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" <eric.lang.bristol.ac.uk> 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" <soemya.kemi.dtu.dk> 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 : http://ambermd.org/tutorials/advanced/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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Received on Tue Dec 13 2016 - 03:30:05 PST
