[gmx-users] disulfide bond, molecule type

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 28 06:24:48 CEST 2011

Hsin-Lin Chiang wrote:
>> 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.

I doubt the chain identifiers are relevant.  Both .gro and .pdb files should 
display properly.  The only odd instance I can think of is that without separate 
chains, some programs may interpret the protein coordinates as a single 
molecule, but I would think that would only happen in the rarest of cases (when 
the termini are so close that the heuristic bond search algorithms think there 
should be a bond between the chains).

When invoking trjconv, did you use any option to modify the periodic representation?

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

I don't understand your question here.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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