VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Dec 12 2017 - 08:43:02 CST

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*) ...

This to me sounds like you have just one thing by the name of resname of
711.

However when you type in:

 "chain A and resname 711" in selection 1 and "chain B and resname 711"

you are looking for two 711s one in each chain A and B. The error of no
atom in selection appears to suggest that while you have a 711 :: protein
~ 711 = -40 kcal/mol there is just one of this (as understood from your
original question.

set sel [atomselect top "resname 711"]
$sel get chain

Only if the second line returns A and B should you expect an answer from ::

Input "chain A and resname 711" in selection 1 and "chain B and resname
711" in selection 2

On Wed, Dec 13, 2017 at 2:25 AM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> I'm sorry, but this doesn't seem to make sense:
> " If chain A and chain B do not both have residues with this name, input
> "chain A" in selection 1 and "chain B" in selection 2 should get same error
> message as
> when input "chain A and resname 711" in selection 1 and "chain B and
> resname 711". "
>
> Why would that be? If chain A and chain B each have many atoms, but none
> are resname 711 (which is a very odd residue name), then you would get
> normal results for the first case, but things would not work for the
> second. Perhaps you could double check what the chain names are for all of
> the residues in your system? Perhaps
> set sel [atomselect top all]
> lsort -unique [$sel get {chain resname resid}]
>
>
> On Tue, Dec 12, 2017 at 2:13 AM, jrhau lung <jrhaulung_at_gmail.com> wrote:
>
>> Dear Giocomo:
>> Thanks for your advice.
>> The protein complex only contains 250 residues, including the ligand
>> 711. The "resname 711" should be correct for the analysis.
>> If chain A and chain B do not both have residues with this name, input
>> "chain A" in selection 1 and "chain B" in selection 2 should get same error
>> message as
>> when input "chain A and resname 711" in selection 1 and "chain B and
>> resname 711".
>>
>> Continue struggling.
>>
>> sincerely,
>> Jrhau
>>
>> 2017-12-12 11:51 GMT+08:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
>>
>>> Perhaps chain A and chain B do not both have residues with this name?
>>> Also, are you sure that you are not interchanging "resname" with "resid"?
>>>
>>> On Mon, Dec 11, 2017 at 9:52 PM, jrhau lung <jrhaulung_at_gmail.com> wrote:
>>>
>>>> Dear João and VMD friends:
>>>>
>>>> I would like to calculate the nonbond energy of a protein complex,
>>>> 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) using
>>>> NAMDenergy plugin. What should I input in selection 1 and selection 2 to
>>>> let result return in one calculation run. Thanks for any help.
>>>>
>>>> Input "protein" in selection 1 and "resname 711" in selection 2 got ~
>>>> -40 kcal/mol
>>>> Input "chain A" in selection 1 and "chain B" in selection 2 got ~ -300
>>>> kcal/mol
>>>> Input "chain A and resname 711" in selection 1 and "chain B and resname
>>>> 711" in selection 2 returned a error message "both selection must
>>>> contain at least one atom"
>>>>
>>>>
>>>> sincerely,
>>>>
>>>> Jrhau
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>> Contractor, National Institutes of Health, Bethesda, MD
>>> http://goo.gl/Q3TBQU
>>> https://github.com/giacomofiorin
>>>
>>
>>
> 

-- 
Best,
/A