From: Sujata Sovani (sujatas_at_scripps.edu)
Date: Thu Mar 03 2011 - 12:15:16 CST

Hi,

I am getting the error below when I try to generate a PSF using psfgen accesing VMD on a cluster of computers (details below). The molecule Col.PDB is 1160 aminoacids long 1179 KB file.
My colleague who takes care of the clusters tried it with two different versions of VMD. But he still gets the error below.

Error--
In the putty command window I see this
PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom 5286
                 cannot be written in PDB format.
                 File will be truncated.

In the VMD window, I get the error message:
-----------
vmd > Info) Using plugin pdb for structure file /tmp/Col.PDB
Info) Using plugin pdb for coordinates from file /tmp/Col.PDB
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 14556
Info) Bonds: 15491
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1164
Info) Waters: 0
Warning) Unusual bond between residues: 499 (protein) and 500 (none)
Warning) Unusual bond between residues: 1159 (protein) and 1160 (none)
Info) Segments: 1
Info) Fragments: 7 Protein: 6 Nucleic: 0
Info) Finished with coordinate file /tmp/Col.PDB.
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: 0
clearing structure, preserving topology and aliases
WORKING ON: 0
pfrag: false ofrag: true allfrag: false osel: protein or nucleic nfrag: false
Info) Opened coordinate file Col.pdb for writing.
PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom 5263
                 cannot be written in PDB format.
                 File will be truncated.
ERROR) write_timestep returned nonzero
Info) Finished with coordinate file Col.pdb.
ERROR: Couldn't write temp files. Do you have enough disk space?
------

Two different ways it was tried
a) the first test was done on a machine with dual quad core Xeon, GeForce 9500 GT running FedoraCore14 with both official packages 1.8.7 and vmd-1.9beta1
b)the second test was done on a machine with dual quad core Xeon, no NVIDIA card running OpenSuse11.3. VMD was compiled from source package version 1.8.7 with MESA library.
On both tests:

/tmp and /var/tmp were both world-writeable
--------

Wondering if this is a bug in VMD. Because the error always (tried 3-4 times) occurs at or near amino acid 413 and at the atom where the Z coordinate changes from -999 to -1000.
Incidentally when I used a smaller version of the same PDB file upto 300 amino acids, I did not get the error and I could get PSF and later was also able to make a water-box.
This is one chain of 1160 aa, eventually I will have 3 chains and the system will be much bigger.

Any help/workaround would be appreciated.

Thank you.

Regards,
Sujata