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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> 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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Received on Tue Jun 12 2012 - 23:30:04 PDT
