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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 13 2012 - 00:00:04 PDT
