error in outputing lowestenergyconformer

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.

Hi,

Try the following syntax:

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

Zsolt

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

in.smiles is the input file (attached).

Zsolt

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

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

thanks

Hi

What a well written great piece of information.