[gmx-users] Cys-Cys Bond

[Mark Abraham]

fulya caglar wrote:
> Hi everone.
> I'm studying on a protein including two chains with *four* disulfide 
> bonds.when I
> watched the simulation I saw that A and B chains were splitting from
> eachother.

Check your topology. This will mean that you didn't define the 
disulfides in the first place. You should also read your pdb2gmx output 
closely, where it should be telling you how many it did find (and create).

> Then I gave that command.
>    pdb2gmx    -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro  -merge  
> -ss  -inter   -ignh.
> But the chains split from eachother again.In specbond.dat only one 
> CYS-CYS bond appears.Should I  add three more lines to the file like this?
> CYS  SG   1     CYS    SG    1   0.2   CYS2   CYS2
>  
> What can I do to identify the  -SS bond other than these?

Identify how far apart those sulfur atoms are in the structure you're 
feeding to pdb2gmx. You may need to edit specbond.dat to increase the 
length that it searches for possible disulfide bonds (search the mailing 
list on this topic). Or you can do a quick geometry optimization with 
restraints on the relevant pairs to bring them close enough that pdb2gmx 
will find them.

Mark