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,
Jorgen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 24 2011 - 08:30:04 PST
