[gmx-users] disulfide bond, molecule type
jiangsl at phys.sinica.edu.tw
Thu Jul 28 17:37:42 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 ......
> 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.
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.
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