AMBER: Fw: pca with ptraj

From: Claire Zerafa <>
Date: Wed, 19 Oct 2005 14:02:08 +0200

----- Original Message -----
From: Claire Zerafa
Sent: Tuesday, October 18, 2005 1:11 AM
Subject: pca with ptraj

Dear all,

I am trying to use pca with amber for the first time. Essentially, I have a series of dynamics .mdcrd files which I want to work with in order to evaluate the most important motions of a protein molecule- in my case the androgen receptor.

I was thinking of using a script as follows
trajin .mdcrd1
trajin .mdcrd 2
reference avg.pdb
rms reference out avg_rms
matrix covar name cvmat
analyse matrix cvmat out top10 vecs 10

Should I use a pdb file that I generated in antechamber after minimisation as a reference pdb file , and is the use of a reference file mandatory- i seem to think not?
I am not sure what the rms reference out avg_rms achieves-?
does matrix covar name cvmat create a covariance matrix for the pca calculation of any name I wish to designate?
and then i guess that analyse matrix cvmat out top10 vecs 10 will calculate the 10 principal components (vectors) from the matrix I designated above

Then, I am not sure- will i get rms fluctuations if i set a script such as the one below, assuming that the fluct files will be the result of running the script above?

trajin .mdcrd
analyse modes fluct file top10 beg 1 end 1 out flct1
analyse modes fluct file top10 beg 2 end 2 out flct2
analyse modes fluct file top10 beg 3 end 3 out flct3
projection modes top10 out proj10 beg 1 end 10

i would really like to understand what beg 1 end 1 out flct 1 achieves, for example..
then what would the command to get it to go be please?
also is it wise to work with a stripped protein- of water that is- i guess that would be sensible- this could be achieved by stripping the waters from the average pdb file?

i know this probably sounds confused. these are all questions that came to mind after reading the manual




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Received on Wed Oct 19 2005 - 13:53:00 PDT
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