Dear CCP4BB members,
I am using the loop building module of new arp/warp 7.0 version in RHEL. I
am sure during installation everthing went well. But when I try to run the
program the following error occured. I think the problem is somewhere in
the xml file format.
Any help is highly appreciated!
Thanks
Karthik
(Sorry for the long log file)
------------------------------------------------------------------------------
#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG loopy
#CCP4I DATE 24 Jul 2007 09:20:39
#CCP4I USER vijay
#CCP4I PROJECT v3
#CCP4I JOB_ID 8
#CCP4I SCRATCH /tmp/vijay
#CCP4I HOSTNAME localhost.localdomain
#CCP4I PID 28599
## This script run with the command ##########
# /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop
-paramfile=/tmp/vijay/v3_8_1_com.tmp
################################################
loop - WRNG* : CConfig::processStream File isn't in proper XML format
loop - WRNG* : Couldn't read XML parameter file for warp::CConfig.
loop - WRNG* : CConfig::processStream Handling parameter file as non-xml.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<arp-warp>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<loop>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<MessageFilename>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.msg
</MessageFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<XMLOutputFilename>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.xml
</XMLOutputFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<AbortLevel> 8 </AbortLevel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<MessageLevel> 4 </MessageLevel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<ProgramName> loopy </ProgramName>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<DictionaryFilename>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/AAbis_extension.XYZ
</DictionaryFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<UniformAtomBFactor> 20 </UniformAtomBFactor>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<UniformAtomRadius> 0.74 </UniformAtomRadius>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<AntiBumpFactor> 1. </AntiBumpFactor>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SymmetryFilename>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/syminfo.lib
</SymmetryFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SpaceGroup> 19 </SpaceGroup>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<XtalCell> 60.489 112.116 133.838 90.00 90.00 90.00 </XtalCell>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<KeepSideChain> 1 </KeepSideChain>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<KeepFragmentLongerThan> 0 </KeepFragmentLongerThan>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<UseCDummyResidue> 1 </UseCDummyResidue>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<StructureFilenameToC>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2C_my_0.3b_cos_log.llh
</StructureFilenameToC>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<StructureFilenameToN>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2N_my_0.3b_cos_log.llh
</StructureFilenameToN>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<CADistance> 3.8 </CADistance>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<RandomGrid> 0 </RandomGrid>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<GridNumber> 378 </GridNumber>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<DisregardNegativeDensity> 1 </DisregardNegativeDensity>, Was
not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<KeepNegDensityHalfway> 0 </KeepNegDensityHalfway>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<NormalizeDensity> 1 </NormalizeDensity>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<BFactorForBuildSideChain> 26 </BFactorForBuildSideChain>, Was
not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LikelihoodThreshold> -4.5 </LikelihoodThreshold>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<WeightDensityLLH> 1. </WeightDensityLLH>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<WeightDistanceLLH> 1. </WeightDistanceLLH>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<WeightStructuralLLH> 1. </WeightStructuralLLH>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<OldComputation> 0 </OldComputation>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<CheckFirstAngle> 1 </CheckFirstAngle>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<UseCubicFitTarget> 1 </UseCubicFitTarget>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<OverlapRejectionThreshold> 0.1 </OverlapRejectionThreshold>,
Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<DummyRejectionThreshold> 0.1 </DummyRejectionThreshold>, Was
not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopBuildAll> 0 </LoopBuildAll>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<ExtendGapSmallerThan> 0 </ExtendGapSmallerThan>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopBothWays> 1 </LoopBothWays>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopToC> 1 </LoopToC>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopLength> </LoopLength>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopOverlap> 0 </LoopOverlap>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopDensityCutoffNo> 100 </LoopDensityCutoffNo>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<MinimalDistance> 0.3 </MinimalDistance>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<MaxNoCAsKept> 6 </MaxNoCAsKept>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<ForceMinCAsKept> 2 </ForceMinCAsKept>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopRMS> 0.7 </LoopRMS>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopStructureThreshold> -1.5 </LoopStructureThreshold>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopStructureCutoffNo> 50 </LoopStructureCutoffNo>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopStructureMinNo> 15 </LoopStructureMinNo>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopMainChainDensNo> 5 </LoopMainChainDensNo>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopsToBuild> C104<8>C112 </LoopsToBuild>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<LoopSequence> PNHVTYSGD </LoopSequence>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<UseLoopSequence> 1 </UseLoopSequence>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<InputPDB>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/04_model.pdb
</InputPDB>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<IncludeChains> </IncludeChains>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<InputMTZ>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/ps39_3_refmac4.mtz
</InputMTZ>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<OutputMapFromMTZ> /tmp/vijay/ps39_3_loopy1.map
</OutputMapFromMTZ>, Was
not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<FWTLabel> FWT </FWTLabel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<PHIWTLabel> PHWT </PHIWTLabel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveResult> 0 </SaveResult>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveBestLoopSets> 1 </SaveBestLoopSets>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveBestNumber> 5 </SaveBestNumber>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveLoopsDir>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac
</SaveLoopsDir>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveLoopsBasename> 04_model_loop </SaveLoopsBasename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveProposedPDBDir>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac
</SaveProposedPDBDir>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveProposedPDBBasename> 04_model_proposed </SaveProposedPDBBasename>,
Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<SaveUseLoopDef> 0 </SaveUseLoopDef>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<WeightMainChain> 1. </WeightMainChain>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
<WeightSideChain> 0. </WeightSideChain>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
</loop>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter file :
</arp-warp>, Was not considered.
loop - WRNG* : CConfig::CConfig : Some argument of the command line (was)
were not parsed by CConfig, ie not understood by libwarp.
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
###############################################################################
### ARP/wARP Program Suite: LOOP BUILDING 0.1 Krista Joosten (17-11-2005)
###
### F77 lib: V. Lamzin
###
############ Copyright 2005 , NKI, A. Perrakis Laboratory
#####################
###############################################################################
<!--SUMMARY_END--></FONT></B>
Starting time : Tue Jul 24 09:20:39 2007
loop - ERROR** : Unable to open file with name : ''. Hence unable to
create a dictionary of Amino Acids!
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command:
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop
-paramfile=/tmp/vijay/v3_8_1_com.tmp
has failed with error message
:51: parser error : StartTag: invalid element name
<LoopsToBuild> C104<8>C112 </LoopsToBuild>
^
Parameter Stream does NOT contain XML!!!
MIGHT ABORT NOW, error message is : ERROR** : Unable to open file with
name : ''. Hence unable to create a dictionary of Amino Acids!
***************************************************************************
#CCP4I TERMINATION STATUS 0 ":51: parser error : StartTag: invalid element
name <LoopsToBuild> C104<8>C112 </LoopsToBuild> ^
Parameter Stream does NOT contain XML!!! MIGHT ABORT NOW, error message is
: ERROR** : Unable to open file with name : ''. Hence unable to create a
dictionary of Amino Acids!"
#CCP4I TERMINATION TIME 24 Jul 2007 09:20:40
#CCP4I MESSAGE Task failed
