Thank you very much for the additional information.
I am using NAB but in the form of make-na by james stroud to get the molecules.
Amber Tools will not work because it will be running on the web.
Won't amber forces alone be realistic enough to handle hyrogen bonding between base pairs in dna strands.
The only purpose right now is to show hydrogen bonds between bases breaking and forming
between dna strands. Will the amber force fields alone be sufficiently accurate for this purpose?
Thanks,
Dan
-----Original Message-----
From: M. L. Dodson <activesitedynamics.comcast.net>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Mon, Mar 15, 2010 2:24 pm
Subject: Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?
On Mar 15, 2010, at 3:58 PM, whimsica.aol.com wrote:
>
> I'm looking for all the parameters necessary to work with the raw amber forces
equation found on
> http://en.wikipedia.org/wiki/AMBER which needs parameters for bonds, angles,
torsions, electrostatic and vanderwalls.
> Are they scattered around in different files like parm99.dat and allnuc94.in?
Where are they? And how do I determine what numbers
> correspond to what? For instance in parm99.dat there are lots of numbers what
are they? Bond Angles? Electrostatic forces?
>
> So far people have just refered me to the documentation.
> I have looked through the docs and the file specification
> and there is not enough information to let me know what the values are.
>
> Here is a line example from parm99.dat
> C -CT 317.0 1.522 JCC,7,(1986),230; AA
>
>
>
> What are these numbers?
>
> Can someone please help me find all the parameters I need to use the original
amber force field equations?
>
> The project is an educational simulation funded by the department of education
to help improve science in the US.
> www.CinematicSciences.com we are using Unity3D as an engine for the
simulations.
>
>
>
> Daniel Savage
> CTO
> CinematicSciences
>
Well, I will assume that you want the results of this exercise to have some
connection to reality (at least reality as represented by simulation with the
AMBER FF). If so, I think this is a project of some substantial duration given
the initial coding (rapid prototyping environment or not) and NECESSARY
validation.
Let me suggest you take another tack rather than reinventing the wheel. The
GPL-licensed AmberTools project (see the AMBER web site) has all the software
needed to do MD simulations. The primary tools in the project you will need for
simple simulations are nab and leap (leap comes in several versions). If you
wait a month or so, I believe the next version of AmberTools will have the
source code for these calculations factored into a library suitable for access
by scripting or prototyping engines. (The list will correct me if I am wrong on
this, but that is my understanding.) This library will already have
computational answers to the questions you are asking embedded in the source
code. The main point, however, is that this software has been extensively
validated.
The main "deficiencies" compared to the regular AMBER simulation engines are
inability to carry out explicit solvent, periodic boundary conditions dynamics
runs and to carry out coupled potential quantum mechanics/molecular mechanics
(QMMM) simulations. (To the list: I know that statement misses a lot of
differences, but these the main ones that would impact this gentleman's
objective, IMO.)
Good luck,
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Mon Mar 15 2010 - 17:30:04 PDT
