VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Jul 03 2020 - 13:01:33 CDT

Dear Kate,
Please see below for answers which I hope will clarify several points.

On Fri, Jul 3, 2020 at 1:55 PM Alilovic,Kata <alilovickata_at_ufl.edu> wrote:

>
> 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.
>

Just to be clear, when you try doing things this way, you are using psfgen,
not autopsf. The error message that you got is informative -- it means you
don't have a topology file matching the name that you specified in the
current working directory. Please specify the full path to that file (and
make sure that you didn't add a '.' to the end of the file name where it
doesn't belong). You should then be able to proceed following the steps in
the tutorial.

>
> 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.
>
Can you specify how you tried to run it? Did you click the 'I'm feeling
lucky" button or go through the interface step by step? Is any output
generated on the console? It should really be quite fast.

> Also when using the Automatic PSF Builder I tried uploading different
> topology files for proteins but it never gives me psf file.
>
I don't know how I can provide any useful reply without knowing what
topology files or what proteins you tried.

>
> Can I use http://www.charmm-gui.org/ website to create psf file and use
> it in vmd ?
>
> This depends very much on your purpose. Use it in vmd? Yes. Use it in
namd? Perhaps someone else with experience using charmm-gui can comment -
there are some subtle formatting differences in psf files between different
software, so I suspect this could cause issues.

Best,
Peter

> 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> 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*
>
>