AMBER Archive (2009)

Subject: Re: [AMBER] How to calculate cavity volume from MD structures?

From: Jason A. Ford-Green (jgreen_at_ccmsi.us)
Date: Wed Jan 21 2009 - 09:39:57 CST

Ben,

 In the VMD (I use version 1.8.6) code you can go to the VMD "Main" window and select Extensions then analysis. From analysis go to the bottom of the drop down tab and select Volmap tool. This extension or plugin gives you some parameter choices for the calculation. It looks as if you can select distance, volume, and occupancy as Volmap types. I have personal experience with the Caver 2.0 plugin in the visualization program PyMol. It works well for qualitative assessment and prediction of cavities with respect to a set of user-defined active site residues. Hope this helps, and good luck with your project. Maybe someone else can chime in on a more refined software, but initially these are pretty good.

Cheers,

Jason Ford-Green

---------- Original Message ----------------------------------
From: ben rodriguez <bramber_at_live.com>
Reply-To: AMBER Mailing List <amber_at_ambermd.org>
Date: Tue, 20 Jan 2009 15:21:43 -0700

>
>Hi,
>
>I am trying to find the volume of a cavity from a series of MD snapshots. My question: is there a tool included in Amber, or otherwise (commercial?) that will perform a volume calculation on a series of structures. I am trying to find the volume of the distal heme pocket of myoglobin mutants.
>
>Thanks,
>
>Ben Rodriguez
>
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