Hi Catherine,
Unfortunately the answer in No. The patch for AMBER 8 cannot be used in
AMBER 10 unless you adapt the code yourself ...
If you don't have or you don't want to use AMBER 8 anymore, RAMD will
also be implemented in the new release of NAMD 2.7 ...
Since the RAMD module is based on the Tcl forces implementation of NAMD,
you can already use it with namd 2.6 ....
You can download the scripts using the link below. You can use these
scripts in NAMD 2.6 or 2.7bX if compiled with tcl support (tcl version
8.3 or 8.4)
I hope the documentation explains well how to run the module...
http://projects.villa-bosch.de/mcmsoft/namd/
If you decide to run RAMD in NAMD with AMBER parameters and you have not
run AMBER simulations in NAMD before, please read *VERY* carefully the
NAMD manual about compatibility with AMBER force fields
Best wishes
Vlad
On 08/09/2010 02:51 PM, Jason Swails wrote:
> Hello,
>
> You have to install and run amber8 to the best of my knowledge. Patches
> written for one version of amber will not work on another, and the RAMD
> functionality has not been preserved.
>
> Hope this helps,
> Jason
>
> On Mon, Aug 9, 2010 at 1:58 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
>
>> Dear All,
>>
>>
>>
>> I found the patch to calculate random acceleration molecular dynamics in
>> amber8 in the AMBER's home website.
>>
>>
>>
>> Is it a built-in protocol in AMBER10 or do I have to install the patch same
>> as amber8 to get it works in AMBER10?
>>
>>
>>
>> Best regards,
>>
>>
>>
>> Catherine
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Mon Aug 09 2010 - 07:00:03 PDT
