[AMBER] pka of CYS

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Mon, 12 Dec 2016 20:14:03 +0000

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.


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Received on Mon Dec 12 2016 - 12:30:02 PST
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