Hi,
On Thu, Jun 4, 2015 at 2:36 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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
>
The 'dihedralscan' command is one of several poorly named commands in
cpptraj. As you can see from the online help and/or the manual, the sole
purpose of 'dihedralscan' is rotating dihedrals in intervals or randomly
(so perhaps the command name should be changed to rotatedihedrals...). If
what you want to do is calculate dihedral angles in a certain residue range
you want the 'multidihedral' command, e.g.
multidihedral MyDihedrals phi psi resrange 60-80 out PhiPsi-60-80.agr
See the manual for full details on the command. Hope this helps,
-Dan
>
> 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
> scanning.
>
> 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.
>
> Regards,
> SB
>
> --
> 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
> in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 04 2015 - 09:00:03 PDT
