Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb

From: Jason Swails <>
Date: Wed, 10 Sep 2014 08:08:41 -0400

On Wed, Sep 10, 2014 at 5:14 AM, <> wrote:

> Looks like the problem exists when the number of water molecules exceed
> more than 9999. Please try to find out why is so?

​You've already heard the explanation about why this is so. I'll chime in
with my 2c and say that ambpdb gives the _desirable_ behavior, in my
opinion. Most programs that I've seen are fairly strict when it comes to
expecting certain items to occupy certain columns in PDB files (they may be
less strict about requiring that all 'mandatory' fields be populated).
 When residue numbers go above 9999, the coordinates will be shifted by 1
character and could yield very strange visualization artifacts.

For instance, if you try viewing the PDB files with VMD, only the one
printed by ambpdb will actually render correctly for precisely this reason.
 In fact, if you use VMD to print out PDB files with atom and residue
numbers that overflow their fields, you may be even more surprised than by
what ambpdb does ;). VMD switches to a hexadecimal integer representation
once numbers no longer fit into their fields. So the residue numbers would
go from 9999 to 2710 and atom numbers would go from 99999 to 186a0 :).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Sep 10 2014 - 05:30:02 PDT
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