AMBER Archive (2008)

Subject: Re: AMBER: Adding New Parameters and Modifying Existing Parameters

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Tue Mar 11 2008 - 11:46:33 CDT

Hi

> I used Amber 9 version on Linux (Fedora Core 7).
>
> I'm working on hydro carbons and planning to use modified Amber
> Force Field in my study but I haven't got enough information about
> "Adding New Parameters and Modifying Existing Parameters"...
> Could you help me and tell in details how to add new parameters and
> modify existing parameters; please?

there are two different things here. How to actually add and change
parameters and how to figure out what good parameters for novel system
would be and how to derive them. The former can be done by either directly
editing the amber forcefield files or, preferably, by generating a frcmod
file for your new compound. The amber tutorial #4 describes this among
other things, so:

http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm

is a good starting point. As to doing it right, i.e. deriving parameters
that make sense and fit well with the rest of the amber ffs, this could be
a major project, involve lots of qm calculations and testing. But if you
study hydrocarbons, these should already be described reasonably well with
the gaff forcefield in amber.

Please not that changing the form of the amber forcefield equation
instead of just parameters would involve lots of work and time...

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

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