Re: [AMBER] help in getting 3D isodensity surface

From: Jason Swails <>
Date: Wed, 11 Mar 2015 10:15:52 -0400

On Wed, 2015-03-11 at 13:39 +0530, Robin Jain wrote:
> Dear all users,
> I have a organic solute (non-spherical) in 64 solvent molecules and I want
> to plot a 3D isodensity surface of solvent around my solute molecule. For
> this i use grid command using cpptraj (version 13.0) as follows-
> *trajin prod.mdcrd*
> *center :1*
> *autoimage*
> *rms mass out rms.dat :1*
> *grid test.xplor 20 2 20 2 20 2 :2-65*
> *go*
> after running i got the file test.xplor and i viewed it with vmd but i got
> a bad plot, which is not showing solvent and solute individual.
> So please help me that what should i do for this.

How did you "view it with VMD"? What do you mean by "bad plot"?

Typically what you (or at least I) do when you want to visualize
volumetric data like solvent distributions, you first load the prmtop
and coordinate file into VMD so you can see the molecule. Then, you
load the .xplor or .dx grid on top of that molecule as volumetric data.
In the representations section of VMD, you can control the isovalue of
the volumetric data, which will adjust the value of the density at each
of the points on the surface.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 11 2015 - 07:30:02 PDT
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