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

PeiQuan Chen gromacs at 163.com
Thu Oct 28 19:52:23 CEST 2004

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.


Thank you in advance!

Sincerely yours
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

More information about the gromacs.org_gmx-users mailing list