[gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang 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.
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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