Dear Amber community member,
I have performed MD simulations and MMPBSA analysis on a series of ligands.
One of the ligand is giving strange values for DeltaGsol i.e. negative
values. Is this an artifact? Are other values in the output reliable?
For other ligands that I considered I'm getting a +ve values
comparable to those shown in MMPBSA tutorial.
I check the mask (protein and ligands) seem to be OK.
Please suggest the source of error in this calculation. The
FINAL_RESULTS_MMPBSA.dat output is shown below.
-----
| Run on Tue Jan 10 02:39:40 IST 2012
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| endframe=50, keep_files=2,
| receptor_mask=:1-54:55-256 ligand_mask=:5001
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&pb
| istrng=0.100,
|/
|--------------------------------------------------------------
|Solvated complex topology file: 2Q5P_MRL24.prmtop
|Complex topology file: 2Q5P_MRL24_nsol.prmtop
|Receptor topology file: 2Q5P_nlig.prmtop
|Ligand topology file: MRL24.prmtop
|Initial mdcrd(s): ./../MRL24_MDruns/MRL24MD3ns.mdcrd
|
|Best guess for receptor mask: ":1-256"
|Best guess for ligand mask: ":257"
|Ligand residue name is "Q24"
|
|Calculations performed using 50 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
WARNINGS:
No ligand_mask set! receptor_mask will be overwritten with best guess.
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2093.7505 21.7155 3.0710
EEL -18552.9025 59.7811 8.4543
EGB -4325.8004 47.9118 6.7758
ESURF 103.7333 1.6328 0.2309
G gas -20646.6530 58.8652 8.3248
G solv -4222.0671 47.9381 6.7795
TOTAL -24868.7201 33.9800 4.8055
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2025.4945 21.5424 3.0465
EEL -18635.7255 57.4636 8.1266
EGB -4194.5339 45.4129 6.4224
ESURF 107.6219 1.5743 0.2226
G gas -20661.2200 56.9144 8.0489
G solv -4086.9120 45.3197 6.4092
TOTAL -24748.1320 33.8452 4.7864
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -3.6728 1.7145 0.2425
EEL 19.3881 2.2401 0.3168
EGB -86.4227 2.1010 0.2971
ESURF 4.2266 0.0390 0.0055
G gas 15.7153 2.4853 0.3515
G solv -82.1961 2.0796 0.2941
TOTAL -66.4808 2.1523 0.3044
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -64.5832 2.8245 0.3994
EEL 63.4350 9.0841 1.2847
EGB -44.8439 8.2478 1.1664
ESURF -8.1152 0.1603 0.0227
DELTA G gas -1.1482 8.9767 1.2695
DELTA G solv -52.9591 8.2483 1.1665
DELTA G binding = -54.1073 +/- 2.8643 0.4051
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2093.7505 21.7155 3.0710
EEL -18552.9025 59.7811 8.4543
EPB -4235.5718 46.8924 6.6316
ECAVITY 72.3376 0.6608 0.0935
G gas -20646.6530 58.8652 8.3248
G solv -4163.2342 46.7680 6.6140
TOTAL -24809.8872 36.2390 5.1250
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2025.4945 21.5424 3.0465
EEL -18635.7255 57.4636 8.1266
EPB -4115.5552 44.3442 6.2712
ECAVITY 74.2708 0.6757 0.0956
G gas -20661.2200 56.9144 8.0489
G solv -4041.2844 44.1913 6.2496
TOTAL -24702.5044 36.1652 5.1145
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -3.6728 1.7145 0.2425
EEL 19.3881 2.2401 0.3168
EPB -82.8169 2.0584 0.2911
ECAVITY 3.3914 0.0384 0.0054
G gas 15.7153 2.4853 0.3515
G solv -79.4255 2.0418 0.2888
TOTAL -63.7103 1.9675 0.2782
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -64.5832 2.8245 0.3994
EEL 63.4350 9.0841 1.2847
EPB -37.1997 7.8910 1.1160
ECAVITY -5.3246 0.0765 0.0108
DELTA G gas -1.1482 8.9767 1.2695
DELTA G solv -42.5243 7.8840 1.1150
DELTA G binding = -43.6725 +/- 3.7422 0.5292
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Thu Jan 19 2012 - 08:00:02 PST
