On Tue, Mar 29, 2016, Michael Shokhen wrote:
>
> I need to calculate rmsd of torsion angle between atoms where one residue
> belongs to ligand and another to protein.
>
>
> rms ToFirst :111.1820 :111.1823 :186.2978 :186.2979 first out rmsd_tors_ser111_ala186.agr time 10000 mass
>
The "rms" command only takes a single mask, not four masks like you have.
What you (may) want is the "dihedral" command, which will create a dataset of
dihedrals (one value for each snapshot in the input trajectory. You could
then analyze that data on your own, or with one of cpptraj's dataset analysis
tools.
If you want the (Cartesian) rmsd of the four atoms listed above relative
to where those atoms were in the first frame, replace the four masks above
with one: ':.1820,1823,2978,2979'. But it doesn't seem (to me!) like this
would be a very useful thing to compute.
[Aside: if you give an atom number, you don't need the residue number as well:
:111.1820 is the same as .1820, assuming that atom 1820 is in residue 111.]
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 29 2016 - 10:00:03 PDT
