Re: [AMBER] pka of CYS

From: Eric Lang <>
Date: Tue, 13 Dec 2016 07:33:05 +0000

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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