AMBER Archive (2008)

Subject: Re: AMBER: PCAL and polar contribution in the output file

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Sun Jun 15 2008 - 08:30:23 CDT

Hi Neha,

PBCAL and the "corrected reaction field energy" are the same but in different units.
PBCAL is given in kcal/mol, the "corrected reaction field energy" in kT/mol.
This is done to be compatible with the DELPHI program since it calculates the reaction field energy in kT/mol as well.
To calculate the "corrected reaction field energy" from PBCAL you simply need to multiply PBCAL with (1000.0 * 4.184 / (T * R)) with the absolute temperature T and the gas constant R. You can reproduce that from the source code if you grep for "kcal2kt" in $AMBERHOME/src/mm_pbsa/mm_pbsa_calceneent.pm and for "kt2kcal" in $AMBERHOME/src/mm_pbsa/mm_pbsa_statistics.pm, respectively.

Cheers!
Hannes

-------- Original-Nachricht --------
> Datum: Fri, 13 Jun 2008 13:42:54 +0800
> Von: "Neha Gandhi" <n.gandhiau_at_gmail.com>
> An: amber_at_scripps.edu
> Betreff: AMBER: PCAL and polar contribution in the output file

> Hi All,
>
> In MM-pbsa analysis, the ouput consists of corrected reaction field
> energy. I am able to calculate non-polar contribution which is
> PBSUR=surface area*0.00542+0.92. Where is the electrostatic solvation
> energy in the output file such as snapshot_rec.all.out? I cannot
> correlate PBCAL with corrected reaction field energy. I appreciate if
> somebody can help me to calculate PBSOL for each snapshot. How PBCAL
> and corrected reaction field energy are related?
>
>
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
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