AMBER: PCA with ptraj

From: ravishk kumar <>
Date: Sat, 28 Jul 2007 17:32:13 +0530

Dear amber users,
Performing essential Dynamics is not possible in amber8??
I tried different ways according to the manual.

Error i get is( and my projection file is empty):
WARNING in ptraj(), transformProjection: no. of atom coords does not agree
with no. of vect elementsignoring command

my file:

trajin amb_eq_pt2.crd
strip :WAT
strip :Cl-
matrix distcovar name mcovar out mcovarnew.dat .CA
analyze matrix mcovar out evecnew.pev name evecs vecs 3
projection modes evecnew.pev out project.ppj beg 1 end 3 .CA

The second time, The following error:

ERROR in safe_malloc: Error in alloc of -14846976 bytes file:
trajin amb_eq_pt2.crd
rms first *
matrix covar name mcovar
analyze matrix mcovar out EVEC.pev vecs 25

What should i do ?
Does anyone faces the same problem. i saw two or three postings.
But there is no reply.

-Thanks and regards

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Received on Sun Jul 29 2007 - 06:07:49 PDT
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