From: Ban Arn (ban.arn_at_gmail.com)
Date: Wed Nov 21 2012 - 08:19:48 CST

Hi Jan

Thanks for suggestion and its easy to run.

I ran the program with 10 pdb structures and as a output I got 41 possible
tunnels.

Its bit hard to guess the possible tunnels for the respective structures.

I have tunnels_xx.pdb.obj 10 files in the tunnel folder
(results->data->tunnel)

I would like to know whether these files have respective tunnel for each
structure and how to visualize these files.

Kindly advice.

Many Thanks
Balaji

On Wed, Nov 21, 2012 at 11:52 AM, Jan Brezovsky <briza_at_chemi.muni.cz> wrote:

> Hello all,
>
> just to add one more alternative program (Caver 3.0) which was designed
> for analysis of MD trajectories.
> http://caver.cz/
>
> Have a nice day,
> Jan
>
> --
> ***************************************
> 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
> ***************************************
>
>
> On 11/21/2012 11:19 AM, Ban Arn 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>wrote:
>
>> this program might work for your needs
>> http://mole.upol.cz/
>>
>>
>> ________________________________________
>> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
>> John Stone [johns_at_ks.uiuc.edu]
>> Sent: Tuesday, November 20, 2012 8:54 AM
>> To: Ban Arn
>> Cc: 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
>>
>> 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/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>>
>
>
>