Hsin-Lin Chiang wrote:
>/
/>>/ 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?
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
>/ 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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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