Hi there
I am using xplor-NIH 3.9 with talosn and ccpnmr to calculate NMR structures. I
am working on two data sets, one of which (50 amino acids) calculates to
completion, and the other (104 amino acids) continually crashes after
calculating the 310th structure. I am running these calculations on an intel
i9-14900K processor with an Nvidia RTX 4080 with 64 GB of RAM. Please see the
error output below:
pass2.py(400): pass
StructureLoop: calculating structure 311
pass2.py(325): from monteCarlo import randomizeTorsions
pass2.py(326): randomizeTorsions(dyn)
pass2.py(330): from torsionTools import setTorsionsFromTable
pass2.py(331): setTorsionsFromTable( dihed.restraintString )
pass2.py(332): pass
pass2.py(334): protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
MMapAlloc::alloc: mmap failed with Cannot allocate memory
munmap_chunk(): invalid pointer
free(): invalid pointer
Aborted (core dumped)
no machines specified. Disabling -parallel...
Xplor-NIH version 3.9
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).
https://bit.niddk.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger
User: jvederas on: jvederas-P(Linux_x86_64 ) at: 7-Jan-25 10:04:44
[stdin](1): xplor.execfile('pass3.py')
pass3.py(2): xplor.requireVersion("3.6")
pass3.py(18): (opts,args) = xplor.parseArguments([
pass3.py(28): quick=False
pass3.py(29): refFilename=None
pass3.py(31): distBlocks=[]
pass3.py(32): for opt in opts:
pass3.py(33): if opt[0]=="quick": #specify -quick to just test that the
script runs
pass3.py(36): if opt[0]=="refFilename":
pass3.py(39): if opt[0]=="dist":
pass3.py(41): if opt[0]=="allDist":
pass3.py(43): if opt[0]=="likelihoodCut":
pass3.py(44): highLikelihoodCutoff=float(opt[1])
pass3.py(45): pass
pass3.py(46): pass
pass3.py(32): for opt in opts:
pass3.py(48): nefFile=args[0]
pass3.py(49): pasdFilenames=args[1:]
pass3.py(57): outFilename = "SCRIPT_STRUCTURE.pdb"
pass3.py(58): numberOfStructures=500
pass3.py(60): if quick:
pass3.py(66): import protocol
pass3.py(68): protocol.initRandomSeed() #set random seed - by time
random seed initialized to 6269484
pass3.py(70): command = xplor.command
pass3.py(74): protocol.initParams('protein')
X-PLOR>param @TOPPAR:protein.par end
ASSFIL: file /usr/local/xplor/xplor-nih-3.9/toppar/protein.par opened.
PARRDR>remark File toppar/protein-4.0.par
PARRDR>remark Xplor-NIH version of CNS protein-allhdg5-4.param
(14-DEC-2022)
PARRDR>remark
PARRDR>remarks file toppar/protein-allhdg5-4.param
PARRDR>remark
PARRDR>remark for file protein-allhdg-ucl.top version UCL date 14-MAR-00
PARRDR>remark for file protein-allhdg-dih-ucl.top version UCL date
07-JUL-01
PARRDR>remark Geometric energy function parameters for distance geometry and
PARRDR>remark simulated annealing.
PARRDR>remark Original author: Michael Nilges, EMBL Heidelberg
PARRDR>remark Modifications: Mark A. Williams, UCL London
PARRDR>remark Several modifications for HADDOCK: Alexandre Bonvin, Utrecht
Uni
PARRDR>!remark Last modification 8-19-2011
PARRDR>
PARRDR>
PARRDR>
PARRDR>set message off echo off end
PARRDR>
PARRDR>
PARRDR>
PARRDR> end
X-PLOR>end
pass3.py(75): from nefTools import readNEF
pass3.py(76): nef = readNEF(nefFile) # generates PSF information
pass3.py(81): from atomAction import genRandomCoords
pass3.py(82): genRandomCoords()
pass3.py(89): from potList import PotList
pass3.py(90): potList = PotList()
pass3.py(94): from simulationTools import MultRamp, StaticRamp, InitialParams,
IVMAction
pass3.py(96): rampedParams=[]
pass3.py(97): highTempParams=[]
pass3.py(98): highTemp1Params=[]
pass3.py(99): highTemp2Params=[]
pass3.py(105): from ivm import IVM
pass3.py(106): dyn = IVM()
pass3.py(107): minc = IVM() # minc used for final cartesian minimization
pass3.py(116): from iupacNaming import toIUPAC
pass3.py(117): toIUPAC()
pass3.py(129): from noePotTools import create_NOEPot, readNEF
pass3.py(130): noe=PotList("dist")
pass3.py(131): if distBlocks is None:
pass3.py(135): for name in distBlocks:
pass3.py(142): potList.append(noe)
