Hi,
First it might be useful for you to become familiar with some of the
tools involved in setting up Amber simulations. In particular tutorial
B1 (
http://ambermd.org/tutorials/basic/tutorial1/) will walk you
through building and simulating a molecule using several programs
available in Amber/AmberTools. Also, the AmberTools 13 manual
(particularly the LEaP section; manual can be found here:
http://ambermd.org/doc12/) contains a lot of useful information on
building parameter and coordinate files for simulations with Amber.
With regards to the link you provided, the CPDI.frcmod file you can
load into tleap with the 'loadamberparams' command, and the mol2 files
can be loaded with the 'loadmol2' command (although again I think it's
worthwhile to go through the tutorial just to get an idea of how LEaP
is actually using the information).
Hope this helps,
-Dan
On Tue, Jun 25, 2013 at 10:18 PM, Parker de Waal
<Parker.deWaal09.kzoo.edu> wrote:
> Hi AMBER Users!
>
> I'm interested in running MD simulations on various heme containing P450
> enzymes and would like to use a set of recently published parameters found
> here -> https://gist.github.com/ParkerdeWaal/d9d838ab0200b4f29450 (source
> found in link as well).
>
> However this is my first experience with AMBER, coming from GROMACS, and do
> not know yet how to use custom parameters such as this yet.
>
> Any assistance would be greatly appreciated!
>
> Best,
> Parker
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jun 25 2013 - 22:00:03 PDT
