Hi,
Not sure if this is the problem, but there is currently an issue with the
order of argument parsing in 'multidihedral' (bugfix pending). Try framing
your command like so instead (it's worth a shot):
multidihedral phihedrals phi out Phi-70-90-test.dat resrange 70-90
The output you get with 'debug actions 1' and 'multidihedral' should look
something like this:
[multidihedral chin out chin.dat resrange 274-306 ]
MULTIDIHEDRAL: Calculating chin dihedrals for residues in range 274-306
Output to chin.dat
Output range is -180 to 180 degrees.
...
ACTION SETUP FOR PARM 'nowat.8OG.parm7' (1 actions):
0: [multidihedral chin out chin.dat resrange 274-306 ]
Warning: Dihedral chin not found for residue 306
ResRange=[274-306] chin, 32 dihedrals.
DIH [chin:274]: :274.4338 :274.4339 :274.4341 :274.4354
DIH [chin:275]: :275.4370 :275.4371 :275.4373 :275.4387
DIH [chin:276]: :276.4403 :276.4404 :276.4406 :276.4420
and so on.
-Dan
On Mon, Jun 8, 2015 at 3:48 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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/
> _______________________________________________
> 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 12 2015 - 13:00:02 PDT
