AMBER Archive (2006)

Subject: Re: AMBER: PCA: can't complete projection

From: Zu Thur Yew (yewzt_at_intern.bii-sg.org)
Date: Tue Aug 08 2006 - 11:42:04 CDT

Hi,

I've now tried other masks (e.g @CA) and it still doesn't work...I then
tried to use the projection modes command by itself rather than as part
of a longer script which included matrix and analyze matrix commands....
instead, other error meesage appeared: "WARNING in ptraj(),
transformProjection: evecs not of type COVAR, MWCOVAR, or IDEA, ignoring
command"

Does that mean that projection is not supported for distcovar?

Thanks for any help!

zt

Vlad Cojocaru wrote:
> 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 .
>
>
> vlad
>
>
>
>
>
> 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*
>>
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>
>

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