VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 06 2009 - 09:55:29 CST

Luis,
  When he says "sourcing" he means that you should download that script
to your local computer, put it in a directory where you can get to it
with VMD, and then run the command "source autopsf.tcl" in the VMD
text console (or TkCon) before you first open up the AutoPSF window
in the graphical user interface. If you're not familiar with VMD
text commands, this might be a good opportunity to briefly try out
one of the VMD tutorials so you become familiar with how to run scripts
like this one.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 06, 2009 at 10:58:19AM +0100, Luis Agullo (LAB) wrote:
> Peter,
>
> I do not completely understand what you mean. Could you explain me what I
> should do step by step? Thank you very much in advance,
>
> Luis
>
>
> > Hi Luis,
> > I found what appears to be the problem -- please try sourcing the
> > autopsf script at www.ks.uiuc.edu/~petefred/autopsf.tcl prior to opening
> > the gui, and things should work again.
> > Thanks for pointing this out.
> > Best,
> > Peter
> >
> > Luis Agullo (LAB) wrote:
> >> Of course! I include one of the pdb used attached to this mail.
> >>
> >> The process is simple, because I use most of the automatic options found
> >> in autopsfgen: I open autopsfgen, load the specific stream file for ATP
> >> in
> >> addition to the standard topology file, select 'Guess and Split Chains'
> >> and afterwards I 'Feel Lucky' and obtain the final autopsf file.
> >>
> >> Using the same procedure, the previous version maintains Mg2+ in the
> >> output files.
> >>
> >> IMPORTANT NOTES:
> >> - I use VMD 1.8.7 for Windows!
> >> - I observed a difference between VMDs when splitting chains (previous
> >> version of VMD recognize the 2 atoms of Mg2+ in positions 6018 and 6019
> >> of
> >> the pdb file; however, the present version found 2 atoms of Mg2+, but at
> >> positions 6018-12037!?; I attached 2 images to show these different
> >> results).
> >>
> >> Luis
> >>
> >>
> >>
> >>
> >>> Hi Luis,
> >>> could you please send me your input pdb and give me an exact set of
> >>> steps for reproducing the problem?
> >>> Thanks,
> >>> Peter
> >>>
> >>> Luis Agullo (LAB) wrote:
> >>>
> >>>> Hello,
> >>>>
> >>>> I have problems with the last version of VMD (VMD 1.8.7). When using
> >>>> autopsfgen with a file including Mg2+ (or Ca2+) cation is excluded
> >>>> from
> >>>> the output file. This does not take place with the previous of VMD
> >>>> version
> >>>> using the same files. I am using the new version for Windows, I have
> >>>> not
> >>>> been able to check this in Linux version.
> >>>>
> >>>> Cheers,
> >>>> Luis
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>> ------------------------------------------------------------------------
> >>>
> >>>
> >>> ------------------------------------------------------------------------
> >>>
> >
> >
> >
> >
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078