[gmx-users] disulfide bond, molecule type

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 28 13:03:03 CEST 2011

Hsin-Lin Chiang wrote:
>> 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?
> I used
> trjconv -pbc mol -center -n index.ndx ......

OK, so this was just a periodicity issue all along.

> Here I chose a-chain for center and protein for output.
>> >/ Do I have any commend can use instead of chain identifier A and B 
>> />/ mannually?
>> />/ 
>> /
>> I don't understand your question here.
> I'm sorry.
> I separate chains manually.
> (Add chain identifier A and B manually in vim)
> Do I have any commend of GROMACS can handle this and I don't need to 
> separate chains manually.

With a merged chain, I think you will always have to add them back in.



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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