pass3.py(143): rampedParams.append( MultRamp(2,30, "noe.setScale( VALUE )") )
pass3.py(147): import pasd
pass3.py(148): pasdTerms=PotList('pasd')
pass3.py(149): potList.append( pasdTerms )
pass3.py(150): for pasdFilename in pasdFilenames:
pass3.py(151): name='_'.join( pasdFilename.split('_')[:-1] )
pass3.py(152): print(f"processing PASD file: {pasdFilename} for spectrum
{name}")
processing PASD file: *pass3.pasd for spectrum
pass3.py(154): from pasdPotTools import create_PASDPot
pass3.py(156): pot = create_PASDPot(name,pasdFilename=pasdFilename)
file not found: *pass3.pasd
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/trace.py", line 180, in run
exec(cmd, dict, dict)
File "<string>", line 1, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/xplorInit.py", line 147, in
execfile
exec(code, globals, locals)
File "pass3.py", line 156, in <module>
pot = create_PASDPot(name,pasdFilename=pasdFilename)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/xplor/xplor-nih-3.9/python/pasdPotTools.py", line 46, in
create_PASDPot
pasd,pasdFilename = fileContentsOrString(pasdFilename,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/xplor/xplor-nih-3.9/python/utils.py", line 218, in
fileContentsOrString
filename = getDBfilename(filenameOrString,dbEnvVar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/xplor/xplor-nih-3.9/python/utils.py", line 190, in
getDBfilename
raise FileNotFoundError(msg)
FileNotFoundError: Could not find *pass3.pasd
HEAP: maximum use= 4201102 current use= 3353249
X-PLOR: total CPU time= 0.3212 s
X-PLOR: entry time at 10:04:44 7-Jan-25
X-PLOR: exit time at 10:04:44 7-Jan-25
Xplor-NIH version 3.9
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).
https://bit.niddk.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger
User: jvederas on: jvederas-P(Linux_x86_64 ) at: 7-Jan-25 10:04:44
[stdin](1): xplor.execfile('makeNEF.py')
makeNEF.py(6): xplor.requireVersion("3.0")
makeNEF.py(11): (opts,args) = xplor.parseArguments([
makeNEF.py(12): ("likelihoodCut","val",
makeNEF.py(11): (opts,args) = xplor.parseArguments([
makeNEF.py(16): likelihoodCut=0.9
makeNEF.py(17): for opt in opts:
makeNEF.py(18): if opt[0]=="likelihoodCut":
makeNEF.py(19): likelihoodCut=float(opt[1])
makeNEF.py(20): pass
makeNEF.py(21): pass
makeNEF.py(17): for opt in opts:
makeNEF.py(24): nefFile=args[0]
makeNEF.py(25): pasdFilenames=args[1:]
makeNEF.py(27): from nefTools import readNEF
makeNEF.py(28): nef = readNEF(nefFile) # generates PSF information
makeNEF.py(35): from iupacNaming import toIUPAC
makeNEF.py(36): toIUPAC()
makeNEF.py(38): from nefTools import genHeader
makeNEF.py(39): nefString = genHeader()
makeNEF.py(43): from nefTools import getBlock, catPrefixes
makeNEF.py(44): shiftsBlock = getBlock(nef,'shifts')
makeNEF.py(45): shiftsPrefix=catPrefixes['shifts']
makeNEF.py(46):
name=shiftsBlock[shiftsPrefix].sf_framecode[0][len(shiftsPrefix)+1:]
makeNEF.py(50): from nefTools import shifts_writeNEF
makeNEF.py(51): nefString += shifts_writeNEF(name,shiftsBlock)
makeNEF.py(55): from nefTools import getBlock, catPrefixes
makeNEF.py(56): dihedralBlock = getBlock(nef,'dihedral','1')
makeNEF.py(57): dihedralPrefix=catPrefixes['dihedral']
makeNEF.py(58):
name=dihedralBlock[dihedralPrefix].sf_framecode[0][len(dihedralPrefix)+1:]
makeNEF.py(60): import nefTools
makeNEF.py(61): dihedral0=nefTools.makeNEF()
makeNEF.py(62): dihedral0[dihedralPrefix+'_'+name] = dihedralBlock
makeNEF.py(64): nefString += "\n" + dihedral0.asString() + "\n"
makeNEF.py(69): prefix=catPrefixes['distance']
makeNEF.py(70): for name in nefTools.getBlockNames(nef,"distance"):
makeNEF.py(83): spectrumNames=[]
makeNEF.py(84): for pasdFilename in pasdFilenames:
makeNEF.py(85): name='_'.join( pasdFilename.split('_')[:-1] )
makeNEF.py(86): print(f"initializing spectrum {name}")
initializing spectrum
makeNEF.py(87): spectrumNames.append( name )
makeNEF.py(89): from nefTools import getBlock, catPrefixes
makeNEF.py(90): block = getBlock(nef,'spectrum',name)
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/trace.py", line 180, in run
