Hello all,
I just wanted to circle back and amend my comments about pKa-ANI - while it
was shown to outperform propka and give decent RMSEs for most residues in
their paper, talking with Professor Roitberg (who advised on pKa-ANI and
was an author of the ANI methods) gave me more clarity on an important
detail: For complicated cases with shifted pKas, a single-structure pKa
method like pKa-ANI is only able to sample one of the conformational
states. However, this leads to a paradox because you need the pKa to get
the correct protonation state, but you can't trust the pKa unless you run
the MD at the correct protonation state. I just wanted to make sure that
this detail was mentioned in the mailing list and archives because it gave
me a better understanding of cpH-MD (hopefully it can do the same for
others).
To quote Prof. Roitberg directly:
If you look closely at the paper, you will see that most of the
experimental pKas are very close to the values in solution, which makes
sense. The interesting prediction are for those that have larger
deviations, such as ASP 26 in Thioredoxin, which is also mentioned in the
paper.
As written, the protocol was this: do regular pKa-ANI, and you get a BAD
prediction for ASP26, who has an experimental pKa of 9.9
Now, you KNOW the experiment, and figure out that the problem is that you
are using a conformation, or did MD with the ASP deprotonated, which, if
the pKa is 9.9, would be wrong, agree?
So, they run MD with ASP26 protonated and deprotonated, and indeed, when
they use the conformations from the MD run protonated, they get a MUCH
better prediction than before.
What is the problem here ? That you know you are wrong ONLY if you have the
experimental data, which defeats the purpose right ? One would like to have
a method that does not need the experiment every time.
Second, clearly the pkA prediction depends on the conformers, which depends
on the protonation state used in the MD. This is a catch-22 problem !. You
do not know the protonation state to run MD until you know the pKa, but
cannot trust the pKa until you run the MD at the correct protonation state.
That is why I said to be careful. In your advise to the person asking, you
said to run MD for 50 ns, then do pKa-ANI, but hopefully you now see the
issue, right?
What protonation state would you use to run that MD ? For most residues you
can just guess, but for the interesting ones, you cannot.
Hence cpHMD (which I agree, is a pain to set up!). It couples conformations
and protonation states directly, and samples the joint energy surface, so
you get all the information together, as you should.
BTW: This discussion has nothing to do with ANI per-se. It applies to ANY
method that predicts pKa from single structures, even if averaged over MD.
On Wed, Feb 21, 2024 at 10:48 PM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> Thank you. I understood my mistake.
>
> On Thu, Feb 22, 2024 at 11:24 AM Dulal Mondal <
> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
> > Thank you for your reply. I tried the grep command on my files and this
> is
> > the output I got:
> > "grep -m1 'Solvent pH:' ../001/cpout.rep.001 ../002/cpout.rep.001
> > ../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
> > ../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
> > ../009/cpout.rep.001 ../010/cpout.rep.001
> > ../001/cpout.rep.001:Solvent pH: 6.40000
> > ../002/cpout.rep.001:Solvent pH: 5.70000
> > ../003/cpout.rep.001:Solvent pH: 5.60000
> > ../004/cpout.rep.001:Solvent pH: 5.90000
> > ../005/cpout.rep.001:Solvent pH: 5.80000
> > ../006/cpout.rep.001:Solvent pH: 6.10000
> > ../007/cpout.rep.001:Solvent pH: 6.00000
> > ../008/cpout.rep.001:Solvent pH: 6.30000
> > ../009/cpout.rep.001:Solvent pH: 6.20000
> > ../010/cpout.rep.001:Solvent pH: 5.90000"
> >
> > I can see two files showing the same pH values of 5.9, although I am
> > unable to understand a few things over here. How exactly is the grep
> > command allocating a specific pH value to a cpout file?
