Dear Amber users,
I am using MMPB/GB SA pymol to calculate free energy decompostion of the
residues within the ligand bound to the receptor in a complex.
I have used this input file for the calculations:
Per-residue GB and PB decomposition
|&general
| endframe=5, verbose=1,
| # entropy=1,
|/
|&pb
| istrng=0.00,
| inp=1,
| radiopt=0
|/
|&decomp
| csv_format = 1,
| idecomp=1, print_res="615-660"
| dec_verbose=1,
and this command line to call for MMPBSA.py calculation:
MMPBSA.py -O -i mmpbsa_2.in -o FINAL_RESULTS_MMPBSA.dat -do
FINAL_DECOMP_MMPBSA.dat -sp all_sol_MMPBSA.top -cp all_nsol_MMPBSA.top -rp
EGFR_MMPBSA.top -lp EGF_MMPBSA.top -y *.mdcrd
I am not getting any result from my per residue decompostion analysis.
I have attached the MMPBSA and ptraj out files.
Would you please guide me with this?
Regards,
Maryam
| Run on Tue Mar 3 15:04:24 2015
|
|Input file:
|--------------------------------------------------------------
|Per-residue GB and PB decomposition
|&general
| endframe=5, verbose=1,
| # entropy=1,
|/
|&pb
| istrng=0.00,
| inp=1,
| radiopt=0
|/
|&decomp
| csv_format = 1,
| idecomp=1, print_res="615-660"
| dec_verbose=1,
|/
|#MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -do
FINAL_DECOMP_MMPBSA.dat -sp inactive_EGFR.prmtop -cp
glycam_1_15_2014_742.prmtop -y inactive_oligo_sol_10frames.mdcrd
|
|
|--------------------------------------------------------------
|MMPBSA.py Version=12.0
|Solvated complex topology file: all_sol_MMPBSA.top
|Complex topology file: all_nsol_MMPBSA.top
|Receptor topology file: EGFR_MMPBSA.top
|Ligand topology file: EGF_MMPBSA.top
|Initial mdcrd(s): oligo_50_60ns_MMPBSA.mdcrd
|
|Receptor mask: ":1-614,662-715"
|Ligand mask: ":615-661"
|
|Calculations performed using 5 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS 225998.2638 16506.5152
7381.9380
EEL -52948.6861 50.8807
22.7545
EPB -8114.9150 29.1758
13.0478
ENPOLAR -41245.2389 64.2273
28.7233
G gas 173049.5777 16514.7122
7385.6038
G solv -49360.1538 80.3309
35.9251
TOTAL 123689.4239 16516.5297
7386.4166
"FINAL_RESULTS_MMPBSA.dat" 101L, 4464C
PPTRAJ: Trajectory Analysis. V12.5
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> [trajin oligo_50_60ns_MMPBSA.mdcrd 1 5 1]
[oligo_50_60ns_MMPBSA.mdcrd] contains 601 frames.
> [noprogress]
noprogress: Progress bar will not be shown.
> [center :1-614,662-715 mass origin]
> [image origin]
> [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
> [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
> [outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb]
> [outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart]
> [outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-5 nobox]
> [strip :615-661]
> [outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb]
> [outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart]
> [outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-5 nobox]
> [unstrip]
> [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
> [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
> [strip :1-614,662-715]
> [outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb]
> [outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart]
> [outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-5 nobox]
> [unstrip]
> [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
> [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
>
INPUT TRAJECTORIES:
[oligo_50_60ns_MMPBSA.mdcrd] is a NetCDF AMBER trajectory, Parm 0 (with
box info) (reading 5 of 601)
Coordinate processing will occur on 5 frames.
PARAMETER FILES:
0: all_sol_MMPBSA.top, 157670 atoms, 49519 res, ortho. box, 48833 mol,
48798 solvent mol, 5 frames
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
No files.
ACTIONS: Initializing 21 actions:
0: [center :1-614,662-715 mass origin]
CENTER: To origin via center of mass using atoms in mask :1-614,662-715
1: [image origin]
IMAGE: To origin based on first atom position using atoms in mask *
2: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
3: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
RMSD: (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), reference is first
frame (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), with fitting,
mass-weighted.
