[gmx-users] How to define the protonated state of a protein

[PeiQuan Chen]

Dear gmx-users，

I am a newbie in protein simulation. So maybe my question is so silly. 
In my protein, there is Asp Glu His Arg and Lys. I what to user pdb2gmx -inter to specify the protonated state of this residue. But I don't have any experience on it. Could anybody give me a help?

The following is my view, is it right? Please help me to correct it?
I assume the pH value is equal 7.

Asp<->Asp-
Glu<->Glu-
Arg<->Asp+
HIS<->HIS+
Lys<->Lys+

Thank you in advance!

Sincerely yours
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PeiQuan Chen
________________________________________________________________________
PeiQuan Chen, Ph.D Student, Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223507510(HOME) (86)23505264 Mobile Phone: (+86)13920675030
pqchen at mail.nankai.edu.cn
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