AW: AW: AW: tclBC incorrect output

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri May 04 2012 - 02:03:02 CDT

Check if the coordinates printed match to another atom in the pdb. So we
know if it is a issue of the atom numbers or the getcoord command. Possibly
the getcoord command starts the atom numbers with zero, while pdb starts
with 1. If so, the atom numbers needs to be decreased by 1. Also, check if
the atomnumbers put from the first part of the script match the right CA
atoms in the pdb.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: P.-L. Chau [mailto:pc104_at_pasteur.fr]
> Gesendet: Freitag, 4. Mai 2012 08:27
> An: Norman Geist
> Cc: Namd Mailing List
> Betreff: Re: AW: AW: namd-l: tclBC incorrect output
>
> Thank you for your message.
>
> I am sorry to say this, but could I say that we are probably going off
> at
> a tangent? I can and shall guarantee that every line of my PDB is an
> ATOM
> line. The first part of the script works fine for my purposes, and I
> shall
> put the improvements you suggested later. But right now I would like to
> concentrate on the part that does NOT work.
>
> As I said in my last reply, changing the first part of the script did
> not
> affect the latter part of the script to print out the coordinates
> correctly. I am concerned with the latter part:
>
> wrapmode cell
> proc calcforces {step unique Rrate Rtarget K} {
> global aalist
> while {[nextatom]} {
> set atomid [getid]
> if { [lsearch $aalist $atomid] >= 0 } {
> set rvec [getcoord]
> puts $rvec
> foreach { x y z } $rvec {break}
> puts "$x $y $z"
> }
> }
> }
>
> I know the aalist is generated correct, but when I ask for the
> coordinates
> to be output, I do not get the correct numbers. Could I ask where I got
> it
> wrong, please?
>
> Thank you very much.
>
> P-L Chau
>
> email: pc104_at_pasteur.fr
> Bioinformatique Structurale
> CNRS URA 2185
> Institut Pasteur
> 75724 Paris
> France
> tel: +33 1 45688546
> fax: +33 1 45688719

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