AMBER Archive (2009)

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

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Nov 24 2009 - 06:36:30 CST


On Tue, Nov 24, 2009, gunajyoti das wrote:

> ¬ Using AMBER10 package I carried out energy minimization on a DNA
> duplex having 10 nucleotides on each of the single strands. The last
> line of output reads as follows
>
> NSTEP ††† ENERGY†††††††††† RMS†††††††††††† GMAX††††††††††††† NAME†††† NUMBER
>
> †500 † † †† -2.2929E+03†††† 5.7810E-01††† 3.4109E+00††††††† N1 † † † † † 362
>
> ¬ 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
> express the total energy of the system in KCal/mol.

The total energy is -2292. kcal/mol, but this is not of any real interest by
itself. It is simply the force field energy part way through a minimization.
You need to find some way to compare two energies in order to gain meaningful
results; that is, the zero of energy is arbitrary.

>
> 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
>
> ††† but the RNA residues were not recognised.

If you use an up-to-date version of AmberTools (including bugfix.12), and use
a pdb file formatted according to version 3 of the PDB standard, LEaP should
correctly recognize DNA, RNA or a mixture of the two. (All current files from
http://www.rcsb.org use a version 3 format.)

...dac

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