Bcut Descriptors: (char, pol, H-bon ,Disp)

User 740a9d8894

16-03-2007 14:51:15


I need to compute the bcut descriptor for the compounds represented by smiles:

Compound 1:


SMILES: [Sb](=O)(O)(O)c1cccc(c1)C=CC(=O)O

Molecular Weight 319.0

Molecular Formula C9H9O5Sb


Compound 2:



Molecular Weight 267.0

Molecular Formula C10H13N5O4


I would like BCUT values (eigenvalues) using this following combination of

(charge-BCUTs, polarizability-BCUTs, H-bond-BCUTS and dispersion Bcuts ).

I mean the atomic properties on the diagonals of four ‘classes’ of Burden matrices: atomiccharges, polarizabilities, H-bond donor- and acceptor-abilities corresponding to the electrostatic, dispersion and H-bonding modes of bimolecular interaction.

Thank you very any help.


ChemAxon efa1591b5a

19-03-2007 09:17:15


these BCUT values can be computed by the generatemd program, you may wish to look at the documentation at http://www.chemaxon.com/jchem/doc/user/GenerateMD.html and specifically http://www.chemaxon.com/jchem/doc/user/GenerateMD.html#BCUT.

Examples about the usage of the program are also given: http://www.chemaxon.com/jchem/doc/user/GenerateMD.html#examples.

Dispersion BCUTs are not yet available, but all other you mention in your post are computed.

I hope this helps. Please get back to the forum in case you need further assistance.



User 740a9d8894

19-03-2007 17:40:27


thanks for the help.

It works using

generatemd c molecules/file.smiles -k BCUT -c config/bcut-charge.xml -D -g -v -o CHarge.txt

generatemd c molecules/file.smiles -k BCUT -c config/bcut-polarizability.xml -D -g -v -o Polarization.txt

generatemd c molecules/file.smiles -k BCUT -c config/bcut-hbond.xml -D -g -v -o Hbond.txt

But when a tested over a file with more than 2000 compounds, the software is not enabling Bcut for all.

Any help to generate Bcut for a file with more than 40,000 compounds ?



ChemAxon efa1591b5a

20-03-2007 08:51:09

That must be a license problem. Did you receive and install your license keys at all?