AMBER Archive (2008)

Subject: AMBER: ptraj analyze modes from nmode

From: Miguel Ortiz-Lombardía (ibdeno_at_gmail.com)
Date: Sat May 31 2008 - 10:40:50 CDT

Hi,

How are modes calculated from nmode analyzed in ptraj?
I have written produce a vec file from nmode with:

nmode -O -i nmode.in -o nmode.out -p protA.prmtop -c protA_mini.rst -v
protA.vec

I had thought that I would be able to process that file in ptraj with:

ptraj protA.prmtop anvecs.ptraj

where anvecs.ptraj is:

analyze modes fluct file protA.vec beg 7 end 56

However, I get this error:

PTRAJ: analyze modes fluct file protA.vec beg 7 end 56
FYI: No evec type found in protA.vec, assuming it is MWCOVAR
FYI: No value for nvectelem found in protA.vec, assuming it is navgelem
WARNING in ptraj(): No input trajectories specified (trajin), aborting...

What am I missing?

Thank you!

Miguel 

-- 
http://www.pangea.org/mol/spip.php?rubrique2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!
Georges Brassens

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