Hi,
If you enter:
debug action 1
before the multidihedral command some extra info including detected
dihedral residue and atom #s should be printed out.
-Dan
On Fri, Jun 5, 2015 at 3:45 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Dear Daniel,
>
> Can I add a print keyword to see the atom numbers which contributes in the
> formation of phi or psi angles?
>
> Thank you once again.
>
> Best regards,
> SB
>
> On Thu, Jun 4, 2015 at 5:49 PM, Soumendranath Bhakat <
> bhakatsoumendranath.gmail.com> wrote:
>
> > 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/
> >
> >
>
>
> --
> 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
Received on Fri Jun 05 2015 - 13:30:03 PDT
