VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Dec 12 2017 - 07:25:16 CST

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
>>
>
>