From: Ebert Maximilian (
Date: Wed Sep 23 2015 - 15:09:55 CDT

Hi John,

for instance in the publication: Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels

Figure 1c) shows on the y axis the free energy and the x axis is the reaction coordinate. the reaction coordinate is along the tunnels identified in ILS. How could I generate such a figure from my DX file. So how can I get the delta G of every point along each channel/path found in ILS.

Thanks for your help,


> On Sep 23, 2015, at 3:33 PM, Ebert Maximilian <> wrote:
> ________________________________________
> From: John Stone
> Sent: Wednesday, September 23, 2015 3:33:09 PM (UTC-05:00) Eastern Time (US & Canada)
> To: Ebert Maximilian
> Cc: <>
> Subject: Re: vmd-l: Implicit Ligand Sampling: How to get energy along a reaction coordinate?
> Max,
> I'm not entirely sure what it is you want out of the plot, so maybe you
> can be more specific about what your input is and how you want it displayed.
> Regarding the 'vol0' and 'interpvol0' atoms selection keywords:
> These select atoms according to the value of voxels in volumetric data
> set 0. The 'vol0' selection samples only the "nearest" voxel to each atom
> as the selection criteria. The "interpvol0" keyword does trilinear
> interpolation among the 8 nearest voxels to each atom, and uses the
> interpolated value.
> Cheers,
> John Stone
> On Wed, Sep 23, 2015 at 07:11:06PM +0000, Ebert Maximilian wrote:
>> Hi there,
>> I did implicit ligand sampling on my simulation and identified some channels. Now I would like to write plot the landscape along these tunnels from the bulk to the center of the protein. How could I do that? Also how can I get the energy value from the PMF in specific coordinate? I saw vol0 and interpvol0. What are the differences?
>> Thank you very much,
>> Max
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