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

From: Jason Swails <>
Date: Tue, 3 Jun 2014 13:59:34 -0400

On Tue, Jun 3, 2014 at 1:44 PM, James Starlight <>

> 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.

​Deprotonated CYS is available in ff99SB (as well as ff12SB and ff14SB).
 You have to rename the residue CYM instead of CYS (CYX is for cysteines
involved in a disulfide bond). Among the various residues that Amber
provides with different protonation states:

ASP - deprotonated aspartate
GLU - deprotonated histidine
CYS - protonated cysteine
LYS - protonated lysine (+1 total charge)
HIS/HIE - histidine protonated at N-epsilon
HID - histidine protonated at N-delta
HIP - histidine protonated at both N-epsilon and N-delta
ASH - protonated aspartic acid
GLH - protonated glutamic acid​
CYM - deprotonated cysteine
LYN - deprotonated (neutral) lysine

The trick in all cases to change the protonation state is to change the
residue name in the PDB to the residue name Amber recognizes as the
"correct" protonation state (correct in the sense that is the protonation
state you want to model).

If one is not on this list (like deprotonated tyrosine), you will have to
derive charges and create a library file for that residue (or find one that
someone else has created already).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jun 03 2014 - 11:30:02 PDT
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