4: [outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb]
Saving frames 1 OUTTRAJ: [_MMPBSA_complex.pdb] is a PDB file,
Parm 0: Writing frames 1
5: [outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart]
Saving frames 1 OUTTRAJ: [_MMPBSA_dummycomplex.inpcrd] is an
AMBER restart file, Parm 0: Writing frames 1
6: [outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-5 nobox]
Saving frames 1 2 3 4 5 OUTTRAJ: [_MMPBSA_complex.mdcrd.0] is an
AMBER trajectory, Parm 0: Writing frames 1 2 3 4 5
7: [strip :615-661]
STRIP: Stripping atoms in mask [:615-661]
8: [outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb]
Saving frames 1 OUTTRAJ: [_MMPBSA_receptor.pdb] is a PDB file,
Parm 0: Writing frames 1
9: [outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart]
Saving frames 1 OUTTRAJ: [_MMPBSA_dummyreceptor.inpcrd] is an
AMBER restart file, Parm 0: Writing frames 1
10: [outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-5 nobox]
Saving frames 1 2 3 4 5 OUTTRAJ: [_MMPBSA_receptor.mdcrd.0] is an
AMBER trajectory, Parm 0: Writing frames 1 2 3 4 5
11: [unstrip]
12: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
STRIP: Stripping atoms in mask [:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
13: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
RMSD: (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), reference is first
frame (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), with fitting,
mass-weighted.
14: [strip :1-614,662-715]
STRIP: Stripping atoms in mask [:1-614,662-715]
15: [outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb]
Saving frames 1 OUTTRAJ: [_MMPBSA_ligand.pdb] is a PDB file, Parm
0: Writing frames 1
16: [outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart]
Saving frames 1 OUTTRAJ: [_MMPBSA_dummyligand.inpcrd] is an AMBER
restart file, Parm 0: Writing frames 1
17: [outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-5 nobox]
Saving frames 1 2 3 4 5 OUTTRAJ: [_MMPBSA_ligand.mdcrd.0] is an
AMBER trajectory, Parm 0: Writing frames 1 2 3 4 5
18: [unstrip]
19: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
STRIP: Stripping atoms in mask [:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
20: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
RMSD: (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), reference is first
frame (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), with fitting,
mass-weighted.
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [all_sol_MMPBSA.top]: Setting up 21 actions.
0: [center :1-614,662-715 mass origin]
:1-614,662-715 (10558 atoms)
1: [image origin]
Number of molecules to be imaged is 48833 based on mask [*]
2: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
Stripping 146400 atoms.
strip.all_sol_MMPBSA.top: Setting up 11400 bonds.
Topology contains 11270 atoms.
715 residues.
11400 bonds.
29 molecules.
3: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
11270 atoms selected.
4: [outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb]
5: [outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart]
6: [outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-5 nobox]
7: [strip :615-661]
Stripping 712 atoms.
strip.strip.all_sol_MMPBSA.top: Setting up 10677 bonds.
Topology contains 10558 atoms.
668 residues.
10677 bonds.
28 molecules.
8: [outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb]
9: [outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart]
10: [outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-5 nobox]
11: [unstrip]
12: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
Stripping 146400 atoms.
strip.all_sol_MMPBSA.top: Setting up 11400 bonds.
Topology contains 11270 atoms.
715 residues.
11400 bonds.
29 molecules.
13: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
11270 atoms selected.
14: [strip :1-614,662-715]
Stripping 10558 atoms.
strip.strip.all_sol_MMPBSA.top: Setting up 723 bonds.
Topology contains 712 atoms.
47 residues.
723 bonds.
1 molecules.
15: [outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb]
16: [outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart]
17: [outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-5 nobox]
18: [unstrip]
19: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
Stripping 146400 atoms.
strip.all_sol_MMPBSA.top: Setting up 11400 bonds.
Topology contains 11270 atoms.
20: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
11270 atoms selected.
----- [oligo_50_60ns_MMPBSA.mdcrd] (1-5, 1) -----
Read 5 frames and processed 5 frames.
ACTION OUTPUT:
OUTTRAJ: [_MMPBSA_complex.pdb] Wrote 1 frames.
OUTTRAJ: [_MMPBSA_dummycomplex.inpcrd] Wrote 1 frames.
OUTTRAJ: [_MMPBSA_complex.mdcrd.0] Wrote 5 frames.
OUTTRAJ: [_MMPBSA_receptor.pdb] Wrote 1 frames.
OUTTRAJ: [_MMPBSA_dummyreceptor.inpcrd] Wrote 1 frames.
OUTTRAJ: [_MMPBSA_receptor.mdcrd.0] Wrote 5 frames.
OUTTRAJ: [_MMPBSA_ligand.pdb] Wrote 1 frames.
OUTTRAJ: [_MMPBSA_dummyligand.inpcrd] Wrote 1 frames.
OUTTRAJ: [_MMPBSA_ligand.mdcrd.0] Wrote 5 frames.
DATASETS:
There are 3 data sets: RMSD_00000,RMSD_00001,RMSD_00002
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Received on Tue Mar 03 2015 - 02:30:10 PST
