[AMBER] Regarding dihedral scanning

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Thu, 4 Jun 2015 10:36:21 +0200

Dear Amberists,

I wish to perform a dihedral scanning within A residues ranging from 60-80
within a beta-hairpin structure. I guess the dihedralscan keyword will find
all possible dihedrals within this residue range

so I guess my input should be something like this

trajin md_total.nc
dihedralscan resrange :60-80 phi out dihedral.dat

But is there any need of specifying the interval and random keywords in
this case. Actually I partially understand the utility of these keywords in

I guess the interval keyword is necessary when we want to create a
trajectory by rotating specified dihedrals in a structure by regular
intervals but hence I just want to scan the trend of regular dihedrals I
don't need to add the interval as well as random keywords.

Please let me know if I understand it correctly or there is any mistake.

Thanks in advance for your support.


Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
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Received on Thu Jun 04 2015 - 02:00:03 PDT
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