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
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
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>>
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Received on Fri Jun 15 2012 - 05:30:03 PDT
