[AMBER] calculate entropy ptraj

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Mon, 24 Jan 2011 17:15:10 +0100

Hi all,

 I am using the quasiharmonic analysis to calcualte the entropy of one
of my molecules. First I start by aligning the whole trajectory
including water like this

center :1-20 mass origin

where the first 20 residues are my peptide. Then I strip of the water

strip :8-99999

and last I calculate the entropy

matrix mwcovar name cc.matrix out cc.matrix
analyze matrix cc.matrix out new.matrix thermo

the problem is I get a lot of warnings which I do not know how to remove

""Warning-- 161 vibrations have low frequencies and may represent hindered
         internal rotations. The contributions printed below assume that these
         really are vibrations.""

Any suggestions would be very much appreciated

Thanks in advance,

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Received on Mon Jan 24 2011 - 08:30:04 PST
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