[gmx-users] disulfide bond, molecule type

[Justin A. Lemkul]

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

-- 
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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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