VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Nov 21 2012 - 10:20:21 CST

The caver and mole tools are nearly identical in function (though the respective authors may highlight the differences). The code base is java vs .NET
They both use pdb files as inputs and both run on linux (.NET with mono/wine).

I should have stated that I have been working with the server version of mole on a linux box for analyzing a VERY large set of md simulations.

The hard part is putting all the data together in an understandable/quantifiable way. Which isn't really the programer's job.

Brian

________________________________
From: Ban Arn [ban.arn_at_gmail.com]
Sent: Wednesday, November 21, 2012 2:19 AM
To: Bennion, Brian
Cc: John Stone; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Hole program for vmd hole tcl script

Hi all

Thanks for the reply.

John, I contacted Oliver through the above mail id, but didnt get any reply from him.

And Brain thanks for the alternative program, however the program works for single pdb structure.

I'm want to calculate the same for simulation trajectories.

Kindly advice.

Many Thanks
Balaji

On Tue, Nov 20, 2012 at 6:14 PM, Bennion, Brian <Bennion1_at_llnl.gov<mailto:Bennion1_at_llnl.gov>> wrote:
this program might work for your needs
http://mole.upol.cz/

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] on behalf of John Stone [johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>]
Sent: Tuesday, November 20, 2012 8:54 AM
To: Ban Arn
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Hole program for vmd hole tcl script

Hi,
  I recommend contacting Olver Smart, the author of HOLE
and ask him where to download it. The link on his page doesn't
work currently:
  http://www.globalphasing.com/people/osmart/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>

On Tue, Nov 20, 2012 at 02:59:20PM +0000, Ban Arn wrote:
> Dear VMD users
> I am looking for download link for HOLE program.
> I came across the following thread in vmd
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3461.html)
> Can anyone help me in this regard.
> Sorry for posting other threads that are not related to vmd.
> Many Thanks
> Balaji 

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