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<pre>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?
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I used<br>
trjconv -pbc mol -center -n index.ndx ......<br>
Here I chose a-chain for center and protein for output.<br>
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<pre>
><i> Do I have any commend can use instead of chain identifier A and B
</i>><i> mannually?
</i>><i>
</i>
I don't understand your question here.
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I'm sorry.<br>
I separate chains manually.<br>
(Add chain identifier A and B manually in vim)<br>
Do I have any commend of GROMACS can handle this and I don't need to
separate chains manually.<br>
<br>
Hsin-Lin<br>
<br>
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<pre>
-Justin</pre>
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