exec(cmd, dict, dict)
File "<string>", line 1, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/xplorInit.py", line 147, in
execfile
exec(code, globals, locals)
File "makeNEF.py", line 90, in <module>
block = getBlock(nef,'spectrum',name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/xplor/xplor-nih-3.9/python/nefTools.py", line 803, in
getBlock
raise Exception(mess)
Exception: getBlock: found more than one block of type: nef_nmr_spectrum
Please choose one of: nef_nmr_spectrum_13CNOESY`1` nef_nmr_spectrum_nnoesy`1`
HEAP: maximum use= 3681502 current use= 3353249
X-PLOR: total CPU time= 0.2600 s
X-PLOR: entry time at 10:04:44 7-Jan-25
X-PLOR: exit time at 10:04:45 7-Jan-25
no machines specified. Disabling -parallel...
Xplor-NIH version 3.9
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).
https://bit.niddk.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger
User: jvederas on: jvederas-P(Linux_x86_64 ) at: 7-Jan-25 10:04:45
[stdin](1): xplor.execfile('fold.py')
fold.py(1): (opts,args) = xplor.parseArguments([
fold.py(12): nefFile=None
fold.py(13): refFilename=None
fold.py(14): distBlocks=[]
fold.py(15): for opt in opts:
fold.py(16): if opt[0]=="nef":
fold.py(17): nefFile=opt[1]
fold.py(18): pass
fold.py(19): if opt[0]=="refFilename":
fold.py(22): if opt[0]=="dist":
fold.py(25): pass
fold.py(15): for opt in opts:
fold.py(16): if opt[0]=="nef":
fold.py(19): if opt[0]=="refFilename":
fold.py(22): if opt[0]=="dist":
fold.py(23): sep=":" if ":" in opt[1] else None
fold.py(24): distBlocks += opt[1].split(sep)
fold.py(25): pass
fold.py(15): for opt in opts:
fold.py(27): from os.path import splitext
fold.py(28): id=splitext(nefFile)[0]
fold.py(32): import protocol
fold.py(33): protocol.initRandomSeed(3421) #explicitly set random seed
random seed initialized to 3421
fold.py(36): protocol.initParams("protein")
X-PLOR>param @TOPPAR:protein.par end
ASSFIL: file /usr/local/xplor/xplor-nih-3.9/toppar/protein.par opened.
PARRDR>remark File toppar/protein-4.0.par
PARRDR>remark Xplor-NIH version of CNS protein-allhdg5-4.param
(14-DEC-2022)
PARRDR>remark
PARRDR>remarks file toppar/protein-allhdg5-4.param
PARRDR>remark
PARRDR>remark for file protein-allhdg-ucl.top version UCL date 14-MAR-00
PARRDR>remark for file protein-allhdg-dih-ucl.top version UCL date
07-JUL-01
PARRDR>remark Geometric energy function parameters for distance geometry and
PARRDR>remark simulated annealing.
PARRDR>remark Original author: Michael Nilges, EMBL Heidelberg
PARRDR>remark Modifications: Mark A. Williams, UCL London
PARRDR>remark Several modifications for HADDOCK: Alexandre Bonvin, Utrecht
Uni
PARRDR>!remark Last modification 8-19-2011
PARRDR>
PARRDR>
PARRDR>
PARRDR>set message off echo off end
PARRDR>
PARRDR>
PARRDR>
PARRDR> end
X-PLOR>end
fold.py(47): from nefTools import readNEF
fold.py(48): nefData = readNEF(nefFile)
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/trace.py", line 180, in run
exec(cmd, dict, dict)
File "<string>", line 1, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/xplorInit.py", line 147, in
execfile
exec(code, globals, locals)
File "fold.py", line 48, in <module>
nefData = readNEF(nefFile)
^^^^^^^^^^^^^^^^
File "/usr/local/xplor/xplor-nih-3.9/python/nefTools.py", line 34, in readNEF
dataString=open(filenameOrString).read()
^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'out.nef'
HEAP: maximum use= 2301505 current use= 2145473
X-PLOR: total CPU time= 0.1220 s
X-PLOR: entry time at 10:04:45 7-Jan-25
X-PLOR: exit time at 10:04:45 7-Jan-25
grep: fold_##.sa.stats: No such file or directory
grep: Filename:: invalid context length argument
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/xplorInit.py", line 147, in
execfile
exec(code, globals, locals)
File "/usr/local/xplor/xplor-nih-3.9/bin/ens2pdb", line 145, in <module>
globList=glob(files[0])
~~~~~^^^
IndexError: list index out of range
grep: fold_##.sa.stats: No such file or directory
grep: Filename:: invalid context length argument
no machines specified. Disabling -parallel...
