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

From: Daniel Roe <>
Date: Wed, 10 Sep 2014 07:43:30 -0600

On Wed, Sep 10, 2014 at 3:22 AM, Thomas Cheatham <> wrote:
> ambpdb is an old program and technically is not doing the wrong thing
> since the PDB format only allows 4-digits for the residue number. You can
> try to fix the program to how you think it should be behave or find a work
> around (such as to use CPPTRAJ or an alternative coordinate format).

Actually cpptraj behaves the same way as ambpdb in this respect:
residue numbers are wrapped to 1 when they become greater than 9999 in
PDB format. However, you can use cpptraj to write out in mol2 format,
which doesn't have the same issue.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Sep 10 2014 - 07:00:02 PDT
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