VMD-L Mailing List

From: Jan Brezovsky (briza_at_chemi.muni.cz)
Date: Wed Nov 21 2012 - 13:39:17 CST

Hi Grace,

just to add some recent informations to yours.

The link you provided points to outdated Mole 1.2 (stand alone), which
suffers from significant imprecisons in geometry of calculated tunnels
(up to 1 A) and lacks robust user friendly clustering of calculated tunnels.
Mole2 (currently available only on-line, no support for MD) and Caver3
(stand alone) both provide proper geometry of tunnels. Caver3.0 is
specificially tuned for analysis of MD (culstering, heat maps, VMD
visulaization,...).

Have a nice day,
Jan

Dne 21. 11. 2012 18:32, Grace Brannigan napsal(a):
> Hi Balaji,
>
> Just to clarify for the list, as shown at the bottom of
>
> http://mole.chemi.muni.cz/web/docs/doc_standalone.php
>
> it is pretty straightforward to use mole to analyze trajectories. I
> believe you have to put your file in AMBER format, however.
>
> cheers,
> Grace
>
>
> On Wed, Nov 21, 2012 at 5:19 AM, Ban Arn <ban.arn_at_gmail.com
> <mailto:ban.arn_at_gmail.com>> wrote:
>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> Phone:
> 217-244-3349 <tel:217-244-3349>
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> <tel:217-244-6078>
>
>
>
>
>
> --
> Grace Brannigan, Ph.D.
> Assistant Professor
> Center for Computational and Integrative Biology (CCIB) &
> Department of Physics
> Rutgers University, Camden, NJ
> (856)225-6780
> www.branniganlab.org <http://www.branniganlab.org>
> 

-- 
***************************************
  Jan Brezovsky, Ph.D.
  Loschmidt Laboratories
  Department of Experimental Biology
  Faculty of Science, Masaryk University
  Kamenice 5/A13-2.19
  625 00 Brno
  Czech Republic
***************************************
  tel. +420-54949-2616
  briza_at_chemi.muni.cz
  http://loschmidt.chemi.muni.cz/peg
***************************************