[gmx-users] disulfide bond, molecule type
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.
I convert .gro to .pdb by trjconv and add chain identifier A and B to
(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
Do I have any commend can use instead of chain identifier A and B mannually?
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