Re: AMBER: Topology file problem in TI !

From: Thomas Steinbrecher <>
Date: Wed, 7 Mar 2007 08:48:10 -0800 (PST)

Hi Pradipta

I'm not sure I can help you with the charge reporting problem, but here
are some thoughts:

> I am using AMBER 8 in a linux machine.

Setup of TI calculations has become much easier in amber 9 (and hopefully
will be even more so in amber10), so if you want to do lots of these
calculations, I would seriously consider upgrading.

> I plan to do both electrostatic and VDW in one step for this model system.
> This is what I did in xleap

Without knowing the specifics of your system, I would advise you against
that, reducing the vdw-repulsion on a charged atom (no matter how small
the charge) can result in serious simulation instabilities. Doing a
transformation in 2 steps (remove charges, then disappear the chargeless
atoms) is annoying to set up, but needs only a little more computer time,
because a charge-change transformation normally has a very linear
dvdl-curve and needs only few lambda points (say, quite speculatively, 5
compared to 20 for the vdw change).

Considering the charge reporting problem, what I would do is make sure
that youre .lib (or .off) files contain the right charges for all atoms,
then you know that it is only a reporting problem in leap. While this
advice just amounts to 'dont trust the charge command', it should not be a
big obstacle in getting your calculation started. Someone else on the list
might help you more here...



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Sun Mar 11 2007 - 06:07:07 PDT
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