[gmx-users] disulfide bond, molecule type

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 28 05:50:37 CEST 2011

Hsin-Lin Chiang wrote:
>> Hsin-Lin Chiang wrote:
>> >/ Hi,
>> />/ 
>> />/ I'm trying to heat a protein.
>> />/ There are two chains, A-chain and B-chain.
>> />/ Two disulfide bonds are between A-chain and B-chain.
>> />/ As I know, I should let A-chain and B-chain belong to the same [molecule 
>> />/ type] in .top file if I want to have the two inter-bonds.
>> />/ 
>> />/ So, I delete the TER line between A-chain and B-chain in .pdb file.
>> />/ And then I use "pdb2gmx -chainsep interactive" on it .
>> />/ 
>> />/ I got the two bonds successfully.
>> />/ But after heating, the length of A-chain and B-chain in VMD was changed.
>> />/ The number of residues in A-chain increase and the ones of B-chain 
>> />/ decrease.
>> />/ It means some residues move from B-chain to A-chain.
>> />/ How should I prevent this kind of error happen.
>> />/ 
>> /
>> The labeling changes?  Is this something VMD is doing or something you can 
>> actually demonstrate in the coordinate file?
> Labeling didn't change.
> I don't know what VMD did.
> It seems to some residues disappear, A-chain was elongated, and B-chain 
> was shortened.
> I also tried Pymol.
> It gave me several small crash peptides.
> But I just tried Ramol, everything looks correct.
> Something wrong in VMD and Pymol may just because A-chain and B-chain 
> curved extremely after heating.
> But I'm still afraid
> Is my output structure wrong by GROMACS?

If you have heated your system severely, you may have generated an unstable 
system that is on the verge of crashing.  VMD seems to allude to some weird 
geometry and PyMOL would seem to confirm that.  I don't know why Rasmol appears 
OK.  If you've somehow "lost" residues then they probably have infinite 
coordinates and your simulation has blown up and is therefore junk.


> Sincerely yours,
> Hsin-Lin
>> >/ Besides, I found even though I only have protein_A which consist both of 
>> />/ A-chain and B-chain.
>> />/ The number of first residue of B-chain is started from 1 in .gro file.
>> />/ I thought it should be equal to "the number of A-chain's residues plus 1".
>> />/ 
>> />/ And it was also strange that the number of first water molecules was 
>> />/ equal to "the number of B-chain plus 1"
>> />/ I thought it should be equal to "the number of A-chain's residues plus 
>> />/ the number of B-chain's residues plus 1"
>> />/ 
>> />/ Is it a bug?
>> />/ 
>> /
>> No, it is the expected output.  By default, pdb2gmx does not renumber residues 
>> consecutively.  This feature was introduced some time ago so that output 
>> selections could easily be made in multiple chain molecules like this one.  If 
>> you want residues renumbered consecutively, either post-process the coordinate 
>> files with genconf -renumber or start over and use pdb2gmx -renum.
> Thank you for your explanation.
>> -Justin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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