AMBER Archive (2008)

Subject: Re: AMBER: TI: perturbation method

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon Mar 31 2008 - 11:32:21 CDT

Dear Fatima,

that depends on which version of Amber you are using. In Amber 9 (and 8?)
you will have to build two different prmtop files (one with the initial
and one with the final charge) and run them using the icfe=1 facilities in
sander. For older versions of amber you would have to build a perturbed
prmtop file.

In my opinion, the easiest way to build the two prmtop files corresponding
to your two endstates is two make two *.lib files for them, e.g.
molecule_charge0.off and molecule_charge1.off. Then read those into leap
to build prmtop0 and prmtop1

Alternatively, if you are using xleap, you can use the edit command to
manually select and modify the charges on some atoms.

Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Mon, 31 Mar 2008, fatima.chami_at_durham.ac.uk wrote:

>
> Dear Amber users,
>
> I need to know which command is used to perturbe the partial charges of a
> molecular structure in 'tleap' in order to calculate the free energy.
>
> best wishes
> Fatima
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