AMBER Archive (2006)

Subject: Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. .

From: David A. Case (
Date: Fri Jul 28 2006 - 09:27:44 CDT

On Thu, Jul 27, 2006, Lwin, ThuZar wrote:
> I also created a prmtop file without the perturbation such as
> saveAmberParm PHE prmtop_wo_perturb.vac
> since to minimize, heat and equilibrate the prmcrd.coul.vac file I
> needed
> the prmtop file without the perturbation.
> Then, when I run sander, I did not get DV/DL printout along with energy
> component terms as shown in the tutorial. I am wondering what I have
> done wrong.

I assume you are using the perturbed prmtop file for this run. My best guess
is that there is no difference between the lambda=0 and the lambda=1 energy.
The DV/DL values are only printed if they are different than zero, so this
would explain the lack of printout.

Run a short calculation (just 10 steps or so, with ntpr=1), first setting
lambda=0, then lambda=1. Make sure that the two endpoints are what you want.
(It is always a good idea to do this for any TI calculation.)


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