AMBER: how to reassign charges

From: Lwin, ThuZar <>
Date: Wed, 9 Aug 2006 13:16:01 -0500

Dr. Case,

     In following the tutorial on Thermodynamic integration, I am able
to reproduce closely to the data in the tutorial. However, I have
question regarding with making the toluene system neutral.

When I compare charges on toluene in tutorial and phenylalanine (in, all atoms are the same except CB which is -0.03430 in
PHE and -0.0828 in toluene. So -0.0485 was added to -0.03430 to make
the toluene neutral. This 0.0485 happens to be the net charge of
toluene after removing N, CA,C=0, the atoms we do not want for toluene.

    I tried to do similar approach using ff03, that is I added the net
charge left on toluene after removing N, CA,C=0 from PHE, to make
toluene neutral to the CB atom.

   In CB of PHE has charge -0.09872. I changed it to
-0.183400 since the net charge on toluene was 0.08468. I then redid the
thermodynamic integration. This time my results are not in agreement
with the experiment. The charging free energy in vacuum now becomes
almost twice the value of charging in vacuum as in tutorial, besides it
is a positive value.

   So my question is how do I appropriately assign the charges on
toluene so that it would be neutral.


Thank you,


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Received on Sun Aug 13 2006 - 06:07:03 PDT
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