[AMBER] Amber14 FEW for 3 trajectory free energy

From: JoAnne Babula <jbabula.umail.iu.edu>
Date: Fri, 5 Aug 2016 10:32:22 -0400


I am currently using Amber14 on a Linux and am wondering if it is possible
for me to use the FEW tool to calculate the binding free energy of a
complex using the 3 trajectory method, but using my own previously
generated simulations as opposed to generating them through the script as
described in the very helpful tutorial A24 (http://ambermd.org/tutorials/
advanced/tutorial24/#section1). I would like to use the script in Section 2
of tutorial A24 to run GBSA analysis on 3 separate simulations (receptor,
ligand, and complex) I have generated previously, but I am unsure how to
specific that I would like these simulations to be used. I noticed the
"trajectory_files" line in the mmpbsa_am1_3trj_pb0_gb2 input file has an
automatically determined path. Is there any way I can alter this to direct
the program to use my three separate trajectories instead? The receptor for
this complex changes conformation when bound by ligand, so I would like to
use the unbound receptor simulation to better estimate the binding free
energy of the complex.
Alternatively, if FEW is not capable of performing this calculation, is
there a different tool in Amber that can?
 Thank you so much.

Very Respectfully,
JoAnne J Babula
IUSM Dept. of Pharmacology
U.S. Army, 1LT, MS
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Received on Fri Aug 05 2016 - 08:00:02 PDT
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