Dear Amber users/developers:
I ran MD simulations of protein-ligand complexes where the ligand has an extra-point on an halogen atom to simulate the sigma hole. I did not have problems to get the MD trajectories (actually I had faced a lot of issues but I could solve it thank to your help).
Now I want to compute the complex free energy with the mm-pbsa.py script but it gives me very large values of the Van der Walls components. Is It due to the extra-point? Could this have something to do with the fact that there is no Van der Walls radius defined for the extra-point ? I have pasted below part of the mm-pbsa output (see also the attach) so you can see what I mean.
I will appreciate any help with this issue.
Emilio
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| startframe=4500, interval=10, endframe=5000, verbose=1,
|/
|&gb
| igb=2, saltcon=0.100
|/
|
|--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: D2h_halo-Br-EP_solvated.top
|Complex topology file: D2h_halo-Br-EP.top
|Receptor topology file: D2h.top
|Ligand topology file: halo-Br-EP.top
|Initial mdcrd(s): ../../md/D2h_halo-Br-EP_md.trj
|
|Receptor mask: ":1-407"
|Ligand mask: ":408"
|Ligand residue name is "LIG"
|
|Calculations performed using 51 complex frames.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 43829506467.0367 11825614435.7874 1655917237.5827
ANGLE 747962.1741 48565.3378 6800.5075
DIHED 21311.4190 428.8652 60.0531
VDWAALS 3236912919534286.5000 22737821235499692.0000 3183931823025937.0000
EEL 3144.4983 2426.4318 339.7684
1-4 VDW 1606799204283528.2500 11359740019800076.0000 1590681770946199.5000
1-4 EEL -4642.1006 4738.0629 663.4615
EGB -54635.2791 15901.4828 2226.6530
ESURF 1063.2668 243.4284 34.0868
G gas 4843755954092058.0000 25263205756246644.0000 3537556387917395.0000
G solv -53572.0123 15721.8033 2201.4928
TOTAL 4843755954038487.0000 25263205756248700.0000 3537556387917683.0000
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 43418016332.9523 11718920749.0411 1640977133.1185
ANGLE 742932.9228 48456.9407 6785.3289
DIHED 21095.2536 420.7170 58.9122
VDWAALS 3236912496720125.0000 22737821281057960.0000 3183931829405371.0000
EEL 3047.4944 2497.3800 349.7031
1-4 VDW 1606799203167423.2500 11359740019956536.0000 1590681770968108.2500
1-4 EEL -4687.4241 4751.7545 665.3787
EGB -54302.9497 15919.1911 2229.1326
ESURF 1056.3959 241.8954 33.8721
G gas 4843755118666268.0000 25263205869856536.0000 3537556403825962.0000
G solv -53246.5538 15740.4896 2204.1094
TOTAL 4843755118613021.0000 25263205869858584.0000 3537556403826248.5000
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 411490134.0844 179876203.5759 25187706.5458
ANGLE 5029.2513 567.4203 79.4547
DIHED 216.1655 24.2846 3.4005
VDWAALS 414716652.8931 2914379082.6808 408094698.6786
EEL 40.1376 62.5781 8.7627
1-4 VDW 1116104.9325 2114712.0416 296118.9155
1-4 EEL 45.3235 31.5759 4.4215
EGB -283.0225 30.1488 4.2217
ESURF 7.2079 1.4647 0.2051
G gas 827328222.7880 2862074597.0851 400770605.7301
G solv -275.8146 30.8545 4.3205
TOTAL 827327946.9734 2862074595.3401 400770605.4857
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 0.0000 0.0000 0.0000
VDWAALS 8097510.2439 51383533.1882 7195133.8170
EEL 56.8663 77.2909 10.8229
1-4 VDW -0.1001 0.7087 0.0992
1-4 EEL -0.0000 0.0001 0.0000
EGB -49.3069 65.5195 9.1746
ESURF -0.3370 0.6486 0.0908
DELTA G gas 8097566.9513 51383530.6414 7195133.4604
DELTA G solv -49.6440 65.6060 9.1867
DELTA TOTAL 8097517.4148 51383532.3387 7195133.6981
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Received on Thu Mar 05 2015 - 14:00:02 PST
