[gmx-users] protonation state

[Erik Lindahl]

David wrote:

>On Sat, 2002-11-09 at 04:11, Wei Fu wrote:
>
>>Hi, all,
>>
>>     When I consider the protonation state on dopamine receptor I found that in "pdb2gmx -inter" there is no option for ARG residue, why so? I think ARG is also an improtant residue for protonation state and I would like to consider its protonation state, how do I consider it?  Or am I wrong?
>>
Just change the name of the residue from ARG to ARGN in the PDB file, 
and pdb2gmx will pick if the neutral version of ARG from the residue 
topology database. At least OPLS/AA has neutral ARG, but I'm pretty sure 
it exists in the other forcefield too.

You will still have to make sure you pick the right proton for the 
change of protonation state by editing the PDB file. This cannot be done 
automatically for obvious reasons.

Cheers,

Erik