[25-I-2013]
Hi everybody,
I'm a newcomer to Thermodynamic Integration calculations and I have been
doing some tests running a TI to transform the alpha anomer of glucose
into the beta anomer to determine the Difference in Free Energy. I am
using Amber11 with AmberTools12 and Glycam06h force field. I am
following the tutorial A9 (
http://ambermd.org/tutorials/):
1) First of all I created the input files for the alpha and beta anomers
and solvated them with TIP3P (glaWAT glbWAT) taking care of all the
requierments needed to avoid problems with common/special atoms.
2) Then I divided TI process into 3 Legs: switching off all the charges in the glucose, mutating atoms (employing soft-core potentials), and then
again switching on the charges (files *.in).
3) I extracted the lines "DV/DL average" and "DV/DL fluctuations" from
output files to create the 3 columns (Lambda, Average, Fluctuation) text file as recommended by the tutorial ("stepX.TIresults.txt").
4) Finally, I processed the lines with the perl script in tutorial ("TotalTI.stepA.txt").
After checking the results I have discovered something strange, and I would like to ask you if I have been anything wrong.
In the first leg, I switch off the charges of the glucose molecule. Since
it is a polar one, interaction with water should be favorable and
therefore going from the molecule with charges (polar) to the molecule
without charges (apolar) should give a positive difference in energy.
Instead, the difference in free energy is about -91.8 kcal/mol (???).
We find exactly the same strange result in the third leg when I apply the
charges. Going from the apolar molecule in water to the polar molecule
should be favoured, however, I again find the wrong sign in the energy
(about +92.5).
I send you attached a tar file with the text documents (submitting scrips, input files, structures, results...)
Does anyone have any clue about what I am doing wrong?
Than you very much.
Kepa K.
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Received on Fri Jan 25 2013 - 06:00:04 PST
