I am relatively new to MMPBSA calculations and trying to run mmpbsa for
protein-protein interactions with 'multiple trajectory protocol'.
I have MD trajectories for complex, ligand and receptor.
Before MD run, I make sure that the # of atoms(complex.pdb) = # of
atoms(receptor.pdb+ligand.pdb).
I used following command to run mmpbsa:
mpirun -np 8 MMPBSA.py.MPI -O -i mmpbsa.in -cp
../preparation/complex-vac1.prmtop -sp complex-bondi.prmtop -rp
rec-bondi.top -lp lig-bondi.top -srp receptor-bondi.prmtop -slp
ligand-bondi.prmtop -y
../mult_traj_prot/complex/04_MD_run/protein_prod_nvt.mdcrd -yr
../mult_traj_prot/receptor/04_MD_run/protein_prod_nvt.mdcrd -yl
../mult_traj_prot/ligand/04_MD_run/protein_prod_nvt.mdcrd
The mmpbsa.in file is as follows:
Input file for running PB
&general
startframe=4100,endframe=5000,interval=100,
verbose=1, entropy=0, debug_printlevel=1,
keep_files=2,
# use_sander=1,
/
&pb
istrng=0.15,inp=2,radiopt=0,
/
The 'FINAL_RESULTS_MMPBSA.dat' is as follows:
| Run on Mon Aug 25 23:55:54 2014
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB
|&general
| startframe=4100,endframe=5000,interval=100,
| verbose=1, entropy=0, debug_printlevel=1,
| keep_files=2,
|# use_sander=1,
|/
|&pb
| istrng=0.15,inp=2,radiopt=0,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: complex-bondi.prmtop
|Complex topology file: ../preparation/complex-vac1.prmtop
|Solvated receptor topology file: receptor-bondi.prmtop
|Receptor topology file: rec-bondi.top
|Solvated ligand topology file: ligand-bondi.prmtop
|Ligand topology file: lig-bondi.top
|Initial mdcrd(s):
../mult_traj_prot/complex_1WDW/04_MD_run_1WDW/protein_prod_nvt.mdcrd
|Initial Receptor mdcrd(s):
../mult_traj_prot/receptor_1V8Z/04_MD_run_1V8Z/protein_prod_nvt.mdcrd
|Initial Ligand mdcrd(s):
../mult_traj_prot/ligand_1GEQ/04_MD_run_1GEQ/protein_prod_nvt.mdcrd
|
|Receptor mask: ":241-1010"
|Ligand mask: ":1-240"
|
|Calculations performed using 10 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 2988.0789 38.8116
12.2733
ANGLE 8143.9588 59.0104
18.6607
DIHED 12376.0183 33.5461
10.6082
VDWAALS -8595.1030 38.6580
12.2247
EEL -75646.4438 116.5307
36.8502
1-4 VDW 3676.1081 15.3841
4.8649
1-4 EEL 45482.4988 51.9816
16.4380
EPB -10160.0940 98.9730
31.2980
ENPOLAR 7306.9811 11.4258
3.6132
EDISPER -3672.3364 11.6806
3.6937
G gas -11574.8840 150.2242
47.5051
G solv -6525.4493 88.0769
27.8524
TOTAL -18100.3333 76.3825
24.1543
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 18370808.2324 2323376.5235
734716.1676
ANGLE nan nan
nan
DIHED nan nan
nan
VDWAALS 36431962.6146 27630.3092
8737.4710
EEL -56648.2693 146.6856
46.3860
1-4 VDW 4994481.4815 8123.9815
2569.0285
1-4 EEL 30409.7021 89.7118
28.3694
EPB -8456.8829 161.5918
51.0998
ENPOLAR 5646.2202 14.7417
4.6617
EDISPER -2599.4915 13.3464
4.2205
G gas nan nan
nan
G solv -5410.1542 161.2324
50.9862
TOTAL nan nan
nan
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 10757348.2738 569117.6697
179970.8093
ANGLE nan nan
nan
DIHED nan nan
nan
VDWAALS 7170069.8982 15984.2203
5054.6543
EEL -17373.0264 109.7643
34.7105
1-4 VDW 983121.3525 1770.9398
560.0204
1-4 EEL 9571.2784 37.7157
11.9268
EPB -3211.3583 117.9810
37.3089
ENPOLAR 1894.8140 10.5365
3.3319
EDISPER -1050.5334 9.8139
3.1034
G gas nan nan
nan
G solv -2367.0778 116.8808
36.9610
TOTAL nan nan
nan
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -29125168.4273 2392064.6716
756437.2673
ANGLE nan nan
nan
DIHED nan nan
nan
VDWAALS -43610627.6159 31920.6952
10094.2101
EEL -1625.1482 217.1273
68.6617
1-4 VDW -5973926.7260 8314.7785
2629.3638
1-4 EEL 5501.5183 110.3303
34.8895
EPB 1508.1472 223.2198
70.5883
ENPOLAR -234.0531 21.4216
6.7741
EDISPER -22.3115 20.2701
6.4100
DELTA G gas nan nan
nan
DELTA G solv 1251.7827 217.7488
68.8582
DELTA TOTAL nan nan
nan
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
I am not sure how to check where exactly it has gone wrong.
