Re: AMBER: PCA: can't complete projection

From: Vlad Cojocaru <>
Date: Tue, 08 Aug 2006 16:56:49 +0200

Dear Zu Thur,

I had the same problem some time ago with ptraj from AMBER8, I told Tom
Cheatham about it but he is busy enough so I guess he forgot, such as
that the ptraj of AMBER9 has the same problem (at least I was told by
somebody else because I didnt manage to test it myself yet). It is a
strange problem that I couldnt figure out yet ... If I use different
masks everything seems fine (just .~H* has created problems for me so far)

Somebody wrote to me sometime ago (that's how I know that ptraj from
Amber9 has the same problem) and told me that he fixed it by changing
the format of the eigenvectors file (at beginning of line 2 adding or
deleting one space). I didnt try it myself yet but it looks like it
worked for the guy who tested it .... Maybe he will join the list with
an answer for the whole list .....

Maybe one should take a look at the formatting read by the projection
command in the ptraj source code .


Zu Thur Yew wrote:

> Hi,
> I'm trying to do PCA on my system....Below is my input file...the mask
> is recognised, but projection couldn't be done.....the error message
> is: "WARNING in ptraj(), transformProjection: file E6PCA2.dat not
> opened, ignoring command"
> I've checked the eigenvector output file and there are eigenvectors..
> Any Help is appreciated!
> zt
> trajin E6_md3.mdcrd
> trajin E6_md4.mdcrd
> strip :WAT
> strip :Na+
> strip :Cl-
> rms first ~.H*
> matrix distcovar name E6distcovar ~.H* byatom
> analyze matrix E6distcovar out E6PCA2.dat vecs 5
> projection modes E6PCA2.dat out E6PROJ.dat beg 1 end 3 ~.H*
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Aug 09 2006 - 06:07:13 PDT
Custom Search