Re: [AMBER] pka of CYS

From: Carlos Simmerling <>
Date: Tue, 13 Dec 2016 06:09:57 -0500

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

On Dec 13, 2016 2:33 AM, "Eric Lang" <> wrote:

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.

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
htm at constph.

I did not come across any article which shows how to calculate pKa for CYS
residues. Kindly, suggest me on this.


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Received on Tue Dec 13 2016 - 03:30:05 PST
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