AMBER: Free energy perturbation in SANDER

From: Chris Moth <>
Date: Thu, 14 Dec 2006 08:21:11 -0600 (CST)

I have done FEP calculations manually.

When perturbing ligands I place place parameter start and end values in
the columns of a spreadsheet, and then calculated intermediate values as
needed for each lambda change from 0 to 1. Then, I apply these immediate
to new prep and forcemod files, and, in turn, create a new prmtop for each
lambda window.

Needed may be calculated by postprocessing each trajectory with multiple
prmtop files. I recall you can use 1 step of minimization to get these
energies out. You will use an input option to _read_ the trajectory file
and report on each frame in it. If you don't find it in the manual, look
at the source code for sander. Or, I can dig it out from my past work.

You will create new atom types in your forcefield setup, so that you can
make your perturbations without affecting the rest of the system.

FEP is a bit of work to setup with AMBER, but once you automate with
scripts, and macros, it is not too bad.

> Dear All
> I want to perform free energy perturbation calculation by SANDER module.
> I know it can be done using GIBBS module in AMBER7, but it's retired in
> SANDER module in AMBER8 can perform TI calculation but not free energy
> perturbation.
> If Free energy perturbation can be performed by SANDER module,
> Please tell me how to do?
> Thanks.
> Yumi
> ****************************************************************************
> **
> Yumi Nukushina
> E-mail :
> ****************************************************************************
> ***
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Received on Thu Dec 14 2006 - 16:48:22 PST
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