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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Received on Tue Nov 24 2009 - 01:30:02 PST
