[gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Thu Jul 28 06:20:06 CEST 2011

> If you have heated your system severely, you may have generated an unstable
> system that is on the verge of crashing.  VMD seems to allude to some weird
> geometry and PyMOL would seem to confirm that.  I don't know why Rasmol appears
> OK.  If you've somehow "lost" residues then they probably have infinite
> coordinates and your simulation has blown up and is therefore junk.
> -Justin
I convert .gro to .pdb by trjconv and add chain identifier A and B to 
.pdb file.
(Because of -chainsep all chain identifier was delete before MD)

Then VMD and Pymol shows correct as Rasmol.
So, maybe the error of snapshot was just because chain identifiers were 
lacked before.

Do I have any commend can use instead of chain identifier A and B mannually?

Sincerely yours,

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