Re: [AMBER] Stacking distance in CPPTRAJ

From: Carlos Simmerling <>
Date: Sun, 13 Dec 2020 06:49:43 -0500

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

On Sun, Dec 13, 2020 at 6:18 AM Athena N <> 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 Sun Dec 13 2020 - 04:00:02 PST
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