AMBER: General Question about AMBER's Free Energy Perturbation Method

From: Chris Moth <>
Date: Wed, 05 Jan 2005 16:06:33 -0600

Ilyas :

If you still are interested in Free Energy Perturbation......

You _can_ do it with Amber 8, manually. I have taken a rather heavy-handed
approach - and it is working out OK on my project (methyl to hydrogen
perturbation in a bound ligand).

I have manually created .prp and .frcmod files to define the
bonds/angles/electrostatics/etc needed for my project as lambda ranges from
0 to 1. A spreadsheet worked well for this. These in turn are used to
create individual prmtop files for each lambda value with leap.

For energetics, you can use the sander IMIN=5 option to post-process each
trajectory using the current, forward, and backward prmtops. I found it
useful to store these energy outputs in 3 separate subdirectories.

Finally, you can compute the frame-by-frame EAMBER energy deltas (between
output files from above) with a few lines of C code - or do it with a
script language that supports floating point - or you can "cut" the values
out, and paste them into a spreadsheet.

I found my boss' (Terry Lybrand) description of FEP helpful in Reviews in
Computational Chemistry, 1990, Wiley & sons

Also, Leach's description in his "Molecular Modelling" (2nd
Edition/Prentice Hall) is helpful.

My calculation has been a lot of work - so if you are getting what you need
from the automated TI capabilities of Amber 8 recommended earlier, I would
not make a change!


At 10:13 PM 12/15/2004, Ilyas Yildirim wrote:
> Dear AMBER Users and Developers,
> I have a general question about AMBER's FEP calculation. I want to make a
>small change on a nucleic acid, and do a FEP calculation from the
>original structure to the newly created structure. In the 'Crown ether in
>vacuum' tutorial, the perturbation is done by using GIBBS. In the initial
>system, there is a Na+ ion, and it is perturbed from Na+ to K+ (and then
>from K+ to Cs+ ion). In this tutorial, 1 atom is changed to another atom.
> My question is as following: Let's say that I have an organic molecule,
>like Guanine, and want to change the amino group (-NH2) to a carbonyl
>group (-O) (Or vice verse). [NH2 -> O or O -> CH2] How can this be
>specified in xleap? Or should I do a [N -> O] or [O -> N] perturbation,
>and then include the hydrogen atoms?
> From GIBBS and XLEAP's interface, I realized that only 1 atom can be
>perturbed. Therefore, I wonder if it is possible to do a
>perturbation like NH2 -> O in AMBER 8. Thanks in advance.
> Ilyas Yildirim
> ---------------------------------------------------------------
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Received on Wed Jan 05 2005 - 22:53:00 PST
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