VMD-L Mailing List

From: Samuel C Flores (samuel.flores_at_yale.edu)
Date: Wed Jun 21 2006 - 14:12:41 CDT

Hi John,

We used pdbalias just as in the ubiquitin tutorial. We figured out that the
usual pdbalias ILE CD1 CD is just to put the input file into the naming
convention used in VMD's topology files; it does not do anything to the
output files.

We ended up using VMD to add hydrogens and perform other operations, then
wrote our own perl script to change the atom names to the amber convention,
which was needed to apply partial charges. Ultimately we are generating
PDBQ and PDBQS files for AutoDock.

We solved our problem using a perl script as described, but it still seems a
bit of a hack -- if there is a way to use pdbalias to change the output
files to some naming convention other than that used in VMD's topology
files, we would like to know about it.

Many thanks

Sam

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Wednesday, June 21, 2006 2:56 PM
To: Samuel C Flores
Cc: 'Juan de Dios Lopez Castro'; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: pdbalias not working

Hi,
  Can you be more specific about the sequence of operations you're
performing, so we can determine if you're using it correctly etc?
If you've already solved your problem, ignore this email.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 15, 2006 at 10:42:06PM -0400, Samuel C Flores wrote:
> For some strange reason pdbalias seems to be doing nothing. I am using it
> pretty much as indicated in the literature, but no amount of futzing will
> get it to affect the output. Is there some magic dance that needs to be
> done?
>
> Sam
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
Of
> John Stone
> Sent: Thursday, June 15, 2006 4:38 PM
> To: Juan de Dios Lopez Castro
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: error Autoimd
>
> Hi,
> What file(s) do you have loaded when this occurs?
> Can you tell us the sequence of operations you're performing that
> leads to this error? What values did you type into the various
> entry fields before submitting the job?
> I'll need to communicate this information to the individual
> that wrote the autoimd plugin.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jun 15, 2006 at 11:04:02AM +0200, Juan de Dios Lopez Castro wrote:
> > Hi all,
> >
> > I have posted a menssage about autoimd. You had asked me about the
> > versión of vmd. I don't know repost, so I going to post it other
> > time.
> >
> > I have tried AUTOIMD on windows and Fedora Core 2. I get always
> > the same error:
> >
> > atomsel: frame -1 out of range for molecule 1
> > atomsel: frame -1 out of range for molecule 1
> > while executing
> > "$all writepdb "$pdbfile""
> > (procedure "initparams" line 49)
> > invoked from within
> > "initparams"
> > (procedure "AutoIMD::submit" line 12)
> > invoked from within
> > "AutoIMD::submit "$AutoIMD::settings::moltenseltext""
> > invoked from within
> > ".autoimd.win.controls.submit invoke"
> > ("uplevel" body line 1)
> > invoked from within
> > "uplevel #0 [list $w invoke]"
> > (procedure "tk::ButtonUp" line 22)
> > invoked from within
> > "tk::ButtonUp .autoimd.win.controls.submit
> > "
> > (command bound to event)
> >
> > The versión of VMD is 1.8.4
> >
> > Thank you
> >
>
> --
> 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
>
> 

-- 
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