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

From: Ross Walker <>
Date: Wed, 11 May 2005 10:13:30 -0700

Dear Li

> 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

See this tutorial,

This explains a "quick and dirty" way of making NMA which is ACE+NME. You
could easily adapt this to include ACE+ALA+NME for alanine dipeptide.

I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Wed May 11 2005 - 18:53:00 PDT
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