[AMBER] Protonated state of GLU, CYS

From: Ngo Son Tung <nstung.ifpan.edu.pl>
Date: Mon, 20 Feb 2012 16:11:45 +0100 (CET)

Dear Expert,

I want to run simulation in constant pH with impicit solvent for Insulin
protein at pH 1.6. I used AmberTool version 1.4 (included in Ambermd 11)
make topology for this protein. I changed GLU to GL4, HIS to HIP ...
(follow Amber11 manual).
                        H
                        |
I found GLU become: R-C-O(+)-H
                      |
                   (+)O-H
                      | H H
                      H | |
and disulfate make by two CYS become: R-S(+)-S(+)-R

I have checked file constph.lib and other. I thinks I got good results.
But I'm not sure 100% because it our of my knowledge. Therefore, I write
the question here to ask about this. So, do you thinks it ok?

Regards, 

-- 
Son Tung Ngo
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Received on Mon Feb 20 2012 - 07:30:02 PST
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