Hello Everyone,
I have recently installed xplor-nih 2.23 on a cluster. I had some problems
running xplor -tcl b/c the cluster runs RHEL 4.0. However, I am now able to
submit jobs via PBS on a headnode running RHEL 5.3 to a computational node
which I'm assuming runs RHEL 5.3. (I had some problems submitting jobs using
a head node with RHEL 5.3 to computational nodes which supposedly ran RHEL
5.3 but gave me the same tcl problems as RHEL 4.0.) Anyway, that is the
background.
So now I'm trying to finish running the pasd/cvn tutorial. I've submitted
the job using the quick flag and everything runs well until the refine.py
command is implemented in the runPASDquick script,
xplor -quick -py refine.py -parallel -machines ${PBS_NODEFILE} >
refine.py.out
At this point my job terminates. I checked the refine.py.out file which
contained this,
process 7: irregular exit.
process 0: irregular exit.
process 3: irregular exit.
process 6: irregular exit.
process 9: irregular exit.
process 8: irregular exit.
process 2: irregular exit.
process 4: irregular exit.
process 5: irregular exit.
This information was not very helpful. I looked at the xplor.log files and
found a failure when xplor ran the refine.py script. It occurred when trying
to run lines 83-85. I've posted the output log file at the end of this
email. I tried commenting out lines 83-85 and reran the refine.py script
however I just ran into a problem later in the script when refRMSD was
undefined. I was hoping someone could help me decipher this error. Is it a
bad cvn_reference.pdb file? It looks ok upon a quick glance. I'm hoping I
can successfully run this tutorial soon so I can get to the actual job at
hand.
Thanks,
Chris Warner
Graduate Student
Chemical & Biological Engineering Department
Iowa State University
User: cwarner on: node150 (x86_64/Linux ) at: 9-Jun-09 12:53:28
connect attempt #0 to node150:9021...
connection fault: (111, 'Connection refused')
connect attempt #1 to node150:9021...
[stdin](1): execfile('refine.py')
refine.py(2): xplor.requireVersion("2.18")
refine.py(14): (opts,args) = xplor.parseArguments(["quick"]) # check for
command-line typos
refine.py(16): quick=False
refine.py(17): for opt in opts:
refine.py(18): if opt[0]=="quick": #specify -quick to just test that
the script runs
refine.py(19): quick=True
refine.py(20): pass
refine.py(17): for opt in opts:
refine.py(24): outFilename = "SCRIPT_STRUCTURE.sa"
refine.py(25): numberOfStructures=100
refine.py(27): if quick:
refine.py(28): numberOfStructures=3
refine.py(29): pass
refine.py(33): import protocol
refine.py(34): protocol.initRandomSeed(3421) #explicitly set random seed
random seed initialized to 3421
refine.py(40): command = xplor.command
refine.py(42): protocol.initParams("protein")
X-PLOR>param @TOPPAR:protein.par end
ASSFIL: file /work/chem_eng3/OLD/cdw/xplor-nih-2.23/toppar/protein.par
opened.
PARRDR>!
PARRDR>! xplor-nih protein parameter file, version 1.0
PARRDR>!
PARRDR>! This file is intended to work with the topology file
protein-1.0.top
PARRDR>!
PARRDR>! This is a re-named copy of the file parallhdg_procheck.pro
PARRDR>!
PARRDR>! We've created this new filename in order to eliminate confusion
PARRDR>! between the various parameter/topology combinations that ship
PARRDR>! with xplor-nih. It has version numbers, and will be updated
PARRDR>! along with the rest of the xplor-nih package.
PARRDR>!
PARRDR>! Its backbone bond lengths and angles are designed to agree with
PARRDR>! the Engh & Huber parameter set (reference below), which is used by
PARRDR>! PROCHECK, among other structure-validation programs.
PARRDR>!
PARRDR>! If you find errors, PLEASE let us know.
PARRDR>!
PARRDR>
PARRDR>
PARRDR>
PARRDR>
PARRDR>remark file protein-1.0.par
PARRDR>remark Changed version of parallhdg_new.pro so that the bond lengths
and angles
PARRDR>remark agree with what PROCHECK expects.
PARRDR>remark JJK 9/14/98
PARRDR>
PARRDR>! file parallhdg_new.pro
PARRDR>! geometric energy function parameters for distance geometry and
PARRDR>! simulated annealing. Modified by G.M.C. to have sigma's of
Param19x and parafloat
PARRDR>
PARRDR>set message off echo off end
PARRDR> end
X-PLOR>end
refine.py(59): protocol.loadPDB("./cvn_pass3_avg.pdb")
loading pdb file: ./cvn_pass3_avg.pdb [psf]PDBTool:read: atom not found in
structure: LEU 36 O
matchInexactAtomEntry: matching entry 36 O to atom 36 OT1
initCoords: still 3 unknown atomic coordinates
[coords]
refine.py(60): xplor.simulation.deleteAtoms("not known")
MAPIC: Atom numbers being modified
refine.py(62): protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
refine.py(68): from potList import PotList
refine.py(69): potList = PotList()
refine.py(73): from simulationTools import MultRamp, StaticRamp,
InitialParams
refine.py(75): rampedParams=[]
refine.py(76): highTempParams=[]
refine.py(82): from posDiffPotTools import create_PosDiffPot
refine.py(83): refRMSD = create_PosDiffPot("refRMSD","name CA or name C or
name N",
refine.py(84): pdbFile='./cvn_reference.pdb',
refine.py(85): cmpSel="not name H*")
loading pdb file: ./cvn_reference.pdb [psf] initCoords: still 5 unknown
atomic coordinates
[coords]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/work/chem_eng3/OLD/cdw/xplor-nih-2.23/python/trace.py", line 180,
in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "refine.py", line 85, in <module>
cmpSel="not name H*")
File "/work/chem_eng3/OLD/cdw/xplor-nih-2.23/python/posDiffPotTools.py",
line 57, in create_PosDiffPot
(len(selection), len(selection2)))
Exception: len(selection) [108] != len(selection2) [303]
PyInterp::command: error executing: >execfile('refine.py')<
HEAP: maximum use= 1987202 current use= 1738674
X-PLOR: total CPU time= 1.0500 s
X-PLOR: entry time at 12:53:28 9-Jun-09
X-PLOR: exit time at 12:54:43 9-Jun-09
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