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.
Thanks.
On Oct 6, 2015, at 2:00 PM, amber-request.ambermd.org wrote:
>> I ran explicit solvent CpHMD (same parameters as in TI calculations) at
>> pH=pKa but I don?t see 50% protonation. It?s stuck at the starting residue
>> state and there is no transition. I guess reference energy value is not
>> right. But I don?t see anything wrong with the reference energy value
>> calculated using sander TI method.
>>
>
> ?You probably have a sign flipped somewhere. If this helps, using the TI
> energy *exactly* as the reference energy results in a pKa of 0. So that
> might be an easy place to start. Assign the TI energy as the reference
> energy, then titrate around pH 0 to see if you get approximately pKa=0. If
> not, try flipping the sign of the reference energy -- if you start seeing a
> more reasonable pKa close to 0, then you obviously flipped the sign
> somewhere by mistake. Once you have that working, you just add
> RT*pKa*ln(10) to the protonated reference energy (residues.py does this for
> you when you specify "deprotonated" and the pKa of the titratable residue).
>
> It takes awhile to really wrap your head around all of the signs and what's
> happening.
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Received on Fri Oct 09 2015 - 07:30:03 PDT
