[gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Thu Jul 28 05:47:56 CEST 2011

> 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?

Sincerely yours,
> >/  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
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