Error with ubqp.pdb in NAMD tutorial

From: Bob Masong (
Date: Mon Oct 24 2011 - 22:43:46 CDT

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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