On Wed, Jul 9, 2014 at 9:44 PM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
> Hi all,
>
> I am trying to run some amoeba computations using amber - I have been able
> to generate the amoeba format and I am not able to find the executable to
> convert it into something readable for amber12 ( this is the version I am
> using) .
>
> I can see that the following file is located here but has not been compile
>
> # file is located here but it is not compiled
> /src/pmemd.amoeba/build_amoeba/tinker_to_amber.f90
>
> do I have to compile it separately and how?
>
If you download AmberTools 14, the tinker_to_amber program is compiled
automatically as part of AmberTools 14 (and there is a section in the Amber
14 manual about using Tinker and tinker_to_amber to create an Amoeba
topology file for use with pmemd.amoeba).
I can't _really_ remember how these programs were built with Amber 12, but
I think you could just run "make" in the src/pmemd.amoeba/build_amoeba
directory. There are a number of improvements included with AmberTools 14,
though (like support for "new" Tinker-style files (both the XYZ and ANALOUT
files have changed recently and require AmberTools 14 to properly read).
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 10 2014 - 03:30:02 PDT
