On Jul 3, 2014, at 11:35 AM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
> Hi all,
>
> I am trying to built some structure to run using the amoeba force field in
> amber. The problem is that I am not even able to generate these parameters
> or load the library.
>
> I start the ambertools and try to source the leaprc.amoeba but the program
> just keeps hanging - 10 minutes and nothing happens. I start the program
> using the following command:
>
> amber12/bin/tleap -s
>
> -I: Adding amber12/dat/leap/prep to search path.
> -I: Adding amber12/dat/leap/lib to search path.
> -I: Adding amber12/dat/leap/parm to search path.
> -I: Adding amber12/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
>
> Welcome to LEaP!
>> source amber12/dat/leap/cmd/leaprc.amoeba
> ----- Source: amber12/dat/leap/cmd/leaprc.amoeba
> ----- Source of amber12/dat/leap/cmd/leaprc.amoeba done
> can't parse echo
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
> Loading library: amber12/dat/leap/lib/amoeba_amino.off
>
>
> I am able to load other libraries and it works fine - am I missing
> something or does it take more than 10 minutes to to load the library.
tleap cannot build a topology file with the Amoeba potential. The sleap program used to be able to (I think), but that project was abandoned some time ago.
If you want to run an Amoeba simulation with Amber, you'll need both Tinker and AmberTools 14. Chapter 16 in the Amber 14 manual is dedicated to showing you how to run the Amoeba potential in Amber. It provides instructions for both the Tinker and Amber side of things (including installing Tinker).
As an aside, "antechamber" will not work with Amoeba -- you'll need to use the Tinker tools to parametrize custom molecules, and that is not covered in the Amber manual.
HTH,
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 03 2014 - 13:00:03 PDT
