[gmx-users] disulfide bonds

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 29 11:16:39 CEST 2012

On 29/04/2012 7:02 PM, Hagit G wrote:
> I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb
> The main problem is: When I use pdb2gmx it adds H atoms to Cys,
> hence the disulfide bonds are no longer conected after energy minimization.
> How can I avoid this addition of H atoms?
> (I tried to make this bond after, but I didn't make it because one Cys
> is in the long chain and the other one is in the short chain)

See http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds 
about requirements for having atoms (and thus chains) in the same 


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