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.
Mark
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