VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Dec 12 2017 - 21:50:52 CST

It is also important to ensure that there is no overlap between the atoms
in selection 1 and those in selection 2.

On Tue, Dec 12, 2017 at 10:41 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> 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>:
>>
>>> Just to add to this, your original question reads:
>>>
>>> ... which contains two protein subunits (chain A and chain B. A and B
>>> also interact each other) and *"**a"* ligand (resname 711 and located
>>> in the middle of the complex and *contact with both chain A and B*) ..--94eb2c0d226694ba1f056030ac96--