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<pre>><i>
</i>>><i> I doubt the chain identifiers are relevant. Both .gro and .pdb files should
</i>>><i> display properly. The only odd instance I can think of is that without separate
</i>>><i> chains, some programs may interpret the protein coordinates as a single
</i>>><i> molecule, but I would think that would only happen in the rarest of cases (when
</i>>><i> the termini are so close that the heuristic bond search algorithms think there
</i>>><i> should be a bond between the chains).
</i>>><i>
</i>>><i> When invoking trjconv, did you use any option to modify the periodic representation?
</i>><i> I used
</i>><i> trjconv -pbc mol -center -n index.ndx ......
</i>
OK, so this was just a periodicity issue all along.
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I'm sorry that I don't understand.<br>
So I did something wrong in PBC by trjconv?<br>
<br>
And I tried another way.<br>
I change the content of .gro file.<br>
I plus the number of residues in A-chain to B-chain's residue
number.<br>
And this new gro file shows the correct snapshot in VMD.<br>
for example<br>
my a-chain has 21 residues, b-chain has 30 residues.<br>
In output .gro file the residue number is 1 to 21 and 1 to 30.<br>
<br>
I'm afraid VMD got confused for the repeat number 1 to 21.<br>
So I change 1-30 in b-chain to 22-51.<br>
Then snapshot in VMD become correct. <br>
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<pre>
><i> Here I chose a-chain for center and protein for output.
</i>>><i> >/ Do I have any commend can use instead of chain identifier A and B
</i>>><i> />/ mannually?
</i>>><i> />/
</i>>><i> /
</i>>><i> I don't understand your question here.
</i>><i> I'm sorry.
</i>><i> I separate chains manually.
</i>><i> (Add chain identifier A and B manually in vim)
</i>><i> Do I have any commend of GROMACS can handle this and I don't need to
</i>><i> separate chains manually.
</i>><i>
</i>
With a merged chain, I think you will always have to add them back in.
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Thank you.<br>
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<pre>
-Justin</pre>
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