Re: [AMBER] tinker to amber format

From: Jason Swails <>
Date: Thu, 10 Jul 2014 03:11:50 -0700

On Wed, Jul 9, 2014 at 9:44 PM, Jorgen Simonsen <> 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 M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jul 10 2014 - 03:30:02 PDT
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