Dear Daniel,
You rock!! Thats exactly what I want. Got confused by seeing the scanning
option.
Tak
/SB
On Thu, Jun 4, 2015 at 5:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 04 2015 - 09:00:05 PDT
