The MMPBSA is not working properly. After narrowing it down, I suspect the problem lies with the protein being counted as two separate molecules (prob the dimer being weird), and the ligand being recognized as another, which could be causing the errors. I figured this out using cpptraj and list, molecule 1: 1-313, molecule 2: 314 - 627, molecule 3 (PFOA): 628. I tried explicitly stating it, but that did not work. What can I do to fix this error?
Input file (mmpbsa.in):
&general
startframe=601, endframe=2000,
strip_mask=":WAT,Na+",
receptor_mask=":1-627",
ligand_mask=":628",
keep_files=2,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1,
/
Terminal:
vishwaa.BCC-A102281:~/amber/TS/R1$ mpirun -np 20 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp R1_solvated.prmtop -cp R1.prmtop -rp R1_rec.prmtop -lp R1_lig.prmtop -y prod.mdcrd
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/vishwaa/amber/amber24/bin/cpptraj
sander found! Using /home/vishwaa/amber/amber24/bin/sander
Preparing trajectories for simulation...
1400 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/vishwaa/amber/amber24/bin/sander
calculating complex contribution...
File "/home/vishwaa/amber/amber24/bin/MMPBSA.py.MPI", line 101, in <module>
app.run_mmpbsa() # for membrane runs by automatically setting the membrane thickness and location.
^^^^^^^^^^^^^^^^
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/main.py", line 225, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 476, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/vishwaa/amber/amber24/bin/sander failed with prmtop R1.prmtop!
Error occurred on rank 6.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
File "/home/vishwaa/amber/amber24/bin/MMPBSA.py.MPI", line 101, in <module>
app.run_mmpbsa() # for membrane runs by automatically setting the membrane thickness and location.
^^^^^^^^^^^^^^^^
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/main.py", line 225, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 476, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
CalcError: /home/vishwaa/amber/amber24/bin/sander failed with prmtop R1.prmtop!
Error occurred on rank 11.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
File "/home/vishwaa/amber/amber24/bin/MMPBSA.py.MPI", line 101, in <module>
app.run_mmpbsa() # for membrane runs by automatically setting the membrane thickness and location.
^^^^^^^^^^^^^^^^
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/main.py", line 225, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py", line 476, in run
raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
[BCC-A102281:10455] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[BCC-A102281:10455] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
vishwaa.BCC-A102281:~/amber/TS/R1$
Output of rank 6 ("MMPBSA_complex_pb.mdout.6"):
-------------------------------------------------------
Amber 24 SANDER 2024
-------------------------------------------------------
| Run on 01/18/2025 at 16:10:12
| Executable path: /home/vishwaa/amber/amber24/bin/sander
| Working directory: /home/vishwaa/amber/TS/R1
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_pb_decomp_com.mdin
| MDOUT: _MMPBSA_complex_pb.mdout.6
|INPCRD: _MMPBSA_dummycomplex.inpcrd
| PARM: R1.prmtop
|RESTRT: _MMPBSA_restrt.6
| REFC: refc
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_complex.mdcrd.6
Here is the input file:
File generated by MMPBSA.py
&cntrl
ntb=0, nsnb=99999, cut=999.0, imin=5,
igb=10, idecomp=1, ipb=2,
dec_verbose=0,
/
&pb
istrng=100.0, radiopt=0, maxitn=1000,
fillratio=4.0,
/
Residues considered as REC
RRES 1 627
END
Residues considered as LIG
LRES 628 628
END
Residues to print
RES 1 628
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 01/17/25 Time = 01:12:41
NATOM = 10051 NTYPES = 19 NBONH = 4986 MBONA = 5196
NTHETH = 11380 MTHETA = 7050 NPHIH = 23035 MPHIA = 22015
NHPARM = 0 NPARM = 0 NNB = 55658 NRES = 628
NBONA = 5196 NTHETA = 7050 NPHIA = 22015 NUMBND = 74
NUMANG = 174 NPTRA = 199 NATYP = 38 NPHB = 0
IFBOX = 0 NMXRS = 25 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
| CMAP information read from topology file:
| Memory Use Allocated
| Real 1557822
| Hollerith 30783
| Integer 583328
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 14569 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
|CMAP: Reticulating splines.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 5, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 50, ntrx = 1, ntwr = 1
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 1, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 10, nsnb = 99999
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
LOADING THE DECOMP ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
Residues considered as REC
Number of atoms in this group = 0
----- READING GROUP 2; TITLE:
Residues considered as LIG
Number of atoms in this group = 0
----- READING GROUP 3; TITLE:
Residues to print
GRP 3 RES 1 TO 628
Number of atoms in this group = 10051
----- END OF GROUP READ -----
There was more stuff here, but just a bunch of atoms and their info.
--
Best,
Vishwaa Kannan
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Received on Sat Jan 18 2025 - 14:00:02 PST
