Apparent logP Discrepancy

To whom it concerns,





I have marvinbeans-4_1_13-linux installed on 2 separate computers. My experiments create SMILES structures whose properties are calculated using the plugins(please see the attached java file My_MolCalculator_Two.java). When I run cxcalc to calculate the logP of the SMILES molecule I get the same value on both machines. But, when I run the java code I get different values for logP.





For example, the SMILES molecule is c12nncc1ncncc2N(CC) and this is saved in the file Individual.sdf.





java chemaxon.marvin.calculations.My_MolCalculator_Two > Test.txt





gives the following results:





MACHINE A : 2, 5, 1, -1.0122, 175.19076 , CCNc1cncnc2cnnc12





MACHINE B : 2, 5, 1, 0.298699, 175.19076, CCNc1cncnc2cnnc12








I would be very grateful if anybody could explain the discrepancy in the logP values.





Thanks,


Miriam O'Riordan

Hi,





When I run your code I get the values of "MACHINE A".


cxcalc also gives me -1.0122 for logP.

Code:

cxcalc logP -p 4 "c12nncc1ncncc2N(CC)" id      logP 1       -1.0122

This is the value you get?





Please run the following commands on both of your machines, and post the results:

Code:

java -version

Code:

uname -a

Regards,


Zsolt

Dear Zsolt,





Thanks for your help. Please find below the output from Machine A and Machine B in response to java -version and uname -a.





java -version Machine A :


java version "1.6.0_03"


Java (TM) SE Runtime Environment (build 1.6.0_03-b05)


Java HotSpot(TM) Client VM (build 1.6.0_03-b05, mixed mode, sharing)





uname -a Machine A:


Linux Machine1 2.6.18-5-686 #1 SMP Fri Jun 1 00:47:00 UTC 2007 i686 GNU/Linux








java -version Machine B :


java version "1.6.0_03"


Java (TM) SE Runtime Environment (build 1.6.0_03-b05)


Java HotSpot(TM) Client VM (build 1.6.0_03-b05, mixed mode, sharing)





uname -a Machine B:


Linux Machine2 2.6.10-2.3.legacy_FC2 #1 Sat Feb 18 21:55:30 EST 2006 i686 i686 i386 GNU/Linux








Regards,


Miriam

Hi,





It seems the problem is not related to the Java implementation you use.





The logP value you get on Machine B (0.298699) is equal to the logP calculated with MarvinBeans 4.0.x version. I think your CLASSPATH environmental variable on Machine B points to an earlier MarvinBeans version. You can check this with

Code:

echo $CLASSPATH

command. After you set the CLASSPATH variable correctly on Machine B you will get the same values on both machines.





Regards,


Zsolt