AMBER Archive (2006)

Subject: AMBER: PCA and projections

From: Miguel Ferreira (
Date: Wed Nov 01 2006 - 08:11:57 CST

Dear amber users,

I want to perform essential dynamics using ptraj and IED software. After
strip the waters and ions of my trajectory I used the following scripts to
calculate the eigenvectors and the corresponding projections:

trajin mds_semH2O.mdcrd.gz
rms first *
matrix covar name mcovar
analyse matrix mcovar out evec.pev vecs 25

trajin mds_semH2O.mdcrd.gz
rms first *
projection modes evec.pev out proj.ppj beg 1 end 25

The first script ran ok and I obtained the evec.pev file. However, the
second script gave me the following error at command line:

--- > 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

Does anyone knows what this means? Any suggestions to solve this problem?

Thanks in advance

MSN Busca: fácil, rápido, direto ao ponto.

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