• Outreach

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Tue Dec 12 2017 - 22:04:57 CST

Dear Ashar:
My protein complex has 3 parts, and are subunit A, subunit B and a
ligand (name XXX). The three parts are not covalent linked to each other
and would like to calculate the nonbond energy between the three.

Since Nondond energy only calculate the energy between selection 1 and
selection 2.
To calculate the nonbond energy between the three. It would need to
collect the nonbond energy between them piece by piece and sum them up.
Hope this is right. Please tell me if I were wrong. Thanks.

sincerely,

Jrhau

2017-12-13 11:41 GMT+08:00 Ashar Malik <asharjm_at_gmail.com>:

> I am not sure what you want to achieve.
>
> chain A and resname XXX --- will only select resname XXX
> chain A or resname XXX --- select all of chain A and all residues resnames
> XXX (not sure if this would double your selection if resname XXX is already
> included in the selection of chain A)
>
> is resname XXX covalantly linked to chain A?
>
> if you want to measure a quantity (say energy) between everything in chain
> A and resname XXX and if resname XXX is also labelled as chain A then you
> should use
>
> selection - 1:: chain A and not resname XXX
> # This will select everything in chain A excluding
> resname XXX
> selection - 2:: resname XXX
> # Will only select resname XXX
>
> You should only use the above if you are absolutely sure there is only one
> residue labelled resname XXX cause if you have multiple you will still get
> an answer - but I am not sure what I would make of it.
>
>
>
>
>
>
> On Wed, Dec 13, 2017 at 4:04 PM, jrhau lung <jrhaulung_at_gmail.com> wrote:
>
>> Dear Ashar:
>> Thanks for your hint. Yes, the complex contains only one ligand.
>> And I realize that using "and" in selection need both selected parts are
>> true.
>>
>> Instead of using "and", input "chain A or resname XXX" in selection
>> 1 and "chain B" in selection 2 works.
>> But I guess the nonbond energy between chain A and ligand XXX is still
>> missing.
>>
>> sincerely
>>
>> Jrhau
>>
>> 2017-12-12 22:43 GMT+08:00 Ashar Malik <asharjm_at_gmail.com>:
>>