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From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Apr 12 2010 - 08:45:13 CDT
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By IUPAC angles I meant the amino acid side-chain (chi_n) angles as defined
by the IUPAC body <http://www.iupac.org/> by the rules defined
here<http://www.chem.qmul.ac.uk/iupac/misc/ppep1.html#160> (this
is quite an old document, but I believe the rules are still valid). The
problem is choosing the "principal torsion angle" as defined
here<http://www.chem.qmul.ac.uk/iupac/misc/ppep1.html#220>.
Basically, heavier atoms have priority, so the principal torsion angle
around one bond is the one formed by the heaviest atoms.
I think I will just have to sit down and define the principal torsion angle
of each amino acid by hand. Then I can define a TCL function that returns a
list quadruples of atoms names comprising all the side-chain principal
torsion angles and use that in a selection macro.
Or even more likely, I will just export the 40000 frames I currently have to
pdb files and analyse them using bioshell. This will be less efficient in
term of processor time, but probably it will be quicker than developing a
new tcl script in terms of my time.
Since atom names differ among various forcefields I think this would be
difficult to implement in a consistent manner using topotools.
thank you for your help,
Ajasja
On Mon, Apr 12, 2010 at 15:08, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, 2010-04-12 at 13:38 +0200, Ajasja Ljubetič wrote:
> > Yes, I have tried that, actually. But I get too many dihedrals (not
> > just the IUPAC Chi1, Chi2 .. Chi4 but all possible dihedral angle
>
> you get all the dihedrals that you feed VMD. like all _good_
> programs, VMD does not make many assumptions about your data.
> it just processes what you give it to work with and then it
> is up to you to tell it how to trim it down. can you please
> explain what you understand under IUPACK dihedrals?
>
> if it is easy enough to implement, i could consider adding
> a special case version for that. or even add some commands
> to the high-level tools that allow to do the whole shebang.
>
> > combinations). I have not yet figured out how to filter them.
> > What is the first value in the list of dihedral angles? The 'topo
> > getdihedrallist -sel "protein and resid 18"' returns a list of lists
> > {unknown 215 217 223 224} {unknown 215 217 219 220} .... Does
> > "unknown" refer to the dihedral name? Or is the type meant to be
> > improper or dihedral angle?
>
> "unknown" refers to the force field type. in charmm class force field
> this type is not stored in the topology file but inferred from the
> atom type and the corresponding parameters are read from the parameter
> file that you have to feed the simulation software. with 'topo
> retypedihedrals' you can generate canonical dihedral types from
> the atom types (note that those are canonicalized, i.e. not simple
> the corresponding atom types concatenated. in other MD programs
> dihedrals are identified with distinct type names or numbers and
> thus VMD allows to store those.
>
> hope that helps,
> axel.
>
> > I'm using the 1.1 version of topotools. And I have loaded the molecule
> > from a psf/pdb combination.
> >
> >
> > Best regards,
> > Ajasja Ljubetič
> >
> > On Mon, Apr 12, 2010 at 12:43, Axel Kohlmeyer <akohlmey_at_gmail.com>
> > wrote:
> > On Mon, Apr 12, 2010 at 4:43 AM, Ajasja Ljubetič
> > <ajasja.ljubetic_at_gmail.com> wrote:
> > > Dear all,
> > > I hope this does not count as a cross post (as I have asked
> > a similar
> > > question on the NAMD mailing list as well).
> > > For each frame of my trajectory I would like to calculate
> > all the
> > > side-chain dihedral angles. Similar to the output of
> > > this webservice. Currently I'm planing to export each frame
> > of
> > > the trajectory to PDB and using the
> > excellent Bioshell to calculate dihedral
> > > angles, but probably it would be faster to do this without
> > all the temporary
> > > PDBs (I will have to analyse a lot of short 10 ns
> > trajectories).
> > > A possible way would be to add labels for all the
> > side-chains using "label
> > > add Dihedrals". Could anyone suggest a simpler way?
> >
> >
> > not sure about simpler, but definitely more efficient would be
> > to use tcl scripting in VMD.
> >
> > you can get the list of dihedrals from the topotools plugin
> > (or even use the generate those, in case you don't have
> > a suitable topology file with existing definitions. topotools
> > commands accept a -sel option that you can give a selection
> > string or a selection command as argument, which would
> > restrict the list to dihedrals fully contained in the
> > sidechain.
> >
> > then you can loop over those and either use the measure
> > or label command to compute the dihedral angle values
> > for your trajectory. probably label would be more efficient.
> >
> > cheers,
> > axel.
> >
> >
> > > Thank you,
> > > Ajasja Ljubetič
> > > Young researcher at Jozef Stefan Instiute,
> > > Slovenia, Ljubljana
> >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> > http://sites.google.com/site/akohlmey/
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
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