Dear Professor Monard,
Thanks for the detailed response. This is very interesting.
I find the Amber default qmcut in QM/MM-GBSA in MMPBSA.py (The cutoff
for the qm/mm charge interactions.) is 9,999 A, which is an usually large
value. We assume adjust the qmcut value into a smaller value and ignore
some longer range electrostatic interactions between non-neutral QM and MM
regions might help. Therefore, we set the qmcut as 8A because all the
charged amino acids in the MM region are at least 11A away from the
non-neutral QM region in the in-house crystal structure. However, in
the situation that qmcut = 8 and QM & MM regions both contain net charges,
we still can see large electrostatic interactions. This might be because
the charged amino acids in the MM region at some points, might be less than
8A away from the QM region in the MD trajectories.
However, if we further test qmcut = 0 ( QM and MM regions both contain
net charges), the large electrostatic interactions in QM/MM-GBSA still
happens, though significantly less frequent. This confuses us, since
qmcut=0 should mute the charge-charge interactions and make dipole-dipole
interactions as the major component. Our guess is that even though
dipole-dipole interactions are less, but still susceptible, to distances.
Therefore, in qmcut=0, as long as both QM and MM regions are non-neutral
and the distances of these two regions are close enough, the large
electrostatic interactions from dipole-dipole interactions might still
happen (though less frequently)? Thanks in advance for enlightening.
Best,
Henry
On Fri, Mar 27, 2015 at 3:27 AM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:
> Hi,
>
> What you see is something very general for QM/MM calculations, although
> I'm not aware of any papers discussing it: you should avoid a
> non-neutral QM region, especially in the case of a charged MM region.
> It comes from the QM/MM electrostatic interactions. The point charges of
> the MM part polarizes the QM part. You can think of your MM point charge
> set in terms of a multipolar development at the center of the MM region
> (total charge + dipole + quadrupole + etc.). You can do the same for the
> QM region. If the MM and the QM regions are charged, the main component
> of the electrostatic QM/MM interaction is a charge-charge interaction
> whose value is the total charge of the QM region times the total charge
> of the MM region divided by the distance between the two centers. If you
> are "lucky", these two centers are close and the electrostatic
> interactions is very large.
>
> In your case, when you use a trajectory, these centers move along the
> trajectory. This will yield large changes if the two centers are close.
>
> If your MM part and the QM part are neutral, then the main interaction
> component is a dipole-dipole interaction that is less susceptible to the
> distance.
>
> If you want to verify my saying, check the total charge of the MM part,
> and make it neutral if it is not.
> You can also turn the MM charges off and check the differences in ESCF.
> I would guess that the numbers will change a lot in the case the QM part
> is charged.
>
> My two cents,
>
> Gerald.
>
>
> On 03/24/2015 06:06 PM, psu4.uic.edu wrote:
> > Dear Amber,
> >
> >
> > We have used a series of protein-ligand binding trajectories to test
> > MM/PBSA, MM/GBSA and QM-MM/GBSA extensively. However, if we include
> NADH,
> > which has net charges equal to -2, into the QM region, EGB and ESCF (QM d
> > Gelectro) don’t converge in some of the test cases (ESCF in dGbind can
> > fluctuate really widely: -700~100 kcal/mol for example ). Therefore the
> > abnormal behavior makes large and positive dGbind (for example, dGbind =
> > 34.37 kcal/mol. For example, the dGbind calculated from MM/GBSA using
> the
> > same trajectories here, is -30 kcal/mol). This happens in igb=1,2,5,7,8
> and
> > various effective radii settings.
> >
> >
> > However, if the net charge is equal to 0 in the QM-MM region (NADH
> not
> > included), QM-MM/GBSA can offer converged and high agreements with
> > experimental data as MM/PBSA and MM/GBSA do, across various igb and
> effective
> > radii setting. Could any guru enlighten? The following is an example
> of
> > QM-MM/GBSA input, which includes the NADH cofactor (residue 101) and the
> > ligand (residue 100). Therefore, the net charges of QM regions in both
> > complex and receptor are -2 since the ligand doesn't have any charge.
> >
> >
> > The test is performed in AmberTools13/ the latest bug fix 26 and
> > Amber12/the
> > latest bug fix 26.
> >
> >
> > &general
> >
> > keep_files=2,interval=10,
> >
> > /
> >
> > &gb
> >
> > igb=8,
> >
> > saltcon=0.100,
> >
> > ifqnt=1,
> >
> > qmcharge_lig=0,
> >
> > qmcharge_com=-2,
> >
> > qmcharge_rec=-2,
> >
> > qm_residues=100,101,
> >
> > qm_theory='PM3',
> >
> > /
> >
> > Best,
> >
> > Henry
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
>
> ____________________________________________________________________________
>
>
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>
--
Pin-Chih Su (Henry Su)
Ph.D. canditate
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
900 South Ashland Avenue, Room 1052
Chicago, IL 60607-7173
office 312-996-5388
fax 312-413-9303
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Received on Thu Apr 02 2015 - 00:30:04 PDT
