Re: [AMBER] tinker to amber format

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 10 Jul 2014 03:11:50 -0700

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?
>

‚ÄčIf 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
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Received on Thu Jul 10 2014 - 03:30:02 PDT
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