[gmx-users] disulfide bonds

Hagit G noolly at gmail.com
Sun Apr 29 11:52:38 CEST 2012

thank you very much

That was what I've tried to use "pdb2gmx    -ss", this is not useful,
'cause it's not in the same unit.
My problem is not the distance.


2012/4/29, Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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
> [moleculetype].
> Mark
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