oops!
Thank you a lot Dan.
I actually had a go, but I forgot to type the internal variable "d1".
Now it worked.
Thanks again.
As far as AmberTools manual is concerned I came across the
`dihedral' occurrence at Pag. 152, 7.6.3 section (CPPTRAJ), where
only atoms are mentioned, whereas in the following section
(distance) also atoms groups are.
All the best,
MP
2011/8/25 Daniel Roe <daniel.r.roe.gmail.com>:
> 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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--
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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Received on Thu Aug 25 2011 - 08:30:05 PDT
