VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Tue Dec 12 2017 - 21:04:04 CST

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*) ...
>
> 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
>