Re: [AMBER] Calculating energies

From: Jason Swails <jason.swails.gmail.com>
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.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Jun 6, 2011, at 4:11 AM, Daniel Schaal <daniel.schaal.uni-bayreuth.de> 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