VMD-L Mailing List
From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Tue Nov 22 2005 - 13:13:15 CST
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Hi,
I'm a new user of VMD. I'm trying to follow the NAMD tutorial to learn how to generate a psf file.
I'm running VMD on a Window XP machine, but NAMD is not installed there.
Here's what I did:
I did not use the files provided for tutorials available at UIUC website. Instead, I went to the Protein Databank to get the pdb file for ubiquitin.
I opened in VMD, and typed
set ubq [atomselect top protein]
$ubq writepdb ubqp.pdb
on the TkConsole.
I know the tutorial at this point tells me to close the console and to use the Unix terminal to type in the remaining commands, but if I try to do it in my DOS window it doesn't work (doesn't even know what package means). So, I keep the TkConsole open and continue typing commands in it:
package require psfgen
topology top_all22_prot.inp (I know it's not the one the tutorial recommends but I couldn't find that one in the CHARMM website. The closest I could find would be top_all27_prot_lipid.rtf but this led to the error message "ERROR! FAILED TO RECOGNIZE CMAP").
alias residue HIS HSE
alias atom ILE CD1 CD
segment U {pdb ubqp.pdb}
The feedback to this instruction is:
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
I'd really appreciate some help here as I have no idea what I'm doing wrong.
Thanks in advance,
Ana
_________________________________
Ana Célia Araújo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
USA
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846
_________________________________
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