[gmx-users] disulfide bond, molecule type

[Hsin-Lin Chiang]

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.

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?

Sincerely yours,
Hsin-Lin