AW: AW: AW: AW: tclBC incorrect output

From: Norman Geist (
Date: Mon May 07 2012 - 00:26:11 CDT


here are some questions that come to my mind:

Does the atom numbers printed match your wanted CA atoms?
Do you start from a unwrapped restart?
->Go to vmd, load your pdb/coor, set your box by "pbc set {x y z}" type "pbc
wrap -now"
->If you now have overlong bonds within your protein, that’s the reason.
Does namd use other unit for the coords internally?
->If someone know, please tell us.
Does namd for some other reason than wrapping updates the coordinates
->When is your script executed, if some steps are already gone, the
coordinates of course don't still match the pdbs one.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: P.-L. Chau []
> Gesendet: Freitag, 4. Mai 2012 09:19
> An: Norman Geist
> Cc: Namd Mailing List
> Betreff: Re: AW: AW: AW: namd-l: tclBC incorrect output
> Thank you for your message.
> > 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.
> The coordinates printed match NONE of the atoms in the PDB file. Could
> I
> ask you if there is some way to check the getcoord command?
> Thank you very much indeed!
> P-L Chau

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