfide bond for the atomic model by vmd eyeball check, then patch the coarse grain model by path...

So, i guess my question is how i can be sure the dirsulfind bond is there in the coarse grain model, by eyeball check in vmd or in certain file.

Any advice is greatly appreciated.

Nancy

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