VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Wed Aug 06 2014 - 10:06:00 CDT

Rangeen,

You have mentioned a couple of different problems in your email below. Regarding:

> And in the tutorial RBCG pdf file I do
> not understand this "If you are using AutoPSF plugin, uncheck “Regenerate
> angles/dihedrals” under Options" because there is no option like that

The section of the tutorial you are describing (at the bottom of page 10 and top
of page 11) is describing the 'Automatic PSF Builder' plugin (also known as
AutoPSF) at that point. If you go to the AutoPSF plugin as described in the
tutorial it does have the Option menu, which has a line for Regenerate
Angles/Dihedrals. The tutorial is telling you to make sure that there is not a
checkmark in front of that line.

The other error you are describing is, most likely, an issue with Windows 7 not
having permissions to write to the proper directory.

Do you have an error earlier in your console saying something like:

ERROR: Couldn't write temp files. Do you have enough disk space?

You will need to be in a directory where you have permission to write as well as
sufficient disk space.

Kirby

On 08/06/2014 06:30 AM, Rangeen Othman wrote:
> Dear VMD users,
>
> Anyone is willing to help, whenever I wanted to build a psf for
> "cg_01-AA-lipoprotein.pdb" on the RBCG tutorial from AutoPSF builder at the
> end give me the following error. And in the tutorial RBCG pdf file I do
> not understand this "If you are using AutoPSF plugin, uncheck “Regenerate
> angles/dihedrals” under Options" because there is no option like that. By
> the way my VMD is 1.9.1. and I am working on windows 7, I have downloaded
> the RBCG files which works on windows as well.
> error deleting "cg_01-AA-lipoprotein_autopsf-temp.pdb": permission denied
> error deleting "cg_01-AA-lipoprotein_autopsf-temp.pdb": permission denied
> while executing
> "file delete $tempfile"
> (procedure "clean_tempfiles" line 3)
> invoked from within
> "clean_tempfiles"
> (procedure "makepatches_gui" line 78)
> invoked from within
> "makepatches_gui"
> (procedure "::autopsf::afterchains_gui" line 103)
> invoked from within
> "::autopsf::afterchains_gui"
> invoked from within
> ".autopsf.chains.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 24)
> invoked from within
> "tk::ButtonUp .autopsf.chains.finish"
> (command bound to event)
>
> I have tried to do for any other examples "protein" it gives me the same
> error. I have uninstalled VMD and installed it again but still the same.
> Please do you have any idea what is this?
>
> Thanks in adavance
> Rangeen
> 

-- 
Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email: kvandivo_at_ks.uiuc.edu          3061 Beckman Institute
http://www.ks.uiuc.edu/~kvandivo/    University of Illinois
Phone: (217) 244-5711                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA