AMBER Archive (2005)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 11 2005 - 12:13:30 CDT

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,
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_Six/index.htm

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
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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