VMD-L Mailing List

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Tue Nov 22 2005 - 13:13:15 CST

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

avilaverde_at_engr.psu.edu

_________________________________