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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Received on Wed Jun 13 2012 - 20:30:03 PDT
