Re: freeware for RNA modeling on Linux (fwd)

From: James W. Caldwell <>
Date: Tue 17 Dec 2002 11:09:37 -0800 (PST)

Please note that the license agreement prohibits you from
redistributing any code which you obtained in the Amber

Also, there is a clause that states that any improvments/alterations
must be communicated back to the amber distributors. Technically,
this applies to any changes regardless. However, we do not enforce
that clause for changes you make locally that stay local.


On Tue, 17 Dec 2002, Joerg-Gerald Siebers wrote:

>Dear all:
>I am writing on a paper regarding Non-Boltzmann MC sampling of
>interactions. I have used parts of the AMBER4.1 source code reagrding
>energy calculation. I modified (simplified) it for my needs. I did not
>about any kind of permission. For this, I apologies. Among scientiest I
>thought this is OK.
>Writing up the paper I feel I should do something about this matter.
>I make a tar-ball of all stuff I used for the program and send it to
>someone you appoint - or to several people.
>As long as "my" stuff is not published I would assume that stuff
>(if it's worth anything). Afterwards you could include it in your
>of programs if you want to or just trash it.
>If you have a better suggestion I am all ears.
>Best wishes
>Joerg-Gerald Siebers
>"David A. Case" wrote:
>> On Tue, Dec 03, 2002, wrote:
>> >
>> > Does anyone know a good freeware (or cheap software --academic use) for RNA
>> > modeling. I have an RNA stem and I would like to attach a loop to it.
>> You could see if Nucleic Acid Builder (NAB) would meet your needs. Info
>> at the web site below.
>> ..dac
>> --
>> ==================================================================
>> David A. Case | e-mail:
>> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>> The Scripps Research Institute | phone: +1-858-784-9768
>> 10550 N. Torrey Pines Rd. | home page:
>> La Jolla CA 92037 USA |
>> ==================================================================

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
Mail Stop 0446                            (email)
513 Parnassus Avenue                      
University of California                  
San Francisco, CA 94143-0446               
Received on Tue Dec 17 2002 - 11:09:37 PST
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