Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)

From: Ilyas Yildirim <>
Date: Wed, 14 Jun 2006 14:46:22 -0400 (EDT)

Dear Kara,

The content of the file u sent looks as follows:

ATOM 2609 ZN ZN 169 26.756 44.995 -1.234MTER MATOM 2610
ZN ZN 170 27.788 42.109 11.205MTER MEND M

When I load this .pdb, it will load only 1 atom. I have changed the way of
look of the contents as follows, and it worked ok (xleap sees 2 ZN atoms
in this case):

ATOM 2609 ZN ZN 169 26.756 44.995 -1.234
ATOM 2610 ZN ZN 170 27.788 42.109 11.205

Are you creating the .pdb files in Windows XP? I am always using joe/vi
kind of program in linux, and they dont put any unknown characters like
'M' in the file. Maybe if u follow Ross' suggestion, that might solve the
problem. Good luck.


On Wed, 14 Jun 2006, Kara Di Giorgio wrote:

> I'm attaching the file. It contains two Zn atoms that are part of my
> protein. I created an atom type for zinc and have a .lib file I'll
> attach also. (I tried this and the message was bounced back.)
> I've used the .lib file before and it worked fine. I actually already
> got the protein loaded into xleap and used it in Amber with some other
> analogs in the binding site. All I'm trying to do now is put some new
> substrates in the binding site. I used Midas to align the two pdb
> files and then was going to cut out the old substrate and replace it
> with the new one to get a pdb file with everything at the correct
> coordinates, something I did for the first analogs. This time, nothing
> will load. I'm not sure if it doesn't like the Midas-generated file,
> or what, as last time I didn't use Midas. However, I don't have access
> to another program to move the new analogs to the old one's site. It's
> frustrating that I can get something to work for one set of things, but
> then not for another, very similar, set of molecules.
> Thanks for the help,
> Kara Di Giorgio

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
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Received on Sun Jun 18 2006 - 06:07:09 PDT
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