Hi,
In addition to what Carlos said, you may want to keep track of the
angle between the rings (to e.g. distinguish edge to face/face to face
stacking). You can get the angle between the ring faces by 1) using
the 'vector' action with the 'corrplane' keyword for the rings, which
will calculate a vector perpendicular to the plane that passes through
the atoms you select, then 2) using the 'vectormath' analysis with the
'dotangle' keyword to calculate the angle between those vectors. One
wrinkle with this however is that there's really no controlling the
direction of the vectors calculated with 'corrplane', so the vectors
may be pointing in the same direction (in which case perfect face to
face stacking would have an angle of 0 deg.) or in opposite directions
(where perfect face to face stacking would have an angle of 180). As
long as you're aware this can happen it's not hard to take it into
account. I've toyed with the idea of making a 'stack' action/analysis
but my to-do list is already pretty sadly neglected...maybe one day...
-Dan
On Sun, Dec 13, 2020 at 6:50 AM Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
>
> if you list several atoms in the group it will calculate the center of mass
> for the group.
> for example, this cpptraj command calculates the distance between the
> centers of mass of the aromatic rings in Phe residues 21 and 45
>
> distance D1 :21.CG,CD1,CD2,CE1,CE2,CZ :45.CG,CD1,CD2,CE1,CE2,CZ out
> distance.FF-COM.dat
>
> On Sun, Dec 13, 2020 at 6:18 AM Athena N <athena.nas01.gmail.com> wrote:
>
> > Hi,
> >
> > I would like to know how could we calculate the stacking distance of a
> > ligand ring to the amino acid/ nucleic acid ring over the trajectory in
> > cpptraj. The “distance” options gives the value between the atoms. But if
> > we have to calculate it using a group, how to do that?
> > Thanks in advance for your help.
> >
> >
> > Regards,
> > Athena
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Received on Tue Dec 15 2020 - 08:00:02 PST
