VMD-L Mailing List

From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Wed Nov 21 2012 - 11:32:27 CST

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> 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
>>
>
> 

-- 
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