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hcounts

Andrew Norgan
hcounts Hi,

I am doing a conversion of a multi-mol2 file to the individual mol2 files with openbabel (openbabel –imol2 $.mol2 -omol2 $.mol2 –m) and in the course of the conversion I receive the warning message “no hcounts”.

The multi-mol2 file was prepared with MOE, and should have all hydrogens explicitly added by MOE before minimization.

Can anyone tell me what “no hcounts” means, and if there is likely a problem with the output files?

Thank you,

Andrew Norgan
Mayo Clinic

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Re: hcounts

Geoffrey Hutchison
I am doing a conversion of a multi-mol2 file to the individual mol2 files with openbabel (openbabel –imol2 $.mol2 -omol2 $.mol2 –m) and in the course of the conversion I receive the warning message “no hcounts”.

Sorry, I just saw this message myself. It's a warning when Open Babel is perceiving amino acid and nucleic acid residues in PDB or mol2 files. It's of no consequence, and I'll remove the message, which I inadvertently left in.

Your output is just fine. But for future reference, you can also use the "copy" format for this -- no transformation of any kind will happen, but babel will filter, join and merge files as requested.

Thanks and best regards,
-Geoff

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