Re: [AMBER] protonate a non standard residu

From: Jason Swails <>
Date: Fri, 12 Nov 2010 11:34:55 -0500

The only way leap knows how to protonate certain species is if a library is
created with the protonated form, and that proton is in the template. My
suggestion is to create such a template with a new name. For instance, you
can follow the protocol used for protonated amino acid residues. I'll use
aspartate as an example.

ASP is an aspartate that is in its most likely protonation state at neutral
pH. Namely, it is deprotonated. ASH is the protonated form of ASP.
Therefore, if you go through a PDB and rename the ASP residues that you want
protonated to ASH, LEaP will add those protons for you, but only because it
was in the ASH template to begin with.

Likewise, if you have residue X, you should create a residue template (mol2,
amber prep, or OFF library) for XH, and load that into leap, taking care to
change the name of the X residue in your PDB to XH.

Hope this helps,

On Fri, Nov 12, 2010 at 11:19 AM, Philippe Pinard <>wrote:

> Dear Amber users
> I have a molecule which contains many non standard residus I created. I
> want to
> protonate these residus at specific N positions, is thee a straightforward
> way
> to do it with leap, without having to protonate by hand all the pdb file?
> Thanks very much in advance for any help
> regards
> PP
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Nov 12 2010 - 09:00:03 PST
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