VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Oct 03 2019 - 11:44:50 CDT

Hi Amir,

How big is your system? This error crops up when any of the fixed format fields can't be written, usually when an atomic coordinate gets to be more than 10000 or less than -1000. Would this be true in your case after translation? If so, using pbctools to rewrap the coordinates would be the next step forward.

-Josh

On 2019-10-03 05:44:31-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Hi all,

I selected my molecule and used writepdb to convert .coor to pdb file but vmd is giving following error :-

PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom 0
                                 cannot be written in PDB format.
                                 File will be truncated.

This has been discussed in mailing list :- https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14674.html
I shifted the origin to center of mass and set occupancy and beta to zero according to answer in above link but still I am getting writepdb failed error.

Thanks in advance,
-Amir