[gmx-users] simulate thiol radical without H

[Andrea Guelfi]

Hi GMXers,

I have a ligand that is not a peptide and has a pKa 8.5, so at
physiological pH it has a thiol radical without it’s hydrogen. 
I have simulated this ligand with –SH within an enzyme without any
problem.  I also have used the PrgDrg program in order to find out
it’s topology.
I would like to simulate a MD with this ligand without it’s hydrogen
(only -S). I have tried to have a topology at PrgDrg without this
particular hydrogen, but it didn’t worked fine.
Does someone have any idea how to solve this problem?

I appreciate your attention,

Andrea