[AMBER] help in getting 3D isodensity surface

From: Robin Jain <robinjain.chem.gmail.com>
Date: Wed, 11 Mar 2015 13:39:48 +0530

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*


*rms mass out rms.dat :1*

*grid test.xplor 20 2 20 2 20 2 :2-65*

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.

Thanking You.
Robin Jain
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Received on Wed Mar 11 2015 - 01:30:06 PDT
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