AMBER: ptraj PCA

From: Vlad Cojocaru <>
Date: Tue, 24 Jan 2006 17:02:20 +0100

Dear ambers,
   When using the inputs below to perform PCA on a protein trajectory
(file.mdcrd containing a full protein but no ions or water), ptraj
always fails to create the projection file (${fname}.ppj -- second
step), the error being listed below. Obviously, the error has something
to do with the mask because if I replace .~H* with .CA, the projection
file is properly created. However I would like to be able to use all the
heavy atoms so that I can visualize the results in IED using a pdb file
with all the heavy atoms in the protein (I believe, IED doesn't allow me
to use a pdb of the entire protein but eigenvectors calculated only for
the CA atoms).
   If somebody has experienced such a problem, could you give me an
advice on how to deal with this?
   I have to mention also that the modesfile ${fname}.pev created in the
first step looks OK with 25 eigenvectors output and in the ptraj log
file of the 2nd step the mask seems to be properly recognized (PTRAJ:
projection modes ${fname}.pev out ${fname}.ppj beg 1 end 25 .~H* \
Mask [~. H*] represents 3736 atoms), with 3736 being the appropriate
number of heavy atoms in my protein. The error comes on STDOUT output.

Thanks in advance


trajin file.mdcrd
rms first .~H*
matrix covar name mc .~H*
analyze matrix mc out ${fname}.pev vecs 25


trajin file.mdcrd
projection modes ${fname}.pev out ${fname}.ppj beg 1 end 25 .~H*

/ptraj error (file ${fname}.ppj is blank -- only the header present)/

FYI: Number of read evecs is 1, number of requested evecs is 25
FYI: Number of read evecs is 1, number of requested evecs is 25
WARNING in ptraj(), transformProjection: no. of atom coords does not
agree with no. of vect elementsignoring command

Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
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Received on Wed Jan 25 2006 - 06:10:06 PST
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