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These instructions are fairly outdated.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
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Received on Thu Mar 20 2014 - 12:30:02 PDT
