i have the pharmocophore part of them protein and some residues around that. i need to find out the H- bonding around that pharmacophore, what are the criteria you are following in PMAPPER to find out the H bond donnor/acceptor???
can u specify any algorithm to find out these things around a pharamcophore??
Pharmacophore definitions are not wired in PMapper, instead, they are provided in external configuration files. We give away two such configurations "we no guarantee", that is, these serve only as examples. They are located in the examples/config folder under the JChem installation directory, one is called pharma_frag.xml the other is pharma_calc.xml. You can take either of these files to build your own pharmacophore definitions on. Both configurations introduce six pharmacophore type: donor, acceptor, plus, minus, aromatic and hydrophobic.
The first shows a purely fragment based approach, while the second relies on our calculator plugins. In this latter one, for instance, donors and acceptors are predicted by the HBDA calculator plugin. If you are interested in learning some details on the underlying algorithm, the Structure based prediction forum area at http://www.chemaxon.com/forum/forum6.html
might be helpful.
For further details on the pharmacophore definitions follow this link: http://www.chemaxon.com/jchem/doc/user/PMapper.html#config
My closing remark is that calculator plugins were developed to handle small molecules thus HBDA may fail on a large protein. In this case the fragment based approach must be followed, that rather easy to implement for amino acids, rules are simple a well-defined. However, HBDA can handle intramolecular bonds which is an advantage.