cxcalc for HBD and HBA

dear support,

To calculate HBD and HBA of structure with cxcalc , should I use the plugin donor or donorcount and acceptor or acceptor count

I try with acceptor and donor and it gives me HBD and HBA at several pH. I would lke only at pH=7.4.

Hi,

You can specify the pH lower an upper limits with "-l" or "--lower", and "-u" or "--upper" command line options.

Example:

$ cxcalc acceptor -l 7.4 -u 7.4 "CCCCN"
id acc acceptorcount accsitecount pH=7,40
1 0;0;0;0;1 1 1 0,00

moha@northtree ~
$ cxcalc donor -l 7.4 -u 7.4 "CCCCN"
id don donorcount donsitecount pH=7,40
1 0;0;0;0;2 1 2 3,00

There is also a "-H" (or "--pH") command line option for specifying one pH only, but it seems to be buggy. We will fix it.

Zsolt

Yes I remark that the option -H gives a bug

but which is the difference between donor and donorcount?

To have HBD at ph=7.4 could I use ?:

cxcalc donorcount -H 7.4 test.sdf ?

"donor" includes four calculations, "don" (donor multiplicity of atoms), "donorcount", "donsitecount", and "msdon". The output of the "donor" calculation is a  table containing the following columns: "id", "don", "donorcount", "donsitecount" and pH-s (pH=0,00 pH=1,00 ...). In Marvin 5.3 we will change this, it will contain only "donorcount" and "donsitecount",  calculations.

"donorcount" is a "single" calculation. It calculates how many hydrogen bond donor atoms are in the molecule.

Zsolt

cxcalc donorcount -H 7.4 test.sdf ?

Yes, it's correct.

Example:

$ cxcalc donorcount -H 14 "CC(O)=O"
id donorcount
1 0

$ cxcalc donorcount -H 1 "CC(O)=O"
id donorcount
1 1

The bug I mentioned before affect only how "msdon" caclulation displays the table.

Zsolt