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
Received on Tue Jun 12 2012 - 23:30:03 PDT
