Dear Amber Users,
This is Voytek Kasprzak from Frederick National Lab (NCI). I am unable to complete a simple
MMPBSA run based on Amber Advanced Tutorial 3 (section 3.4) in Amber 16 or Amber 14.
My case is similar but not the same as a post on the PB failure from yesterday.
I am analyzing a trajectory of an RNA fragment with a small ligand (~60 atoms), that was
subjected to explicit solvent PME MD simulation in Amber 16. All topology files
(complex in solvent, complex without solvent, receptor alone and ligand alone) were created
in one LEaP session with the same PBRadii - a potential issue, as the end of the FILE.o*
shown below seems to suggest (see 1. below)
After completing successfully the GB-based section of the MMPBSA.py.MPI run (10,000 input
frames on 16 cores), the program crashes reproducibly as it gets to the PB-based calculations.
The error message states that "No radius assigned for atom 3 C5' CI" is the problem,
and one PB output file _MMPBSA_complex_pb.mdout.2 shows an aborted start of that section
(see 2. below). C5' is the third atom in the RNA/lifand prmtop file (oddly, no complaints
about the first two atoms: HO5' and O5'). The input file is shown in point 3.
Should I create separate no-solvent topology files with PBRadii set to bondi since that is
the common denominator for igb=2 and pbsa runs? What would you recommend for RNA/DNA-ligand
complexes? What are the consequences of having solvent run based on one set of radii and
solvent-free parts on another?
If my interpretation of the error messages is incorrect, what else could be the problem?
Best regards, Voytek
Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
kasprzaw.mail.nih.gov
http://binkley2.ncifcrf.gov/users/kasprzak
==================================================================
1. Error message:
File "/opt/nasapps/production/amber/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/nasapps/production/amber/amber16/bin/mmpbsa_py_energy failed with prmtop RNA-LIGAND-nosolv.prmtop!
PB Bomb in pb_aaradi(): No radius assigned for atom 3 C5' CI
Error occured on rank 2.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 1.
==================================================================
2. Last PB output before the crash (_MMPBSA_complex_pb.mdout.2):
Reading parm file (RNA-LIGAND-nosolv.prmtop)
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=1
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_complex.mdcrd.2)
Processing frame 1
iter Total bad vdW elect nonpolar EPB frms
eff.c(2717) enb14 --> 571.724
eff.c(2718) eel14 --> -6929.892
==================================================================
3. MMPBSA input file (same as in the tutorial) mmpbsa.in:
Input file for running PB and GB (100ns in 10K frames)
&general
endframe=10000, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.15
/
&pb
istrng=0.15,
/
==================================================================
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Received on Wed Apr 11 2018 - 08:00:02 PDT
