Re: [AMBER] Molecule volume in cpptraj?

--
Gustavo Seabra.
On Fri, Feb 26, 2021 at 9:45 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> do...
>
> -Dan
>
> On Thu, Feb 25, 2021 at 1:56 PM Gustavo Seabra <gustavo.seabra.gmail.com>
> 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.
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