VMD-L Mailing List

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Sun Feb 24 2008 - 20:42:44 CST

Hi,

I have similar questions regarding the usage of "measure sasa". Hope someone
can enlighten me.

-DX

On Thu, Feb 7, 2008 at 12:45 PM, Manali Mehendale <manali_at_adrik.bchs.uh.edu>
wrote:

> 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
>
>