Re: [AMBER] pka of CYS

From: Eric Lang <>
Date: Tue, 13 Dec 2016 13:43:44 +0000

Hi Carlos,
I think that as long as Cys is defined as being a titrable residue, the
partial charge on each atom of the residue for the two states (protonated
and deprotonated) are defined in (which is part of
Parmed). In particular the charge on the titrable hydrogen becomes 0.00 in
the deprotonated form and the charges on all atoms of the side chains are
changed to reflect the deprotonation. Overall during CpHMD the hydrogen are
not actually removed (i.e. changing from one residue type to another e.g.
CYS to CYM) but instead the hydrogen in "masked" by zeroing its charged and
changing the charge of adjacent atoms. It is a change of state (state 1 to
state 0 for the deprotonation of Cys) for a single residue type (CYS)
I believe however that the the Van der Waals radius does not change between
the protonated and deprotonated form as it does not seem to have an impact
on the quality of the result (as shown in the original Mongan paper where
the effect of the VdW radius of the titrable hydrogens in Lys (non-zero)
was compared with the radius of titrable hydrogens in Glu and Asp (where is
is zero)).
Please Jason, correct me if what I said is wrong or incomplete.

On 13 December 2016 at 11:09, Carlos Simmerling <
> wrote:

> I don't think that will work. The parameters for Cys without the bond are
> not at all the same as a deprotonated (negatively charged) Cys. You will
> need to find or make Cys- parameters, and then develop the reference
> energies needed for the pka calculations. Someone else may have better info
> (Jason?).
> On Dec 13, 2016 2:33 AM, "Eric Lang" <> wrote:
> Hi,
> You just need to add CYS to the list of titrable residues (using the
> resname flag for example) when you generate your cpin file with cpinutil.
> Eric
> On 12/12/2016 20:16, "Sowmya Indrakumar" <> wrote:
> Dear All,
> I am trying to calculate pka of CYS in a given protein at constph. I simply
> keep the bonded CYX-CYX as non-bonded CYS-CYS and remove the conect record
> from the PDB file before making the *.parm7 and *.rst7 files for MD.
> I am following whats mentioned in the given link to calculate the Pka of
> ASP,GLU and HIS :
> dvanced/tutorial18/section1.
> htm <> at
> constph.
> I did not come across any article which shows how to calculate pKa for CYS
> residues. Kindly, suggest me on this.
> Thanks
> Sowmya
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Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Tue Dec 13 2016 - 06:00:03 PST
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