RE: AMBER: Basic AMBER question

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 11 Jul 2007 13:07:42 -0700

Hi Lili,
 
Amber's GAFF force field is designed to tackle organic molecules. Take a
look at tutorial B4
(http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm) which covers
how to use AMBER's antechamber tool coupled with the GAFF force field on
stand alone organic molecules. Note the typical caveat applies that this is
an automated tool for assigning parameters - while it typically does a good
job that is no substitute for judicial review...
 
Note you should also read up on molecular mechanics and molecular dynamics
so you understand the issues involved. I recommend as a start you take a
look at:
 
Leach "Molecular Modelling: Principles and Applications"
 
I would also see:
 
D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr.,
A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular
simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).
 
and
 
J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot.
Chem. 66, 27-85 (2003).
 
As well as look for some course notes on Molecular Dynamics and published
reviews.
 
Good luck...
 
Ross
 

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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Lili Peng
Sent: Wednesday, July 11, 2007 12:16
To: amber.scripps.edu
Subject: AMBER: Basic AMBER question


Dear AMBER users,

This is probably a very basic question addressing the fundamentals of AMBER.

Currently I've drawn a structure consisting of an amino acid chain and
organic molecules (consisting of benzene rings and a carbohydrate). I used
Accelrys' DS Visualizer to draw the structure in .PDB format. Now I'm
attempting to perform an energy minimization in AMBER, but I'm getting
errors such as "FATAL: Atom .R<MOL 2>.A<C104 23> does not have a type." I
Googled this error and I found some infromation about incorporating .lib
files. I figured this has to do with the different types molecules in my
structure - or does it?

Basically, I'd like to know if AMBER can be used to simulate a complex
structure consisting of different types of molecules? I've read that AMBER
is primarily used for simulation on proteins and DNA, but what if I wanted
to do simulate organic molecules? I've read into other literature, and from
what I've gathered there are other force fields such as ECEPP and Compass
that are better suited for organic molecules.

Anyway, I'm probably asking a very basic question, but I'd like to whether I
need to back up a few steps before I proceed further with using AMBER.

Thanks all,
Lili





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