AMBER Archive (2008)

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

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Sun Jun 15 2008 - 08:56:20 CDT

Hi Hannes,

Thanks for your reply. I have another small query about MM-PBSA
implemented in Amber 9. The default output using PBSA solver in AMBER,
what are the units? Kcal/mol or KJ/mol? The default tutorials say
Kcal/mol and whereas some papers where they use delphi report kJ/mol.

Many thanks!

Cheers,
Neha

On Sun, Jun 15, 2008 at 9:30 PM, Hannes Kopitz <Hannes.Kopitz_at_gmx.de> wrote:
> 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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-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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