[gmx-users] disulfide bond, molecule type
jiangsl at phys.sinica.edu.tw
Fri Jul 29 04:17:18 CEST 2011
> 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.
> >/ 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.
Thank you for your help.
I think I have no problem now.
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