Thanks, you really help me a lot.
I made new prmtop which has no Cl- ion. I think this may be comparable
with the trajectory which has been dropped the Cl- by strip_mask. But
the prmtop still does not match the trajectory. So I have to keep the
Cl- in the trajectory. But this affect the energy. Maybe next time I
would not add any countered ions at the beginning. ps: Is the
countered ions very important to the system?
On 6/15/12, Bill Miller III <brmilleriii.gmail.com> wrote:
> 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.
>> >>>>>
>> >>>>> _______________________________________________
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>> >>>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>> 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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>
>
> --
> 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 - 05:30:05 PDT
