Dear All,
We have just installed xplor-nih-2.25 on our linux cluster using SGE
(version6.2) for job submission. Version 2.24 works fine however, version 2.25
fails. I've attached below the log file from one of the jobs which gives
typical output from a failed run. This was an attempt to run anneal.py from the
eginput/protG directory on one of our structure calculations. Any suggestions
would be gratefully received.
Yours,
Fred Muskett
Xplor-NIH version 2.25
C.D. Schwieters, J.J. Kuszewski, Progr. NMR Spectr. 48, 47-62 (2006).
N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003).
http://nmr.cit.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger
User: fwm1 on: comp12 (x86_64/Linux ) at: 9-Mar-10 14:11:40
connect attempt #0 to comp12:9021...
[stdin](1): execfile('anneal2.py')
anneal2.py(9): outFilename = "pdcd4_STRUCTURE.pdb"
anneal2.py(10): numberOfStructures=100
anneal2.py(11): seed=3421
anneal2.py(12): simWorld.setRandomSeed(seed) #set random seed
anneal2.py(14): command = xplor.command
anneal2.py(19): from noePot import NOEPot
anneal2.py(20): from xplorPot import XplorPot
anneal2.py(21): from rdcPotTools import create_RDCPot
anneal2.py(22): from varTensorTools import create_VarTensor
anneal2.py(23): import varTensorTools
anneal2.py(24): from ivm import IVM
anneal2.py(25): from potList import PotList
anneal2.py(26): import protocol
anneal2.py(31): protocol.initParams("protein") Traceback (most recent call
last):
File "<string>", line 2, in <module>
File "/opt/xplor-nih/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "anneal2.py", line 31, in <module>
protocol.initParams("protein")
File "/opt/xplor-nih/python/protocol.py", line 178, in initParams
addParams(file)
File "/opt/xplor-nih/python/protocol.py", line 160, in addParams
file = genTopParFilename(file,True)
File "/opt/xplor-nih/python/protocol.py", line 101, in genTopParFilename
raise Exception(mess)
Exception: genTopParFilename: could not find name protein.par as a structure
type
or as file in the current dir, or in TOPPAR
PyInterp::command: error executing: >execfile('anneal2.py')<
HEAP: maximum use= 609307 current use= 597475
X-PLOR: total CPU time= 0.3900 s
X-PLOR: entry time at 14:11:40 9-Mar-10
X-PLOR: exit time at 14:11:48 9-Mar-10
######################################################################
Dr F.W.Muskett
Structural Biology Manager
Dept. of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Road
Leicester? LE1 9HN? UK
Tel. +44 (0)116 229 7096
Mob. +44 (0)790 990 7330
Fax? +44 (0)116 229 7018
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Times Higher Education Award for Outstanding Student Support 2009-10
Times Higher Education University of the Year 2008-9
