Polypeptide alpha-helix with Amber 3.0
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 ^at^ SEISMO.CSS.GOV