AMBER Archive (2006)

Subject: Re: AMBER: solvation and His protonation

From: Jardas sucuriba (
Date: Tue Oct 31 2006 - 07:07:24 CST


Thanks Dr. Case.
I have a very basic question about histidine protonation. What is the
preferable form of a surface-accessible histidine?


>From: "David A. Case" <>
>Subject: Re: AMBER: solvation and His protonation
>Date: Mon, 30 Oct 2006 16:34:05 -0800
>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
> > So, I have residues with the same number. I wonder if someone could tell
> > if this is a problem just with ambpdb or if the top and crd files are
> > 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
>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
>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
>to make modifications to the ambpdb program.
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