Dear Bala,
Think very carefully about what you mean by an average structure. An average
structure is typically not very meaningful since it is just an average of
the cartesian coordinates visited during a simulation. E.g. If I have a
methyl group that is free to rotate around a C-C bond then the average
position of those 3 hydrogens will be a point at the centre of rotation.
Thus when looking at the average structure we would see what looks like a
very very weird chemical group but really all it is telling us is that the
methyl group is unrestrained and the hydrogens are degenerate.
A good example of this is given in the following tutorial.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/index.ht
m
If you want a structure that has some physical meaning then you may want to
consider cluster analysis and then take the structures that closest to each
of the clusters you calculate.
You may also want to revisit your ptraj script. I am not sure what you are
hoping to see by averaging with the waters in place and then stripping them?
What is the reasoning behind this?
All the best
Ross
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
C Balasubramanian
Sent: Monday, November 21, 2005 05:51
To: amber.scripps.edu
Subject: AMBER: average struct without solvent
Dear users,
I hve run a 1.5ns simulation on a 12 mer DNA in explicit solvent with PBC. i
wanted to calculate the average structure without (excluding) solvent and
ions. the following is the input i gave to ptraj. I am getting the structure
but it is highly scattered and not a proper one. Someone please help me on
this.
trajin mde.mdcrd
trajin mdp1.mdcrd
trajin mdp2.mdcrd
average avgst.pdb pdb nowrap
center :1-24
image familiar
strip :WAT
strip :Na+
thanks,
Bala
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Received on Mon Nov 21 2005 - 16:53:02 PST
