VMD-L Mailing List

From: Alilovic,Kata (alilovickata_at_ufl.edu)
Date: Fri Jul 03 2020 - 12:55:10 CDT

Dear Peter ,

I am using pdb file from Protein Data Bank. I saved 1UBQ using Tk console as instructed. (https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html)
When using Tk Console for generating PSF file I used lines from the tutorial :
package require psfgen
topology top_all27_prot_lipid.inp.

After writing the line for topology file I get the error unable to open topology file top_all27_prot_lipid.inp. Molecule destroyed by a fatal error. Use resetpsf to start over.

 I tried creating PSF file for 3GHG, 1CAG, 1CSN and it did not work.

When using Automatic PSF Builder I get 7 suggested topology files automatically as input files. If I load them all, it is taking forever. If I leave only topology file for protein it runs but I do not get psf file.
Also when using the Automatic PSF Builder I tried uploading different topology files for proteins but it never gives me psf file.

Can I use http://www.charmm-gui.org/ website to create psf file and use it in vmd ?

Thank you,

Kate

________________________________
From: Peter Freddolino <petefred_at_umich.edu>
Sent: Thursday, July 2, 2020 8:05 PM
To: Alilovic,Kata <alilovickata_at_ufl.edu>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Unable to create PSF file

[External Email]
Dear Kate,
Can you tell us what pdb you're trying to use? Does it work with a simple example like the ubiquitin PDB from the tutorials? What text is written to the console when you run it?
Thanks,
Peter

On Thu, Jul 2, 2020 at 7:19 PM Alilovic,Kata <alilovickata_at_ufl.edu<mailto:alilovickata_at_ufl.edu>> wrote:
I run into an issue when creating a psf file while using Automatic PSF Builder. After I upload the PDB file and set the PSF builder, VMD shuts down and in the terminal, it says process completed. I do not get psf file in the end. When I load pdb file and run Automatic PSF Builder I get autopsf-temp_top, autopsf-temp.xbgf, and autopsf_formatted.pdb file. Also when I try using the Tk Console following the example given in the tutorial I get an error saying that it can not open the topology file and that molecule destroyed is destroyed by fatal error. I have the newest version of VMD for Mac.
I would appreciate any advice on how to solve this.

Best,
Kate