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.
Hsin-Lin
-Justin
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