Molecular volume and Log D

Hi. Which descriptor in Geometry plugin is for molecular volume. I saw there was volume within Geometry, is that one I should use?

Another question is that, for the LogD, I only want calculator to get LogD under 7.4, and output into a SDF file. But after i input "cxcalc  -S -o xxx.sdf  Log D -H 7.4 xxx.sdf" in the command line, in the result SDF file, there is 7.4 before each Log D value. How could I remove the 7.4 and just have Log D value under the LogD tag in the SDF file.

 

Thanks. 

geneman wrote:

Hi. Which descriptor in Geometry plugin is for molecular volume. I saw there was volume within Geometry, is that one I should use?

 
If you want to calculate van der Waals volume then yes, you shoud use Geometry plugin.

geneman wrote:

Another question is that, for the LogD, I only want calculator to get LogD under 7.4, and output into a SDF file. But after i input "cxcalc  -S -o xxx.sdf  Log D -H 7.4 xxx.sdf" in the command line, in the result SDF file, there is 7.4 before each Log D value. How could I remove the 7.4 and just have Log D value under the LogD tag in the SDF file.

This will do:

cxcalc -S -o out.sdf -t "logD at pH 7.4" logp -H 7.4 in.sdf

in.sdf is the input, out.sdf is the output.

Zsolt