AMBER: Thermodynamic integration using the amber 9

From: Vitor Manuel Sousa F?x <>
Date: Mon, 29 May 2006 14:41:14 +0100

Ti Calculations using the amber9

I would like to calculate the binding constant between a
synthetic receptor and an aromatic substrate using the
same methodology described in the amber tutorial ˇ°toluene
to nothingˇ±. However I would like to do this
transformation in a single step in which the charges and
the vdw parameters are changed simultaneously. So, the
question is it possible to do this with amber 9 using a
single prompt file (with information about vdw and charge
variations) created via saveamberparmpert command in
xleap. If the, the answer is yes, which klambda is the
most suitable one, 7 ?...

Alternatively, we have to create prmtop files
corresponding to initial (substrate) and end (nothing,
with all atoms replaced by dummies) stages and to use the
ˇ°multistage protocolˇ± as suggested in amber9 manual.
However, for me it is not no clear how to do to create the
prmtop files. In other words to use saveamberparm instead
of saveamberparmpert, is it necessary include the charge
variations. The lib files corresponding to the
transformation ethane to methane reported with software
package amber9/test/ti_eth2meth_gas would be a useful
contribute for a complete understanding of this issue.

Thank you very much in advance for some help from the
amber stuff


Prof. Vitor Felix
Department of Chemistry
University of Aveiro
3810-193 Aveiro
Tel: 351 234 370 729
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Received on Wed May 31 2006 - 00:11:57 PDT
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