AMBER Archive (2009)

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

From: gunajyoti das (guna_das78_at_yahoo.co.in)
Date: Tue Nov 24 2009 - 03:14:06 CST

Hi Amber users,
  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.

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.
 
    With warm wishes, thanking in advance.

Gunajyoti Das
NEH University
Shillong-22
India

 

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