Re: [AMBER] pka of CYS

From: Sowmya Indrakumar <>
Date: Tue, 13 Dec 2016 15:21:59 +0000

Dear All,
Thank you for your suggestions.

I included CYS in the list of -resnames and could create the *.cpin. I could run the minimisation properly using sander, but running heating step using pmemd.cuda gave this error message *STOP PMEMD Terminated Abnormally!*
The above MD is been run for implicit solvent, but this doesn seem to work if I use explicit solvent (i get the same error message).
Kindly, suggest me.

From: Adrian Roitberg []
Sent: Tuesday, December 13, 2016 3:18 PM
Subject: Re: [AMBER] pka of CYS


Have you tried just using CYS as a titratable residue ?

If you try -l

you will see that CYS is already properly defined as titratable, with
all parameters already there.

You can also look at

This is a paper by Jason Swails and myself, were there are some
calculations for Cysteine.


On 12/13/16 8:43 AM, Eric Lang wrote:
> 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.
> Eric
> 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
>> _______________________________________________
>> AMBER mailing list
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>> AMBER mailing list

Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
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Received on Tue Dec 13 2016 - 07:30:02 PST
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