AMBER Archive (2006)

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

From: Kara Di Giorgio (
Date: Wed Jun 14 2006 - 12:20:40 CDT

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

  • application/octet-stream attachment: znnew.pdb

On Jun 13, 2006, at 2:25 PM, Ilyas Yildirim wrote:

> 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
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