Thanks, Jason! I appreciate your help.
Geoffrey
On Thu, Mar 20, 2014 at 3:26 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, 2014-03-20 at 14:50 -0400, Geoffrey Gray wrote:
> > I am trying to use the AMOEBA force field with the Amber package, but
> > cannot determine how to build the necessary topology/coordinate files.
> The
> > documentation says that I need to use sleap, which is not present after I
> > compile AmberTools 13, and when I try to use tleap, I receive an error.
> How
> > can I prepare these files? Thank you in advance for your help.
>
> These instructions are fairly outdated. You need to use a set of
> programs included with pmemd.amoeba (tinker_to_amber) in order to
> generate the topology file. You also need the Tinker program suite
> installed (you specifically need to use the "analyze" program) in order
> to generate the intermediate files that tinker_to_amber needs.
>
> The process is not very well-documented, but there is a README file in
> $AMBERHOME/src/pmemd.amoeba/build_amoeba/examples/JAC that explains the
> process. You need to build tinker_to_amber first, though. The command
> below should do it:
>
> cd $AMBERHOME/src/pmemd.amoeba/build_amoeba
> make all
>
> This will create tinker_to_amber inside that directory.
>
> Hopefully the instructions will be clearer in the upcoming Amber
> release.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 20 2014 - 15:00:02 PDT
