[gmx-users] Amber and protonation state

Arik Cohen acohen at biochem.duke.edu
Fri Feb 26 09:42:59 CET 2010

Dear users,

I would be most thankful for any comment or advice on the following 

1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield. 
While executing the pdb2gmx command as: pdb2gmx -f 1bgq.pdb -water tip3p 
the -his option does not work regardless of the choice in the 
protonation state

2. Is there any way to change the protonation state not via an 
interacticve mode and thus to enable to run the pdb2gmx in an automatic 
way(echo 10 | pdb2gmx ... | -his echo 2 will not work of course)

Thanks a lot


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