The receptor and ligand part ANGLE and DIHED shows "nan" values and "G gas
" is also "nan".
Based on previous mailing lists, I tried to run following:
$ mmpbsa_py_energy -O -i ../_MMPBSA_pb.mdin -o mdout -p ../rec-bondi.top -c
../_MMPBSA_receptor.pdb -y ../_MMPBSA_receptor.mdcrd.0
And the output file 'mdout' is as follows:
Reading parm file (../rec-bondi.top)
title:
default_name
mm_options: e_debug=3
mm_options: ipb=2
mm_options: inp=2
mm_options: epsin=1.000000
mm_options: epsout=80.000000
mm_options: smoothopt=1
mm_options: istrng=150.000000
mm_options: radiopt=0
mm_options: dprob=1.400000
mm_options: iprob=2.000000
mm_options: npbopt=0
mm_options: solvopt=1
mm_options: accept=0.001000
mm_options: maxitn=1000
mm_options: fillratio=4.000000
mm_options: space=0.500000
mm_options: nfocus=2
mm_options: fscale=8
mm_options: bcopt=5
mm_options: eneopt=2
mm_options: cutnb=0.000000
mm_options: sprob=0.557000
mm_options: cavity_surften=0.037800
mm_options: cavity_offset=-0.569200
Processing ASCII trajectory (../_MMPBSA_receptor.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB
frms
eff.c(2713) enb14 --> 4993813.636
eff.c(2714) eel14 --> 30337.653
eff.c(2829) enb --> 36387739.033
eff.c(2830) eel --> -56679.137
eff.c(2831) e_pb --> -8375.899
eff.c(2832) esurf --> 5658.214
eff.c(2833) evdwnp --> -2597.279
ff: 0 -nan -nan 41381552.67 -26341.48 3060.93
-8375.90 -nan
BOND = 17419498.5891 ANGLE = -nan DIHED =
-nan
VDWAALS = 36387739.0325 EEL = -56679.1366 EPB =
-8375.8992
1-4 VDW = 4993813.6358 1-4 EEL = 30337.6530 RESTRAINT =
0.0000
ECAVITY = 5658.2136 EDISPER = -2597.2792
Processing frame 2
eff.c(2713) enb14 --> 4985260.185
eff.c(2714) eel14 --> 30481.724
eff.c(2829) enb --> 36423252.161
eff.c(2830) eel --> -56502.637
eff.c(2831) e_pb --> -8693.038
eff.c(2832) esurf --> 5663.572
eff.c(2833) evdwnp --> -2605.459
BOND = 24005312.9441 ANGLE = 520147.0127 DIHED =
21988.4024
VDWAALS = 36423252.1613 EEL = -56502.6372 EPB =
-8693.0380
1-4 VDW = 4985260.1854 1-4 EEL = 30481.7238 RESTRAINT =
0.0000
ECAVITY = 5663.5718 EDISPER = -2605.4586
MM/PBSA processing done!
Although, I am getting "MM/PBSA processing is done !" ther are still "-nan"
values in the output.
How can I fix this problem ?
Is my protein-protein complex system is too large ?
OR I missed something here ?
I am using AMBER14 with MMPBSA.py 14.0 version.
Any suggestion please !!
Thanks you in advance.
-- Joshi
--
--------------------------------------------------------------
Dhananjay Joshi
Graduate Student
TIGP, Academia Sinica,
Academia Sinica, Taipei-115, Taiwan
--------------------------------------------------------------
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Received on Mon Aug 25 2014 - 10:00:02 PDT
