Hi Dan,
I added something like this
trajin md_totalsparse.nc
debug action 1
multidihedral phihedrals phi resrange 70-90 out Phi-70-90-test.dat
Am I doing anything wrong as the atom numbers corresponding to phi dihedral
is not printing out.
Thanks in advance.
/SB
On Fri, Jun 5, 2015 at 10:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
--
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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Received on Mon Jun 08 2015 - 03:00:03 PDT