> >
> > On Thu, Feb 22, 2024 at 2:12 AM He, Amy <he.1768.buckeyemail.osu.edu>
> > wrote:
> >
> >> Hi Dulal,
> >>
> >>
> >>
> >> A quick way to find two replicas with the same pH is to print the
> initial
> >> “Solvent pH” in the individual cpout files, something like this:
> >>
> >> *grep* *-m1* *'Solvent pH:'* ../001/cpout.rep.001 ../002/cpout.rep.001
> >> ../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
> >> ../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
> >> ../009/cpout.rep.001 ../010/cpout.rep.001*
> >>
> >>
> >>
> >> cphstats can’t handle two replicas with the same pH. With these, the
> >> sizes of samples at each pH will become unequal, and that can change the
> >> error estimates of the pKa fitting, too.. although in my opinion it’s
> not
> >> wrong to have replicas this close (it’s just like the extreme case of
> >> unequally spaced replicas)
> >>
> >>
> >>
> >> But if this is not something you planned, make sure to check the inputs
> >> and outputs. Do you have multiple files that match
> ../010/cpout.rep.001*?
> >> Also, cphstats tries to make sure each replica has a unique pH, but it
> >> can’t tell whether the outputs were from the same replica exchange
> >> calculation or not. So we need to make sure these are correct
> >>
> >>
> >>
> >> Hope this is mildly helpful!
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> --
> >>
> >> Amy He
> >>
> >> Hadad Lab @ OSU
> >>
> >> He.1768.osu.edu
> >>
> >>
> >>
> >>
> >>
> >> *From: *Dulal Mondal via AMBER <amber.ambermd.org>
> >> *Date: *Wednesday, February 21, 2024 at 1:46 AM
> >> *To: *Adrian Roitberg <roitberg.ufl.edu>, AMBER Mailing List <
> >> amber.ambermd.org>
> >> *Subject: *Re: [AMBER] Constant pH remd
> >>
> >>
> >>
> >> Not clear sir.
> >>
> >> On Tue, 20 Feb, 2024, 11:38 pm Adrian Roitberg via AMBER, <
> >> amber.ambermd.org>
> >> wrote:
> >>
> >> > the error is clear, right ?
> >> >
> >> >
> >> > Error: Same pH (5.9) found twice!
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On 2/20/24 5:16 AM, Dulal Mondal via AMBER wrote:
> >> > > [External Email]
> >> > >
> >> > > Dear Experts,
> >> > > I run the constant pH remd with 10 replicas from pH 5.5 to 6.4 with
> >> 0.1
> >> > pH
> >> > > gap. I type the following command
> >> > > *cphstats --fix-remd prod001 ../001/cpout.rep.001
> ../002/cpout.rep.001
> >> > > ../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
> >> > > ../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
> >> > > ../009/cpout.rep.001 ../010/cpout.rep.001*
> >> > > But it show the following error message.
> >> > > Error: Same pH (5.9) found twice!
> >> > > Thanking You
> >> > > --
> >> > > *With regards,*
> >> > > *Dulal Mondal,*
> >> > > *Research Scholar,*
> >> > > *Department of Chemistry,*
> >> > > *IIT Kharagpur, Kharagpur 721302.*
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > >
> >>
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> >> <
> https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2m0EMW4bCEjJifX24_plQ504saKXGYNH1CQ-BHZDLVfm0VCPE4zxvSu70KoA-Ynr7Rim3tqfdhIabyM_0uXUHltqnoA$
> >
> >> >
> >> > --
> >> > Dr. Adrian E. Roitberg
> >> > V.T. and Louise Jackson Professor in Chemistry
> >> > Department of Chemistry
> >> > University of Florida
> >> > roitberg.ufl.edu
> >> > 352-392-6972
> >> >
> >> >
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> >
> >>
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> >> <
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> >
> >> >
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >>
> >>
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> >> <
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> >
> >>
> >
> >
> > --
> > *With regards,*
> > *Dulal Mondal,*
> > *Research Scholar,*
> > *Department of Chemistry,*
> > *IIT Kharagpur, Kharagpur 721302.*
> >
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
> _______________________________________________
> AMBER mailing list
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Received on Thu Feb 22 2024 - 17:30:02 PST
