VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 27 2009 - 12:21:49 CDT

Hi,
  This error means that you have one or more atom data fields that contain
values that are not representable in a legal PDB file, and that the file will
be truncated at the point where this error occured. If you have atoms with
very large magnitude x/y/z coordinates, or a large magnitude occupancy or
beta field, that's the cause of your problem. The easiest way to correct
this is to translate the coordinates so that the center of mass of
your structure is at the origin, and to make sure you don't have any
out-of-range occupancy or beta values.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 27, 2009 at 01:18:15PM -0400, Christine Horejs wrote:
> Hi,
> yes, this is what I did initially, but I got the following error message:
> PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom 0
> cannot be written in PDB format.
> File will be truncated.
> ERROR) write_timestep returned nonzero
> Do you know what the problem is?
> Thank you for your help,
> Christine
> 2009/10/27 John Stone <johns_at_ks.uiuc.edu>
>
> Hi,
> If you've loaded it into VMD, you can select the molecule, and use
> the "save coordinates" item in the File menu to do this, selecting the
> final frame.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Oct 27, 2009 at 12:50:06PM -0400, Christine Horejs wrote:
> > Dear all,
> > I have a lammpstrj file and I would like to save the last frame of
> the
> > simulation, meaning the final configuration of the protein, as a
> pdb file.
> > Does anyone know how to do that?
> > Thank you so much and have a great day,
> > Christine
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078