AMBER Archive (2003)

Subject: AMBER: PMF calculations

From: Sébastien Canneaux (sebastien.canneaux_at_univ-reims.fr)
Date: Tue Sep 09 2003 - 07:29:36 CDT

Dear Amber's users,

I try to run a PMF calculation with the gibbs program.
My system consists of an organic molecule (in vacuo), near a bulk of
water.

To draw the organic molecule in the bulk of water, I must fix a dummy
atom.
(I define the dummy atom without charges nor VDW parameters).

When I fix this dummy atom with the ''ibelly'' option, (I define my
internal constrain between one atom of my solute and the dummy atom),
the free energy is equal to zero.

When I fix the dummy atom with the ''ntr'' option, (I define my
internal constrain between one atom of my solute and the dummy atom),
the step of PMF calculation don't run.

Which is methodology to carry out this kind of calculation, and to
prepare the coordinate / topologie files.

Can anybody help me in understanding the problem ?

Thank you very much in advance

Sébastien.


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