Yes, the chloride ions will have an effect on the energy. In general,
MM-PB(GB)SA is not parameterized to include explicit ions. We generally
advise that users remove all ions from their trajectories (which is why
that is the default strip_mask for MMPBSA.py) before performing MM-PBSA
calculations since the PB or GB model should include ionic strength
effects, although obviously not in an explicit manner.
I hope that helps.
-Bill
On Fri, Jun 15, 2012 at 8:01 AM, qiao xue <xueqiaoup.gmail.com> wrote:
> Thanks, I modified the strip_mask to ":WAT" Now, the result seems
> good. I still have a question. Now in the system, Cl- exists. But what
> I want is the free energy between ligand and protein. Does the Cl-
> ions have any effect on the energy?
>
> On 6/14/12, Cao Yang <muxiachuixue.163.com> wrote:
> > The problem is caused by Cl- of your system. Just as Bill said, in
> default,
> > MMPBSA strips the Cl- and thus leading to the inconsistence between your
> > prmtop file and mdcrd file. Read the strip_mask variable of &general in
> > AmberTools manual and you would have some idea.
> >
> >
> >
> >
> >
> > At 2012-06-13 19:53:23,"Bill Miller III" <brmilleriii.gmail.com> wrote:
> >>Energies this high are usually indicative of an inconsistency between the
> >> prmtop and trajectory files. You should try visualizing the trajectories
> >> produced by MMPBSA.py with the corresponding prmtop files to see if
> >> anything looks wrong.
> >>
> >>-Bill
> >>
> >>
> >>
> >>On Jun 13, 2012, at 2:32 AM, qiao xue <xueqiaoup.gmail.com> wrote:
> >>
> >>> I do not want to include Cl-, I thought the problem may be caused by
> >>> Cl- in the beginning. But I have dropped Cl-, the problem still exist.
> >>> So I do not know what this problem is.
> >>>
> >>> On 6/13/12, Bill Miller III <brmilleriii.gmail.com> wrote:
> >>>> MMPBSA.py, by default, removes all the ions from the original
> >>>> trajectory.
> >>>> You will need to specify the strip_mask control variable in your input
> >>>> file
> >>>> so that MMPBSA.py does not remove the chloride ion that you are
> >>>> attempting
> >>>> to include in the calculation.
> >>>>
> >>>> -Bill
> >>>>
> >>>> On Wed, Jun 13, 2012 at 2:03 AM, qiao xue <xueqiaoup.gmail.com>
> wrote:
> >>>>
> >>>>> Hello all,
> >>>>> I take a MD simulation of a protein contained Fe ion. This protein
> >>>>> is a receptor. And there are several ligands. So in some of them I
> add
> >>>>> countered ions Cl-. Then I did MMPBSA calculation for these
> >>>>> protein-ligand complex. All the systems with countered ion Cl- is
> >>>>> abnormal. Like this
> >>>>>
> >>>>>
> >>>>> Differences (Complex - Receptor - Ligand):
> >>>>> Energy Component Average Std. Dev. Std.
> Err.
> >>>>> of
> >>>>> Mean
> >>>>>
> >>>>>
> -------------------------------------------------------------------------------
> >>>>> BOND 0.0000 0.0001
> >>>>> 0.0000
> >>>>> ANGLE -0.0000 0.0000
> >>>>> 0.0000
> >>>>> DIHED -1.9605 1.1967
> >>>>> 0.2443
> >>>>> VDWAALS 37918031025063.1484 125947828014390.9375
> >>>>> 25708992737255.8711
> >>>>> EEL 175.6232 121.1990
> >>>>> 24.7396
> >>>>> 1-4 VDW -831.8288 3735.5515
> >>>>> 762.5163
> >>>>> 1-4 EEL 0.0808 0.1088
> >>>>> 0.0222
> >>>>> EGB 63.4121 68.6816
> >>>>> 14.0196
> >>>>> ESURF -3.4046 1.7772
> >>>>> 0.3628
> >>>>>
> >>>>> DELTA G gas 37918031024810.1719 125947828014502.9375
> >>>>> 25708992737278.7305
> >>>>> DELTA G solv 60.0075 68.3297
> >>>>> 13.9477
> >>>>>
> >>>>>
> >>>>> DELTA G binding = 37918031024879.3438 +/- 125947828014482.4219
> >>>>> 25708992737274.5430
> >>>>>
> >>>>>
> -------------------------------------------------------------------------------------------------------------
> >>>>>
> >>>>> The VDWAALS is very huge. I am sure the parameters strip_mask is
> >>>>> correct. I use the default parameters. It contains Cl-. Then I have
> >>>>> tried to drop the Cl- from the trajectory. And I use the new prmtop
> >>>>> file which has no countered ion. But the result is still wrong.
> >>>>>
> >>>>> But the system without countered ion Cl- is good. The result is this:
> >>>>>
> >>>>> Differences (Complex - Receptor - Ligand):
> >>>>> Energy Component Average Std. Dev. Std.
> Err.
> >>>>> of
> >>>>> Mean
> >>>>>
> >>>>>
> -------------------------------------------------------------------------------
> >>>>> BOND -0.0000 0.0000
> >>>>> 0.0000
> >>>>> ANGLE 0.0000 0.0000
> >>>>> 0.0000
> >>>>> DIHED -0.0676 0.0682
> >>>>> 0.0014
> >>>>> VDWAALS -56.3502 3.2913
> >>>>> 0.0658
> >>>>> EEL -20.1411 4.8748
> >>>>> 0.0975
> >>>>> 1-4 VDW 3.0567 1.1338
> >>>>> 0.0227
> >>>>> 1-4 EEL 0.1026 0.0240
> >>>>> 0.0005
> >>>>> EPB 50.0003 4.5535
> >>>>> 0.0911
> >>>>> ECAVITY -4.8209 0.1075
> >>>>> 0.0021
> >>>>>
> >>>>> DELTA G gas -73.3996 5.4641
> >>>>> 0.1093
> >>>>> DELTA G solv 45.1794 4.5587
> >>>>> 0.0912
> >>>>>
> >>>>>
> >>>>> DELTA G binding = -28.2202 +/- 4.8647
> >>>>> 0.0973
> >>>>>
> >>>>>
> >>>>>
> ------------------------------------------------------------------------------------------------------------------
> >>>>>
> >>>>> This VDWAALS seems good.
> >>>>>
> >>>>>
> >>>>> This input file is same:
> >>>>> &general
> >>>>> endframe=2500, keep_files=2,
> >>>>> /
> >>>>> &gb
> >>>>> igb=2, saltcon=0.100,
> >>>>> /
> >>>>> &pb
> >>>>> istrng=0.100,
> >>>>> /
> >>>>>
> >>>>> -----------------------------------------------------------
> >>>>>
> >>>>> The two systems is the same protein. The ligands are very normal. The
> >>>>> most different thing is the countered ion. I think this may be caused
> >>>>> by Cl- at first. But I have droped this ion. I do not know why this
> is
> >>>>> still wrong. I hope someone could help me.
> >>>>> Thank you very much!
> >>>>>
> >>>>>
> >>>>> Xue Qiao.
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Bill Miller III
> >>>> Quantum Theory Project,
> >>>> University of Florida
> >>>> Ph.D. Graduate Student
> >>>> 352-392-6715
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>> _______________________________________________
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> >>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Jun 15 2012 - 05:30:04 PDT
