---------- Forwarded message ----------
From: <wmsmith.uci.edu>
Date: Wed, May 23, 2012 at 10:48 AM
Subject: Re: Fwd: [AMBER] Amber tools 12 and esp visualization in VMD and
PyMol
To: "Ray Luo, Ph.D." <ray.luo.uci.edu>
Cc: Wesley Smith <wmsmith.uci.edu>, Sudarshan Debnath <
sudarshandebnath.ku.rediffmail.com>, Ray Luo <ray.luo.uci.edu>
Dr. Sudarshan Debnath,
I loaded the pbsa_phi.dx along with the molecule's .rst and .top files
in VMD and loaded the radii from the .top file using the tkconsole. I
displayed the potential as a color map for the VDW surface.
Everything seems to be working normally.
I reduced the color scale by a factor of 10 to compensate for point charge
singularity since the contrast looked low. I have attached a screenshot
for you.
Color scale was set to -20177.00,13444.00 under the trajectory tab.
This was reduced from -201778.73,134441.28 which had low contrast.
See AmberTools12 manual sections 8.4.2 - 8.4.12 for details on loading and
displaying the pbsa_phi.dx file in VMD.
-Wesley Botello-Smith
> Here is the file again in msdoc version ...
>
> Ray
>
> ---------- Forwarded message ----------
> From: Sudarshan Debnath <sudarshandebnath.ku.rediffmail.com>
> Date: Wed, May 23, 2012 at 6:10 AM
> Subject: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol
> To: amber.ambermd.org
>
>
> Dear Wes,
> Here I attached the content pbsa.dx file in MS-word. Please
> extract
> it if possible.
>
> best regards,
> Sud.
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>
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Received on Wed May 23 2012 - 11:30:04 PDT
