AMBER Archive (2009)

Subject: Re: [AMBER] How to get total energy of asystem

From: steinbrt_at_rci.rutgers.edu
Date: Tue Nov 24 2009 - 03:43:06 CST

Hi,

>  500        -2.2929E+03     5.7810E-01    3.4109E+00       
...
>  Here what does the E+03,  E-01 and E+00 mean and if I want to get the
> total energy of the system, how should I proceed from here. I want to

The E+XX means the number is in exponential format, so 2.3E+03 means
2.3*10^3, or 2300 kcal/mol.

> Further, instead of the DNA duplex if I want to consider a RNA duplex then
> what Force Field should I use. I tried to use ff99SB, using the following
> command
>
> $AMBERHOME/exe/xleap -s -f
> $AMBERHOME/dat/leap/cmd/leaprc.ff99SB

Amber normally assumes a nucleic acid to be DNA. RNA residues are in
ff99SB, to distinguish them they are called RA, RC etc. in leap. You have
to adjust your input file to explicitly name the residues as RNA.

Also, if you are doing nucleic acid simulations, you might want to
consider the parmbsc parameter adjustment set by Orozco et al.(check
ambermd.org for information), which is an improved nucleid acid force
field.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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