VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 29 2008 - 13:11:37 CST

Hi,
  At present, the only way to do this would be to temporarily build a
new structure containing both the inhibitors and the protein of interest,
and run the SASA calculation on the merged structure. Let us know if you
need help doing that. There's a new VMD plugin that automates merging
multiple structures, if you would like to try it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Feb 24, 2008 at 06:42:44PM -0800, Dong Xu wrote:
> 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
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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