>/ />>/ 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.
I'm sorry that I don't understand. So I did something wrong in PBC by trjconv?
And I tried another way. I change the content of .gro file. I plus the number of residues in A-chain to B-chain's residue number. And this new gro file shows the correct snapshot in VMD. for example my a-chain has 21 residues, b-chain has 30 residues. In output .gro file the residue number is 1 to 21 and 1 to 30. I'm afraid VMD got confused for the repeat number 1 to 21. So I change 1-30 in b-chain to 22-51. Then snapshot in VMD become correct.
>/ 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.
Thank you.
-Justin
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