[gmx-users] disulfide bond, molecule type

[Hsin-Lin Chiang]

> No.  You said before you had broken chains.  Applying trjconv -pbc mol fixes
> this issue.  Molecules can be "broken" across periodic boundaries and is an
> entirely normal phenomenon.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> >/  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.
> /
> Then this was primarily VMD's issue.
>
> -Justin
Thank you for your help.
I think I have no problem now.

Hsin-Lin

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