Dear All,
The standard MMPBSA calculations for a protein-protein complex went well.
Binding energy (-8 kcal/mol) started to converge at 200 frames.
Thus I started the quasi-harmonic (entropy=1) simulation.
But I'm not sure if the calculation is running at all.
I also tried with just 2 frames with the following input, but cpptraj has
been running for more than 20 minutes with no output.
Traj processing is still at 0 %.
Can someone on the list please suggest how to make sure if the calculation
is running ok? How long it can be expected to take? I have receptor and
ligand sizes of 143 and 91 residues respectively.
The prmtop files are unlikely to the source of error since the GB and PBSA
calculations ran well with these files.
Looking forward to valuable suggestions from the experts and users on the
list.
thanks and best regards
The input file and command are shown below.
mpirun -np 2 MMPBSA.py.MPI -sp ../1hga-3ner-solv.prmtop -cp
1hga-3ner-complex.prmtop -rp 1hga-recp1.prmtop -lp 3ner-lig1.prmtop -y ../
1hga-3ner-solv-prod300-reimaged.nc -i mmpbsa-quasihar.in -O -o
FINAL-MMPBSA-RESULTS-quasihar-nf200endfr2000.dat >
mmpbsa-quasihar-nf200endfr2000.out &
(base) [exx.c107739 MMPBSA]$ more mmpbsa-quasihar.in
Input file for running nmode and GB
&general
endframe=2000, verbose=2, interval=1000,
entropy=1,
/
&gb
igb=5,
/
(base) [exx.c107739 MMPBSA]$
(base) [exx.c107739 MMPBSA]$ more _MMPBSA_cpptraj_entropy.out
CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.09)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 04/18/21 00:18:14
| Available memory: 20.431 GB
Reading '1hga-3ner-complex.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
Warning: Amber topology flag 'CMAP_COUNT' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_RESOLUTION' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_01' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_02' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_03' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_04' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_05' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_06' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_07' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_08' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_09' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_10' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_11' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_12' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_13' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_14' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_INDEX' is unrecognized and will be
skipped.
INPUT: Reading input from '_MMPBSA_cpptrajentropy.in'
[trajin _MMPBSA_complex.mdcrd]
Reading '_MMPBSA_complex.mdcrd' as Amber Trajectory
[reference _MMPBSA_avgcomplex.pdb]
Reading '_MMPBSA_avgcomplex.pdb' as PDB
Setting active reference for distance-based masks:
'_MMPBSA_avgcomplex.pdb'
[rms mass reference :1-235]
RMSD: (:1-235), reference is "_MMPBSA_avgcomplex.pdb:1" (:1-235),
mass-weighted.
Best-fit RMSD will be calculated, coords will be rotated and
translated.
[matrix mwcovar name comp.matrix :1-235]
MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
Matrix data set is 'comp.matrix'
Start: 1 Stop: Final frame
Mask1 is ':1-235'
[analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce]
Warning: The 'analyze' prefix is no longer necessary and may be soon
deprecated.
Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
Changed DataFile '_MMPBSA_complex_entropy.out' type to Evecs file
for set Modes_00004
DIAGMATRIX: Diagonalizing matrix comp.matrix and writing modes to
_MMPBSA_complex_entropy.out
Calculating all eigenvectors.
Calculating thermodynamic data at 298.15 K, output to STDOUT
Storing modes with name: Modes_00004
[rms mass reference :1-143]
RMSD: (:1-143), reference is "_MMPBSA_avgcomplex.pdb:1" (:1-143),
mass-weighted.
Best-fit RMSD will be calculated, coords will be rotated and
translated.
[matrix mwcovar name rec.matrix :1-143]
MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
Matrix data set is 'rec.matrix'
Start: 1 Stop: Final frame
Mask1 is ':1-143'
[analyze matrix rec.matrix out _MMPBSA_receptor_entropy.out thermo reduce]
Warning: The 'analyze' prefix is no longer necessary and may be soon
deprecated.
Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
Changed DataFile '_MMPBSA_receptor_entropy.out' type to Evecs file
for set Modes_00007
DIAGMATRIX: Diagonalizing matrix rec.matrix and writing modes to
_MMPBSA_receptor_entropy.out
Calculating all eigenvectors.
Calculating thermodynamic data at 298.15 K, output to STDOUT
Storing modes with name: Modes_00007
[rms mass reference :144-235]
RMSD: (:144-235), reference is "_MMPBSA_avgcomplex.pdb:1" (:144-235),
mass-weighted.
Best-fit RMSD will be calculated, coords will be rotated and
translated.
[matrix mwcovar name lig.matrix :144-235]
MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
Matrix data set is 'lig.matrix'
Start: 1 Stop: Final frame
Mask1 is ':144-235'
[analyze matrix lig.matrix out _MMPBSA_ligand_entropy.out thermo reduce]
Warning: The 'analyze' prefix is no longer necessary and may be soon
deprecated.
Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
Changed DataFile '_MMPBSA_ligand_entropy.out' type to Evecs file
for set Modes_00010
DIAGMATRIX: Diagonalizing matrix lig.matrix and writing modes to
_MMPBSA_ligand_entropy.out
Calculating all eigenvectors.
Calculating thermodynamic data at 298.15 K, output to STDOUT
Storing modes with name: Modes_00010
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: 1hga-3ner-complex.prmtop, 3704 atoms, 235 res, box: None, 2 mol
INPUT TRAJECTORIES (1 total):
0: '_MMPBSA_complex.mdcrd' is an AMBER trajectory, Parm
1hga-3ner-complex.prmtop (reading 2 of 2)
Coordinate processing will occur on 2 frames.
REFERENCE FRAMES (1 total):
0: _MMPBSA_avgcomplex.pdb:1
Active reference frame for distance-based masks is
'_MMPBSA_avgcomplex.pdb:1'
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '1hga-3ner-complex.prmtop' (6 actions):
0: [rms mass reference :1-235]
Target mask: [:1-235](3704)
Reference mask: [:1-235](3704)
1: [matrix mwcovar name comp.matrix :1-235]
Mask [:1-235] corresponds to 3704 atoms.
2: [rms mass reference :1-143]
Target mask: [:1-143](2214)
Reference mask: [:1-143](2214)
3: [matrix mwcovar name rec.matrix :1-143]
Mask [:1-143] corresponds to 2214 atoms.
4: [rms mass reference :144-235]
Target mask: [:144-235](1490)
Reference mask: [:144-235](1490)
5: [matrix mwcovar name lig.matrix :144-235]
Mask [:144-235] corresponds to 1490 atoms.
----- _MMPBSA_complex.mdcrd (1-2, 1) -----
0%
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 17 2021 - 09:00:02 PDT
