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Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Sat, Jan 18, 2025 at 1:34 PM Vishwaa Kannan via AMBER <amber.ambermd.org>
wrote:
> 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 - 15:00:03 PST