[AMBER] Parametrization of the protein with the assigned protonation states

From: James Starlight <jmsstarlight.gmail.com>
Date: Tue, 3 Jun 2014 19:44:07 +0200

Dear Amber users!

I'd like to assign protonation states of the titrable residues of my
protein using proPKa server and make further parametrization of its outtput
pdb consisted of protein with hydrogens using some of the amber parameter
sets keeping all hydrogens and protonation states predicted by ProPKa. I've
tried to do such task using amber99sb ff but some residues like
deprotonated CYS have not been recognized by that param set. What exactly
force field should I use ? Has the amber itself program for such
calculations instead of using proPK?


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Received on Tue Jun 03 2014 - 11:00:02 PDT
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