Doubt:: JChem>>screenmd

Quote:

Dear Sir, I am JChem(Ver.5.1.4) user. I have doubt in JChem>>screenmd program. I want to run screenmd with LogD Descripto. For that I tried following command screenmd database_combo2.mol2 input_glp22.smiles -C -k LogD logd.xml -g -o Old_LogD -o sdf Old_LogD.sdf <span style="font-size: 10pt; font-family: Verdana;">[  In the corrent working directory have following files:

Database Name - <span style="font-size: 10pt; font-family: Verdana;">database_combo2.mol2


Query - <span style="font-size: 10pt; font-family: Verdana;">input_glp22.smiles


 logd.xml – this xml file I got from ‘\examples\config’ folder


]





<span style="font-size: 10pt; font-family: Verdana;">But after


running this command, following error is coming.











<span style="font-size: 10pt; font-family: Verdana;">[screenmd]$ screenmd database_combo2.mol2 input_glp22.smiles -k LogD logd.xml -g -o LogD_OP -o sdf LogD_OP.sdf


<span style="color: red;">java.lang.ArrayIndexOutOfBoundsException:-1


        at chemaxon.calculations.PolarGroups.setAtomicGroups(PolarGroups.java:1193)


        at


chemaxon.calculations.PolarGroups.setGroups(PolarGroups.java:1153)


        at


chemaxon.calculations.logP.initArrays_new(logP.java:5625)


        at


chemaxon.calculations.logP.initlogP_new(logP.java:5667)


        at


chemaxon.calculations.logP.calclogPMicro_new(logP.java:5973)


        at


chemaxon.calculations.logP.calclogPMicro(logP.java:3800)


        at


chemaxon.calculations.logP.calcWeightedlogPMicro(logP.java:3721)


        at


chemaxon.calculations.logP.calclogPMicro(logP.java:3793)


        at


chemaxon.calculations.logD.calclogDatFixpH(logD.java:450)


        at


chemaxon.descriptors.scalars.LDParameters.generate(LDParameters.java:113)


        at


chemaxon.descriptors.scalars.LogD.generate(LogD.java:125)


        at


chemaxon.descriptors.MDFileReader.readFromMolecule(MDFileReader.java:308)


        at


chemaxon.descriptors.MDFileReader.next(MDFileReader.java:229)


        at


chemaxon.descriptors.MDSimilarity.compare(MDSimilarity.java:515)


        at


chemaxon.descriptors.ScreenMD.compare(ScreenMD.java:340)


        at


chemaxon.descriptors.ScreenMD.main(ScreenMD.java:229)


chemaxon.descriptors.MDGeneratorException: Parameters are not set


properly.


        at


chemaxon.descriptors.scalars.LDParameters.generate(LDParameters.java:117)


        at


chemaxon.descriptors.scalars.LogD.generate(LogD.java:125)


        at


chemaxon.descriptors.MDFileReader.readFromMolecule(MDFileReader.java:308)


        at


chemaxon.descriptors.MDFileReader.next(MDFileReader.java:229)


        at


chemaxon.descriptors.MDSimilarity.compare(MDSimilarity.java:515)


        at


chemaxon.descriptors.ScreenMD.compare(ScreenMD.java:340)


        at


chemaxon.descriptors.ScreenMD.main(ScreenMD.java:229)


Error in MDMolFileReader.next(), reason: Parameters are not set


properly.


chemaxon.descriptors.MDReaderException: Error in


MDMolFileReader.next(), reason: Parameters are not set properly.


        at


chemaxon.descriptors.MDFileReader.readFromMolecule(MDFileReader.java:329)


        at


chemaxon.descriptors.MDFileReader.next(MDFileReader.java:229)


        at


chemaxon.descriptors.MDSimilarity.compare(MDSimilarity.java:515)


        at


chemaxon.descriptors.ScreenMD.compare(ScreenMD.java:340)


        at


chemaxon.descriptors.ScreenMD.main(ScreenMD.java:229)





[screenmd]$











 


<span style="font-size: 10pt; font-family: Arial; color: #006666;">Whats the error in the command line?


Can you find it out why this type of error are coming?





<span style="font-size: 10pt; font-family: Arial; color: #006666;">Thanks in advance,


Remya.

Dear Remya,


my colleague who can answer this is on holiday until next Monday, 1st March, he will answer to you as soon as he is back.


Kind Regards.


