error in outputing lowestenergyconformer

User 5a88369158

10-03-2010 15:10:29

I am trying to calculate the lowest energy conformation for a series of compounds and i am using the command line to do this.


I have a text file with compound name followed by the smiles string (attached).


I can calculate the lowest energy conformation for just one compound and the result is shown in the command line but I cannot output this information to an output file and I cannot calculate ithe lowest energy conformation for a series of compounds.


I am using the following command


cxcalc test.txt lowestenergyconformer -f outputtest.sdf


When I try to input a text file with multiple compounds, i get an error saying


C:\Program Files\ChemAxon\JChem\bin>cxcalc conformers.txt lowestenergyconformer
Exception in thread "main" chemaxon.formats.MolFormatException: conformers.txt:
Cannot recognize format (?)
        at chemaxon.formats.recognizer.RecognitionSubsystem.getFormat(Recognitio
nSubsystem.java:185)
        at chemaxon.formats.MolInputStream.initTextFormat(MolInputStream.java:23
4)
        at chemaxon.formats.MolInputStream.init(MolInputStream.java:134)
        at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:116)
        at chemaxon.formats.MolImporter.init(MolImporter.java:469)
        at chemaxon.formats.MolImporter.init(MolImporter.java:425)
        at chemaxon.formats.MolImporter.<init>(MolImporter.java:258)
        at chemaxon.formats.MolImporter.<init>(MolImporter.java:227)
        at chemaxon.marvin.Calculator.run(Calculator.java:1026)
        at chemaxon.marvin.Calculator.main(Calculator.java:1506)
C:\Program Files\ChemAxon\JChem\bin>


 


When I try a single compound, I get an output in the command line but I want to save the energy result to an output file, i get an error.

ChemAxon e08c317633

10-03-2010 15:36:38

Hi,


Try the following syntax:


cxcalc -o out.sdf lowestenergyconformer -f sdf in.smiles


Zsolt

User 5a88369158

10-03-2010 16:01:41

i can get an output sdf file that shows the lowest energy conformer and the energy for that conformer but the 'in.smiles' does not work


 


also, how can i do this for multiple compounds


 


the above command line code worked for a text file with just one compound but i get an error when i have multiple compounds as shown in the attached file


thanks

ChemAxon e08c317633

10-03-2010 16:21:26

in.smiles is the input file (attached).


Zsolt

User 5a88369158

11-03-2010 00:28:12

im sorry i dont understand your reply


i want to calculate the lowest energy conformer and the energy associated with it for a series of compounds


i thought i could make a text file with smiles strings for all the compounds and output the energy to a text file as well, if this is not possible, i would like to input a text file with smiles strings and get an 3D output


 


thank you

ChemAxon e08c317633

12-03-2010 10:46:33

Sorry, I attached the wrong file. Command


cxcalc -o out.sdf lowestenergyconformer -f sdf in.smiles


will do exactly what you need. "in.smiles" is the input file (it contains 10 SMILES strings), "out.sdf" is the output file in SDF format, which will contain the  generated 3D structures (both attached). Energies are stored in SDF fields (see the attached image).


I hope this helps.


Zsolt

User 5a88369158

12-03-2010 14:16:47

thanks

10-05-2010 14:36:21

Hi


What a well written great piece of information.