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

From: Thomas Cheatham <>
Date: Wed, 10 Sep 2014 03:22:18 -0600 (MDT)

> Looks like the problem exists when the number of water molecules exceed
> more than 9999. Please try to find out why is so? is simply overflow of the PDB format which cannot accomodate RESID's
greater than 9999 as per the standard (search the WWW for PDB format)...
The only "correct" way around this would be to start to use chain ID's.

> > There is problem when pdb file is created using "ambpdb" command. The ATOM
> > numbers are correct but Water residues (WAT) are not numbered correctly.
> > In the test.pdb file after resid 9999, residue numbering starts again with
> > 0, 1, 2......3216. This number does not match with topology file. When I
> > tried with other PDB file it shows the same thing. That is after resid
> > 9999, renumbering starts again.

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).


AMBER mailing list
Received on Wed Sep 10 2014 - 02:30:02 PDT
Custom Search