AMBER Archive (2007)

Subject: AMBER: mm_pbsa: missing values in ras-raf tutorials

From: merc mertens (merc.mertens_at_gmx.net)
Date: Fri Oct 19 2007 - 03:28:09 CDT

dear list,

i have been trying to use the mm_pbsa utility from amber for the calculation of binding free energies between a protein-ligand complex. during my calculations i get messages in the log-file like:

No values for MM_ELE existing -> Skipping

or:

No values for GB_GBSOL existing -> Skipping

I thought these missing values might be related to my system (e.g. wrong generation of coordinates), but when i looked into the log-files from the ras-raf tutorial

like
$PATH_TO_AMBER/amber9/src/mm_pbsa/Examples/03_MMPBSA_Binding/mm_pbsa.log.save

i saw exactly the same messages. does anyone have any explanation for this?
are these missing values not important for the outcome of the calculation? does the tutorial contain errors?

thanks for any help,
merc 

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