Re: Error with ubqp.pdb in NAMD tutorial

From: Jens K. Munk (
Date: Tue Oct 25 2011 - 02:10:22 CDT

Hi Bob,

The command to write data in variable "ubq" to a .pdb file is:

> $ubq writepdb ubqp.pdb

The dollar sign calls the variable "ubq" and is important.



Venlig hilsen / Kind Regards
M. Sc. Jens K. Munk
Department of Basic Sciences and the Environment
Room T432
Phone +45 3533 2429
Thorvaldsensvej 40
DK-1870 Frederiksberg
>>> Bob Masong <> 25-10-2011 05:43 >>>
Hello VMD,
I am a novice user of VMD and NAMD. In the past I was successful with my first
run of NAMD, however of late I am struggling to run the tutorials included with
NAMD. I went through the tutorial believing that all is well and now it was
time to run this command: " vmd -dispdev text -e ubq.pgn ". This is
where I ran into a wall. I got an error and the output looked like this:
reading topology file
> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
>>>>>> Includes phi, psi cross term map (CMAP) correction
July 2004   
All comments to ADM jr. via the CHARMM web site: 
parameter set discussion forum
Created by CHARMM version 31 1
cross-term entries present in topology definitions
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment U
ERROR: Unable to open pdb file ubqp.pdb to read residues
MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
ERROR: failed while building segment
MOLECULE MISSING!  Use resetpsf to start over.
MOLECULE MISSING!  Use resetpsf to start over.
MOLECULE MISSING!  Use resetpsf to start over.
MOLECULE MISSING!  Use resetpsf to start over.
I thought I had done something wrong so I checked my steps carefully but I
repeated the previous steps many many times over and over and this did not
change anything. I decided to take a look at the file "ubqp.pdb" and
I found out that the file had no coordinates in it, in fact the pdb file
contained only two lines and looked like this:
original generated coordinate pdb file
Immediately I realized that VMD was not able to write the pdb file. Thus, I
went back and repeated the steps that involved the creation of ubqp.pdb and
nothing worked.
When I follow the commands in the namd-tutorial file I get an error message
that I have ignored for sometime. It did not bother me in the past but now I
have to ask.
Below is the output in the window of TkConsole whiles trying to create
loading history file ... 32 events added
Main console display active (Tcl8.5.6 / Tk8.5.6)
(1-1-build) 33 % set ubq [atomselect top protein]
>Main< (1-1-build) 34 % ubq writepdb ubqp.pdb
invalid command name "ubq"
>Main< (1-1-build) 35 % writepdb ubqp.pdb
Info: writing pdb file ubqp.pdb
Info: pdb file complete.
>Main< (1-1-build) 36 % 
The error I get after line 34 does not show up after I type in line 35. I'm not
sure why this is but I did everything as specified by the tutorial but it still
does not work. The pdb file created by VMD in the TkConsole is an empty file.
Please Help.
Bob M.

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