AMBER Archive (2006)

Subject: Re: AMBER: Difficulty loading a pdb file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jun 13 2006 - 16:25:27 CDT

Can u copy/paste or send the .pdb file u are trying to load in xleap?

On Tue, 13 Jun 2006, Kara Di Giorgio wrote:

> I have a pdb file containing just two atoms and when I load it in xLeap
> it makes a file with just one of the atoms.
>
> (I'm working with part of my full pdb file as I'm trying to narrow down
> where the problem is.)
>
> My pdb file was generated with Midas on a SGI, but I'm using xLeap on a
> Mac. I'm using TextEdit to edit the pdb files.
>
> I was having similar problems late last week with a different file and
> my computer-scientist husband looked at two files, on that worked and
> one that didn't (both looked identical on visual inspection) and
> applied a file comparison program. He found that the line return
> character was different. I resolved that problem by pasting the
> "important" information from the one that didn't work in to the older
> file that did keeping the beginning and end of the lines the same.
> I've tried that for this and can't get it to work.
>
> Has anyone else ever had this problem? If so, how did you deal with
> it? Why would it load only one of two atoms and give no error message?
> The leap log says "terminal/last, was not found in name map. total
> atoms in file: 1."
>
> Any help would be greatly appreciated.
>
> Kara Di Giorgio
> University of the Pacific
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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