AMBER Archive (2006)

Subject: RE: AMBER: Difficulty loading a pdb file

From: Ross Walker (
Date: Wed Jun 14 2006 - 09:05:34 CDT

Dear Kara,

> 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.)

Check the atom and residue names. If the atoms are in the same residue and
have the same name Leap will just assume they are duplicates and discard the
second one. Although you should see a message about this when you load the

> 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.

This can sometimes cause problems as well. The files should be in Unix text
format. Try running:

dos2unix my.pdb

this will strip and extra carriage returns from the ends of lines.
I can't offer much more advice without see the pdb in question I am afraid.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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