From: Jens K. Munk (jkm_at_life.ku.dk)
Date: Tue Oct 25 2011 - 02:10:22 CDT
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 Ph.D.-student Department of Basic Sciences and the Environment KU-LIFE Room T432 Phone +45 3533 2429 Thorvaldsensvej 40 DK-1870 Frederiksberg Denmark >>> Bob Masong <mack5sum5_at_hotmail.com> 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 top_all27_prot_lipid.inp > 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: www.charmm.org 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: REMARK original generated coordinate pdb file END 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 ubqp.pdb: 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] atomselect0 >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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