AMBER: Basic AMBER question

From: Lili Peng <>
Date: Wed, 11 Jul 2007 12:15:48 -0700

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,

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Received on Sun Jul 15 2007 - 06:07:10 PDT
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