Re: [AMBER] Molecule volume in cpptraj?

From: Daniel Roe <>
Date: Fri, 26 Feb 2021 09:44:45 -0500

Hi Gustavo,

There's an approximate molecular volume calculation that is done via
the 'volmap' command. It will create a dataset named <name>[totalvol]
and output the value at the end of the run like so:

<#> occupied voxels, voxel volume= <voxelvol> Ang^3, total volume
<totalvol> Ang^3

All this is doing of course is summing over occupied voxels and
multiplying by the voxel volume. If your spacing is small enough this
should be a reasonable estimate of the molecular volume (as defined by
whatever radii set you're using in 'volmap'). I haven't really tested
the values obtained this way against better volume calculations so use
at your own risk. Molecular volume calculation is one of those things
I've always wanted to do better but never seem to find the time to


On Thu, Feb 25, 2021 at 1:56 PM Gustavo Seabra <> wrote:
> Hi all,
> Does cpptraj offer any way to calculate an approximate molecular volume or
> surface area for a specified mask (ligand)?
> Thanks,
> --
> Gustavo Seabra.
> _______________________________________________
> AMBER mailing list

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Received on Fri Feb 26 2021 - 07:00:02 PST
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