VDWSA and wateraccessiblesurfacearea fail but logp, logD OK

User 677b9c22ff

25-11-2009 19:17:34

Hi,

the following mols (DrugBank) fail in vdwsa, wateraccessiblesurfacearea. First and last are OK. Marvin 5.2.2

CCO
NC(Cc1cnc[nH+]1)C=O
NC1=Nc2ncc(CCC3=CC=C(C=C3)C(=O)NC(CCc3nnnn3)C(O)=O)c2C(=O)N1
CC1=C(CCC(O)=O)C2=Cc3nc(C=C4N=C(C=C5NC(=CC1=N2)C(C=C)=C5C)C(C=C)=C4C)c(C)c3CCC(O)=O
NC1=Nc2ncc(CCC3=CC=C(C=C3)C(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)c2C(=O)N1
OC1C(COP(O)(O)=O)NC(C1O)c1cnc2C(=O)NC=Nc12
CCO

Topology and logP are ok.

Z:\drugbank>cxcalc logp plattindex wateraccessiblesurfacefail.smi
id      logP    Platt index
1       -0.16   2
2       -1.30   24
3       0.14    100
4       6.56    136
5       -1.82   164
6       -4.56   76
7       -0.16   2
Z:\drugbank>

Now the VDWSA fail.

Z:\drugbank>cxcalc vdwsa  wateraccessiblesurfacefail.smi
id      Van der Waals surface area (3D)
1       102.92
Error at molecule: 2 ID = 2
java.lang.ArrayIndexOutOfBoundsException: 19
java.lang.ArrayIndexOutOfBoundsException: 19
        at chemaxon.calculations.Charge.calcMajorResonanceCharge(Charge.java:931)
        at chemaxon.calculations.MolSurfaceArea.calcCharge(MolSurfaceArea.java:282)
        at chemaxon.calculations.MolSurfaceArea.initCalc(MolSurfaceArea.java:248)
        at chemaxon.calculations.MolSurfaceArea.calcVDWSA(MolSurfaceArea.java:219)
        at chemaxon.marvin.calculations.MSAPlugin.run(MSAPlugin.java:223)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
        at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
        at chemaxon.util.concurrent.processors.SingleThreadedProcessor.getNext(SingleThreadedProcessor.java:67)
        at chemaxon.marvin.Calculator.run(Calculator.java:1134)
        at chemaxon.marvin.Calculator.run(Calculator.java:1096)
        at chemaxon.marvin.Calculator.main(Calculator.java:1660)
2
Exception in thread "main" java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 19
        at chemaxon.marvin.Calculator.outputOnlyPlugin(Calculator.java:1462)
        at chemaxon.marvin.Calculator.consume(Calculator.java:1397)
        at chemaxon.marvin.Calculator.run(Calculator.java:1134)
        at chemaxon.marvin.Calculator.run(Calculator.java:1096)
        at chemaxon.marvin.Calculator.main(Calculator.java:1660)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 19
        at chemaxon.calculations.Charge.calcMajorResonanceCharge(Charge.java:931)
        at chemaxon.calculations.MolSurfaceArea.calcCharge(MolSurfaceArea.java:282)
        at chemaxon.calculations.MolSurfaceArea.initCalc(MolSurfaceArea.java:248)
        at chemaxon.calculations.MolSurfaceArea.calcVDWSA(MolSurfaceArea.java:219)
        at chemaxon.marvin.calculations.MSAPlugin.run(MSAPlugin.java:223)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
        at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
        at chemaxon.util.concurrent.processors.SingleThreadedProcessor.getNext(SingleThreadedProcessor.java:67)
        ... 3 more
Z:\drugbank>

Now thewateraccessiblesurfacearea fail:

Z:\drugbank>cxcalc  wateraccessiblesurfacearea  wateraccessiblesurfacefail.smi
id      ASA     ASA+    ASA-    ASA_H   ASA_P
1       229.68  170.00  59.68   182.57  47.11
Error at molecule: 2 ID = 2
java.lang.ArrayIndexOutOfBoundsException: 19
java.lang.ArrayIndexOutOfBoundsException: 19
        at chemaxon.calculations.Charge.calcMajorResonanceCharge(Charge.java:931)
        at chemaxon.calculations.MolSurfaceArea.calcCharge(MolSurfaceArea.java:282)
        at chemaxon.calculations.MolSurfaceArea.initCalc(MolSurfaceArea.java:248)
        at chemaxon.calculations.MolSurfaceArea.calcSASA(MolSurfaceArea.java:193)
        at chemaxon.marvin.calculations.MSAPlugin.run(MSAPlugin.java:226)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
        at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
        at chemaxon.util.concurrent.processors.SingleThreadedProcessor.getNext(SingleThreadedProcessor.java:67)
        at chemaxon.marvin.Calculator.run(Calculator.java:1134)
        at chemaxon.marvin.Calculator.run(Calculator.java:1096)
        at chemaxon.marvin.Calculator.main(Calculator.java:1660)
2
Exception in thread "main" java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 19
        at chemaxon.marvin.Calculator.outputOnlyPlugin(Calculator.java:1462)
        at chemaxon.marvin.Calculator.consume(Calculator.java:1397)
        at chemaxon.marvin.Calculator.run(Calculator.java:1134)
        at chemaxon.marvin.Calculator.run(Calculator.java:1096)
        at chemaxon.marvin.Calculator.main(Calculator.java:1660)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 19
        at chemaxon.calculations.Charge.calcMajorResonanceCharge(Charge.java:931)
        at chemaxon.calculations.MolSurfaceArea.calcCharge(MolSurfaceArea.java:282)
        at chemaxon.calculations.MolSurfaceArea.initCalc(MolSurfaceArea.java:248)
        at chemaxon.calculations.MolSurfaceArea.calcSASA(MolSurfaceArea.java:193)
        at chemaxon.marvin.calculations.MSAPlugin.run(MSAPlugin.java:226)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
        at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
        at chemaxon.util.concurrent.processors.SingleThreadedProcessor.getNext(SingleThreadedProcessor.java:67)
        ... 3 more
Z:\drugbank>

Cheers

Tobias