AMBER Archive (2006)

Subject: AMBER: Difficulty loading a pdb file

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Tue Jun 13 2006 - 13:20:41 CDT

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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