AMBER Archive (2005)

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

From: FyD (fyd_at_u-picardie.fr)
Date: Wed May 11 2005 - 11:06:27 CDT

Quoting Li Su <suli_at_msu.edu>:

> 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
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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