AMBER Archive (2008)

Subject: AMBER: Ptraj pucker for pyranose

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Mon Oct 13 2008 - 04:43:33 CDT

Hi,
I am using Amber 9 and needs to calculate puckering for 6 member ring system
from md trajectory.
How do I calculate puckering for pyranose ie. O5/C1/C2/C3/C4/C5 in a six
member ring system? I checked amber 9 manual where pucker takes 5 atoms. Has
anybody tried for Cremer-Polpe for six member?

Your help is much appreciated. 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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