VMD-L Mailing List

From: Sergio Anis (sergioanis_at_ispwest.com)
Date: Tue Nov 22 2005 - 15:58:42 CST

it's a version incompatibility problem, you can either delete all the CMAP references in the topology file or, the best option is to look for the topology file included in the tutorial's files

cheers
sergio

Ana Celia Araujo Vila Verde wrote:
> 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
>
> _________________________________
>
>
>