Re: [AMBER] Calculating energies

From: Jason Swails <>
Date: Mon, 6 Jun 2011 06:02:07 -0700

It sounds like you want to do an MMPBSA-like calculation.

Without post-processing, it's impossible. You would have to use ptraj to strip the solvent, create a compatible prmtop, and use the imin=5 functionality of sander to do this, picking either an implicit solvent model or run in vacuum.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
On Jun 6, 2011, at 4:11 AM, Daniel Schaal <> wrote:
> Dear all,
> I am new to AMBER and i am running a MD of a peptide in solution with a waterbox TIP3PBOX.
> When using the process_mdout.perl on the "xxx.out-file" after the production run,  i get the energies of the whole system.
> Is there a possibility to extract only the contribution to the energy of the peptide, so to speak neglecting the solvents energy.
> Cheers
> D.S.
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Received on Mon Jun 06 2011 - 06:30:02 PDT
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