Adrian

Hi,





please consult with the relevant user documentation that explains command line arguments, you may wish to follow this link: http://www.chemaxon.com/jchem/doc/user/ScreenMD.html#usage about usage of screenmd command line, or alternatively check the examples provided: http://www.chemaxon.com/jchem/doc/user/ScreenMD.html#examples.





Regarding your particular command, -C is not a valid option, -k logD can however be followed by an optional -c flag, in which case the XML configuration file name is mandatory after the -c flag.





Finally, please provide full details in your profile in order to qualify for the free support via this forum.





Regards,





Miklos

Dear Sir,





I followed your instruction, but still i am facing some error.





I tried to run 'sreenmd' program with 'LogD' option in the JChem5.1.4 Version.





Following command i used for running the same [input file and logd.xml files are attached with this mail for your referance]:-





 >> screenmd database_combo2.mol2 input_glp22.smiles -L 1.0 -k LogD -c logd.xml -k LogP -k Mass -k Heavy -g -o screenmd_OP1 -o sdf screenmd_OP2.sdf





I am gettign following error message after running this command in command line and 2 output is generated with the names 'screenmd_OP1' and 'screenmd_OP2.sdf'.








Note: This same screenmd command with same input files is working in JChem 3.2.6 Version and getting the result. Problem with JChem5.1.4 Ver.











========================Error========================





java.lang.ArrayIndexOutOfBoundsException: -1


        at chemaxon.calculations.PolarGroups.setAtomicGroups(PolarGroups.java:1193)


        at chemaxon.calculations.PolarGroups.setGroups(PolarGroups.java:1153)


        at chemaxon.calculations.logP.initArrays_new(logP.java:5625)


        at chemaxon.calculations.logP.initlogP_new(logP.java:5667)


        at chemaxon.calculations.logP.calclogPMicro_new(logP.java:5973)


        at chemaxon.calculations.logP.calclogPMicro(logP.java:3800)


        at chemaxon.calculations.logP.calcWeightedlogPMicro(logP.java:3721)


        at chemaxon.calculations.logP.calclogPMicro(logP.java:3793)


        at chemaxon.calculations.logD.calclogDatFixpH(logD.java:450)


        at chemaxon.descriptors.scalars.LDParameters.generate(LDParameters.java:113)


        at chemaxon.descriptors.scalars.LogD.generate(LogD.java:125)


        at chemaxon.descriptors.MDFileReader.readFromMolecule(MDFileReader.java:308)


        at chemaxon.descriptors.MDFileReader.next(MDFileReader.java:229)


        at chemaxon.descriptors.MDSimilarity.compare(MDSimilarity.java:515)


        at chemaxon.descriptors.ScreenMD.compare(ScreenMD.java:340)


        at chemaxon.descriptors.ScreenMD.main(ScreenMD.java:229)


chemaxon.descriptors.MDGeneratorException: Parameters are not set properly.


        at chemaxon.descriptors.scalars.LDParameters.generate(LDParameters.java:117)


        at chemaxon.descriptors.scalars.LogD.generate(LogD.java:125)


        at chemaxon.descriptors.MDFileReader.readFromMolecule(MDFileReader.java:308)


        at chemaxon.descriptors.MDFileReader.next(MDFileReader.java:229)


        at chemaxon.descriptors.MDSimilarity.compare(MDSimilarity.java:515)


        at chemaxon.descriptors.ScreenMD.compare(ScreenMD.java:340)


        at chemaxon.descriptors.ScreenMD.main(ScreenMD.java:229)


Error in MDMolFileReader.next(), reason: Parameters are not set properly.


chemaxon.descriptors.MDReaderException: Error in MDMolFileReader.next(), reason: Parameters are not set properly.


        at chemaxon.descriptors.MDFileReader.readFromMolecule(MDFileReader.java:329)


        at chemaxon.descriptors.MDFileReader.next(MDFileReader.java:229)


        at chemaxon.descriptors.MDSimilarity.compare(MDSimilarity.java:515)


        at chemaxon.descriptors.ScreenMD.compare(ScreenMD.java:340)


        at chemaxon.descriptors.ScreenMD.main(ScreenMD.java:229)





====================End of the Error============================





Sir, Please guide me to find out and resolve this problem.














Thanks in advance,





Remya Francis M.

Dear Remya,





please update your JChem installation to the most recent major release 5.2, that should resolve the problem you encountered.





HTH





Miklos