AMBER Archive (2002)

Subject: Re: total energies during MM-PBSA

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Fri Nov 01 2002 - 11:29:33 CST

Dear Giulio,
I've written a script that grabs, calculates, and outputs gas, nonpolar, and
solvation energy for each snapshot.

It works like this:

./script-name xxx.all.out

and it writes out 3 files- xxx.all.out.gas xxx.all.out.nonpol and
xxx.all.out.sol with gas, nonpolar, and solvation energy for each snapshot.

I hope this is what you were looking for.

All the best,

     Martin Lepsik

P.S. This is the script:

#!/bin/tcsh
sed 's/1-4 /1-4/g' $1 > tmp
awk '/^ [BV1]/ {print gas = gas + $3 + $6 + $9} {gas = 0}' tmp > tmp1
paste -s -d " \n" tmp1 > tmp2
awk '{print $1 + $2 + $3}' tmp2 > ${1}.gas
awk '/surface/ {print 0.00542 * $4 + 0.92}' $1 > ${1}.nonpol
awk '/^ c/ {print 0.59616 * $5}' $1 > ${1}.sol
paste -d '" "' ${1}.gas ${1}.nonpol ${1}.sol > tmp
awk '{print $1 + $2 + $3}' tmp > ${1}.all

----------------------------------------------------------------------------
---------------------------------------------------------------------------- 

----
Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem
----- Original Message -----
From: "Giulio Rastelli" <rastelli.giulio_at_unimo.it>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Sunday, October 27, 2002 7:20 PM
Subject: total energies during MM-PBSA

> Dear all,
> is it possible to print out the total energies (stability calcs) of a
> system
> during the MD trajectory with mm_pbsa? The statistics file reports the
> averaged values, the *com_all* file reports all the individual terms,
> but for
> a huge number of snapshots it is impratical to get the total. Also, may
> be
> somebody out there made a script to get the total energy during the
> trajectory...
> Thank you very much for your help, really appreciated!
> Giulio
> --
>
> Giulio Rastelli
> Dipartimento di Scienze Farmaceutiche
> Universita di Modena e Reggio Emilia
> Via Campi 183
> 41100 Modena - ITALY
> -------------------------------------
> tel 0039-059-2055145
> fax 0039-059-2055131
> -------------------------------------