Re: [AMBER] How to compute pairwise interaction between masks

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Mon, 13 Sep 2021 11:50:53 +0000

Hello Dr. Horn,
Just a quick question when you compute LIE values do you provide all the protein heavy atoms as mask, or do you only use binding site residues as your surrounding mask for the ligand?
Say my ligand is residue 190 and my protein atoms are residue 1-189
So do you use :1-189 as mask in LIE or just the 12-16 residues specific to the binding pocket anchoring the ligand in your cpptraj LIE command?
I wanted to cross check I am doing it the right way.
Regards
Debarati


Also Thanks to Mathew for the question!
From: Dr. Anselm Horn<mailto:anselm.horn.fau.de>
Sent: 13 September 2021 05:12
To: amber.ambermd.org<mailto:amber.ambermd.org>
Subject: Re: [AMBER] How to compute pairwise interaction between masks

Dear Mathew,

maybe the cpptraj-command lie (linear interaction energy) does what you
want (see p. 703, section 34.11.41 Amber21 manual).
With lie you can compute the electrostatic and vdW interaction energy
between two groups of atoms defined by Amber masks. The calculation is
done in cpptraj and is very fast.

Alternatively, you maybe could use the cpptra-command energy (see p.
689, section 34.11.30 Amber21 manual) to compute the interaction energy
of your two sets of atoms by hand.

While I haven't used the energy command so far, I have successfully
applied the lie feature to compute interaction energies between groups
of atoms within a system over the course of a trajectory.

Best,

Anselm



On 09/10/2021 11:26 PM, Matthew Guberman-Pfeffer wrote:
> Dear Amber Community,
>
> I want to compute the interaction energy between two masks, not for the atoms within a given mask (i.e. something akin to the PairInteraction feature of NAMD). Is there a way to do this in CPPTRAJ? Iíve looked at the pairwise function, but that feature doesnít seem to compute the energy between two masks.
>
> Best,
> Matthew
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Mon Sep 13 2021 - 05:00:02 PDT
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