[gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Thu Jul 28 06:57:06 CEST 2011

> 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 ......
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.


> -Justin
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