On Fri, Oct 9, 2015 at 10:02 AM, Arjun Sharma <arjunsharma83.gmail.com>
wrote:
> Dear Jason,
>
> I tried what you suggested in the previous post but that didn’t help. I
> checked for any flipped signs but everything looks fine. Here is my cpin
> file. It is just a residue long (monomer) (CH3)3-C-COOH with pKa = 4.65.
> &CNSTPH
>
> CHRGDAT=-0.18,0.6,0.6,0.6,-0.1,-0.18,0.6,0.6,0.6,-0.18,0.6,0.6,0.6,0.7,-0.8,
>
> -0.8,0.0,0.0,0.0,0.0,-0.18,0.6,0.6,0.6,0.0,-0.18,0.6,0.6,0.6,-0.18,0.6,0.6,0.6,
> 0.52,-0.44,-0.53,0.45,0.0,0.0,0.0,-0.18,0.6,0.6,0.6,0.0,-0.18,0.6,0.6,0.6,
> -0.18,0.6,0.6,0.6,0.52,-0.44,-0.53,0.0,0.45,0.0,0.0,-0.18,0.6,0.6,0.6,0.0,
>
> -0.18,0.6,0.6,0.6,-0.18,0.6,0.6,0.6,0.52,-0.53,-0.44,0.0,0.0,0.45,0.0,-0.18,
>
> 0.6,0.6,0.6,0.0,-0.18,0.6,0.6,0.6,-0.18,0.6,0.6,0.6,0.52,-0.53,-0.44,0.0,0.0,
> 0.0,0.45,
> PROTCNT=0,1,1,1,1,
> RESNAME='System: Unknown','Residue: PTN 1',
> RESSTATE=0,
> STATEINF(0)%FIRST_ATOM=1, STATEINF(0)%FIRST_CHARGE=0,
> STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=20,
> STATEINF(0)%NUM_STATES=5,
> STATENE=0,-59.8513,-59.8513,-59.8513,-59.8513,
> TRESCNT=1,CPHFIRST_SOL=21, CPH_IGB=2, CPH_INTDIEL=1.0,
>
> I tried solvent pH = 0 with actual TI energy (not pKaRTln10 added), I get
> the following calcpka.dat and population.dat
>
> Solvent pH is 0.000
> PTN 1 : Offset -inf Pred -inf Frac Prot 0.000 Transitions 0
>
> Average total molecular protonation: 0.000
>
> Residue Number State 0 State 1 State 2 State 3
> State 4
>
> -----------------------------------------------------------------------------------
> Residue: PTN 1 1.000000 (0) 0.000000 (1) 0.000000 (1) 0.000000 (1)
> 0.000000 (1)
> ~
>
> and when I flip signs of TI energy, I get exactly same calcpka.dat as
> above and the following population.dat
> Residue Number State 0 State 1 State 2 State 3
> State 4
>
> -----------------------------------------------------------------------------------
> Residue: PTN 1 0.000000 (0) 0.508502 (1) 0.000000 (1) 0.000000 (1)
> 0.491498 (1)
>
> I’m not sure if it makes any sense. I don’t see predicted pka value even
> when I flip signs of reference energy.
> I would appreciate your help.
>
Your TI energy is obviously wrong, then. I'm not sure how you did your
TI, but it's far easier to do it "wrong" than "right" :)
- You have to do it in implicit solvent, using the igb=2 model
- You have to make sure it uses exactly the same residue definition (for
instance, you can't compute a reference energy for AS4 by doing your
reference calculation on ASH)
- You have to use the same GB radii as you get from cpinutil.py (did you
adjust cpinutil.py to write out a prmtop file with carboxylate oxygens for
your residue reduced to 1.3 Angstroms? and did you use the prmtop with the
reduced radii in order to compute your reference energies?).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 09 2015 - 08:00:04 PDT
