Re: AMBER: PCA with ptraj

From: Chris Moth <>
Date: Sun, 29 Jul 2007 07:27:32 -0500 (CDT)

A few thoughts on the second example.

The return of the negative from malloc may indicate that you may have a
larger problem than your machine architecture can support.

If you remove all atoms but CA, can you diagonalize then?


> 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
> go
> What should i do ?
> Does anyone faces the same problem. i saw two or three postings.
> But there is no reply.
> -Thanks and regards

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Aug 01 2007 - 06:07:06 PDT
Custom Search