AMBER Archive (2005)

Subject: Re: AMBER: nmode entropy calculations in MMPBSA

From: david.evans_at_ulsop.ac.uk
Date: Fri Feb 25 2005 - 08:14:55 CST

Hi,

I noticed this before. I think it is just a glitch in the perl script
which pulls values
from the output files.
mm_pbsa_calceneent.pm: line 382
This matches two lines from a typical nmode output, only the second
of which
is the rotational entropy you want. Fortunately, the routine that
reads in the
*all.out file ignores all but the last rotational entry, so I think
it doesn't matter.

Dave 

--
David Evans
School of Pharmacy
University of London

---- Message from Fabien Cailliez <Fabien.Cailliez_at_ibpc.fr> at
2005-02-25 11:20:23 ------
>Dear all,
>
>I want to calculate entropies using the nmode module in MMPBSA
calculations.
>I am wondering about the signification of one term in the output
*all.out :
>NM
>1
>rotational 0.00004
>Total 3083.839
>translational 52.992
>rotational 52.080
>vibrational 2978.767
>
>There are 2 "rotational" terms. I guess the important one is the
second 
>(52.080) bu t
>what is the meaning of the first one which is always very close to 0
?
>
>Thanks for your answers,
>Fabien
>
>-- 
>__________________________________________________________________
>Fabien Cailliez	   Tel : 01 58 41 51 63	   
>Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
>IBPC	13, rue Pierre et Marie Curie   
>75005 Paris	    
>__________________________________________________________________
>
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