Actually both ptraj and cpptraj take four atom masks (each of 1 or
more atoms) to describe dihedrals, which is stated in the AmberTools
manual (here is the excerpt for ptraj):
"Calculate the dihedral angle for the four atoms listed in mask1
through mask4 (representing rotation about the bond from mask2 to
mask3). If more than one atom is listed in each mask, treat the
position of that atom as the center of mass of the atoms in the mask."
So something like "dihedral d1 :1 :2 :3 :4" will use the centers of
mass of the atoms in residues 1, 2, 3, and 4 to calculate the
dihedral.
-Dan
On Thu, Aug 25, 2011 at 10:34 AM, Massimiliano Porrini
<M.Porrini.ed.ac.uk> wrote:
> Dear all,
>
> I would need to work out the time series of the dihedral angle
> of a quadruple of centres of mass of groups of atoms
> (rather than of single atoms).
>
> I had a look at the AmberTools manual (and at the mailing list
> archives) and as far as I understood
> the Mask of groups of atoms works only for the "distance" command.
>
> Any hint would be really appreciated.
>
> Cheers,
> MP
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
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>
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Received on Thu Aug 25 2011 - 08:30:04 PDT
