AMBER Archive (2006)

Subject: Re: AMBER: solvation and His protonation

From: David A. Case (
Date: Mon Oct 30 2006 - 18:34:05 CST

On Sat, Oct 28, 2006, Jardas sucuriba wrote:
> a) I solvated my protein with a truncated octahedron of waters, with a
> total number of waters around 14000. When I used ambpdb to create the
> corresponding pdb file the numbering of residues started again after 9999.
> So, I have residues with the same number. I wonder if someone could tell me
> if this is a problem just with ambpdb or if the top and crd files are also
> wrong? Is sander able to interpret each residue as unique when running
> the MD?

The topology and coordinate files should be fine. The PDB format allows only
four digits for residue number, so it is not possible to have a conforming
file with more than 9999 residues. The ambpdb program just starts over again,
as you have seen. If users on the list have a better idea, (or a better
understanding of what *should* be done per the PDB standard), I would be happy
to make modifications to the ambpdb program.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to