Re: AMBER: Asking how to creat alanine "dipeptide" in amber8

From: FyD <>
Date: Wed, 11 May 2005 18:06:27 +0200

Quoting Li Su <>:

> Sorry to bother. I'm wondering how to creat a structure of alanine
> dipeptide in amber. For alanine dipeptide is not a real dipeptide and
> actually is N-acetyl-alanine-N'-methylamide, I can't load the correct
> structure into amber. I have used INSIGHT II to creat the pdb file for the
> alanine dipeptide. But I can not use it directly as the input file for amber
> Leap, for it is not composed of regular residues thus some atoms can't be
> recognized. And I also tried antechamber, it seemed to me I had to treat the
> whole "alanine dipeptide" as a unit, say just like a organic small molecule.
> And also if I do this way, I still meet some problem in using the prmtop and
> inpcrd files generated this way when launching Sander.
> So I'm wonder if somebody knows the situation can reply the email. Thanks a

The diff. between PDB atom names in insightII & AMBER/LEaP are the hydrogen atom
names: Just save your di-peptide in insightII without the hydrogens and load the
corresponding PDB file in LEaP. Then, LEaP will add the missing hydrogens using
its own hydrogen atom name convention.

Regards, Francois

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
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Received on Wed May 11 2005 - 17:53:00 PDT
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