VMD-L Mailing List

From: Manali Mehendale (manali_at_adrik.bchs.uh.edu)
Date: Thu Feb 07 2008 - 14:45:37 CST

Hi,

I want to calculate the sasa of multiple inhibitors that bind to a protein
at the same place.
So essentially i want to do the following:

measure sasa 1.4 $allsel -restrict $sel

where $allsel would be my protein pocket + inhibitor and $sel just the
inhibitor.

According to my understanding $sel should be a subset of $allsel.
However my protein is a pdb and inhibitors are separate mol2 files.

How can i accomplish my goal ?

One way i thought of was to write a temp pdb file of the protein+inhibitor
do the calculation and delete the temp file.

Is this the only way ? Am i missing some other way to get this done ?

Thanks,
Manali