[gmx-users] disulfide bond, molecule type
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
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?
> >/ 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.
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