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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