Xplor-NIH version 3.9
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).
https://bit.niddk.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger
User: jvederas on: jvederas-P(Linux_x86_64 ) at: 7-Jan-25 10:04:45
[stdin](1): xplor.execfile('refine.py')
refine.py(1): (opts,args) = xplor.parseArguments([
refine.py(12): numberOfStructures=100
refine.py(13): nefFile=None
refine.py(14): refFilename=None
refine.py(15): distBlocks=[]
refine.py(16): for opt in opts:
refine.py(17): if opt[0]=="nef":
refine.py(18): nefFile=opt[1]
refine.py(19): pass
refine.py(20): if opt[0]=="refFilename":
refine.py(23): if opt[0]=="dist":
refine.py(26): pass
refine.py(16): for opt in opts:
refine.py(17): if opt[0]=="nef":
refine.py(20): if opt[0]=="refFilename":
refine.py(23): if opt[0]=="dist":
refine.py(24): sep=":" if ":" in opt[1] else None
refine.py(25): distBlocks += opt[1].split(sep)
refine.py(26): pass
refine.py(16): for opt in opts:
refine.py(28): if nefFile is None:
refine.py(34): pdbFilesIn = args
refine.py(35): if len(pdbFilesIn) == 0:
refine.py(43): import protocol
refine.py(44): protocol.initRandomSeed(3421) #explicitly set random seed
random seed initialized to 3421
refine.py(47): protocol.initParams("protein")
X-PLOR>param @TOPPAR:protein.par end
ASSFIL: file /usr/local/xplor/xplor-nih-3.9/toppar/protein.par opened.
PARRDR>remark File toppar/protein-4.0.par
PARRDR>remark Xplor-NIH version of CNS protein-allhdg5-4.param
(14-DEC-2022)
PARRDR>remark
PARRDR>remarks file toppar/protein-allhdg5-4.param
PARRDR>remark
PARRDR>remark for file protein-allhdg-ucl.top version UCL date 14-MAR-00
PARRDR>remark for file protein-allhdg-dih-ucl.top version UCL date
07-JUL-01
PARRDR>remark Geometric energy function parameters for distance geometry and
PARRDR>remark simulated annealing.
PARRDR>remark Original author: Michael Nilges, EMBL Heidelberg
PARRDR>remark Modifications: Mark A. Williams, UCL London
PARRDR>remark Several modifications for HADDOCK: Alexandre Bonvin, Utrecht
Uni
PARRDR>!remark Last modification 8-19-2011
PARRDR>
PARRDR>
PARRDR>
PARRDR>set message off echo off end
PARRDR>
PARRDR>
PARRDR>
PARRDR> end
X-PLOR>end
refine.py(58): from nefTools import readNEF
refine.py(59): nefData = readNEF(nefFile)
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/trace.py", line 180, in run
exec(cmd, dict, dict)
File "<string>", line 1, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/xplorInit.py", line 147, in
execfile
exec(code, globals, locals)
File "refine.py", line 59, in <module>
nefData = readNEF(nefFile)
^^^^^^^^^^^^^^^^
File "/usr/local/xplor/xplor-nih-3.9/python/nefTools.py", line 34, in readNEF
dataString=open(filenameOrString).read()
^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'out.nef'
HEAP: maximum use= 2301505 current use= 2145473
X-PLOR: total CPU time= 0.1135 s
X-PLOR: entry time at 10:04:45 7-Jan-25
X-PLOR: exit time at 10:04:45 7-Jan-25
grep: refine_##.sa.stats: No such file or directory
grep: Filename:: invalid context length argument
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/xplor/xplor-nih-3.9/python/xplorInit.py", line 147, in
execfile
exec(code, globals, locals)
File "/usr/local/xplor/xplor-nih-3.9/bin/ens2pdb", line 145, in <module>
globList=glob(files[0])
~~~~~^^^
IndexError: list index out of range
Thank you kindly for your assistance
Tyler
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