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

From: Dr. Anselm Horn <anselm.horn.fau.de>
Date: Mon, 13 Sep 2021 15:19:43 +0200

Dear Debarati,

there is no general answer for that, both approaches are IMHO valid:
In the one case you compute the interaction between your ligand and the
complete protein, in the other case specifically for the binding pocket
- or even single residues.
Of course, you have to be aware, where your values originate from, and
consider this in your interpretation.

Best regards,

Anselm


On 09/13/2021 01:50 PM, Debarati DasGupta wrote:
> 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
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>>
>
>
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>
> †
>


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Received on Mon Sep 13 2021 - 06:30:02 PDT
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