From chemistry-request*- at -*ccl.net Tue Apr 23 21:38:29 1991
Date: Wed, 24 Apr 91 11:14:37 +1000
From: apa -A_T- ccadfa.cc.adfa.oz.AU (Alan P Arnold)
Subject: Polypeptide alpha-helix with Amber 3.0
To: chemistry: at :ccl.net
Status: R

Thanks to all those who replied to my earlier request for
creating MIN coordinate files from MD trajectories.

Now, another problem.  I have created an 8-mer of Alanine
with neutral terminii, using Amber.  The starting 'conformation'
created by LINK/EDIT/PARM is an extended chain.  I want to
get the (Ala)8 into an alpha-helix.  Naively, I thought that
using constraints on the H-bond distances between the ith NH
and i+3'th carbonyl-O (of about 2.0A with 'energy' of 10kcal)
should spring the peptide pretty close to alpha-helical.  No way.
Further contstraining the H-bond angles to near 180deg as well
as H-bond distance constraints still doesn't work.  All this
'constraining' is done in PARM.

I am obviously doing something wrong here.  How do I force such
a peptide into an alpha-helix? 

A secondary question obviously arises - what is the likelihood
that MIN (or any minimiser) will find the alpha-helical conformation
starting from an extended chain?

Thanks again.

----
Alan Arnold             	     |  Phone: +61 62 68 8080
Chem. Department,University College  | ACSNET: apa ^%at%^ ccadfa.oz 
Australian Defence Force Academy     |   UUCP: ...!seismo!munnari!ccadfa.oz!lpb 
CANBERRA  ACT 2600 Australia         |   ARPA: apa%ccadfa.oz -8 at 8- SEISMO.CSS.GOV