[gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx

Mark Abraham Mark.Abraham at anu.edu.au
Sun May 24 08:02:25 CEST 2009

Chih-Ying Lin wrote:
> Hi
> after the command pdb2gmx,
> the protein will be added appropriate H,
> So, does pdb2gmx add H (protonate) based on pH =7.0 ?

No. You should choose the protonation state based on your understanding 
of the conditions you wish to model, and instruct pdb2gmx accordingly. 
Read pdb2gmx -h. Do some tutorials - this sort of thing is covered there.


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