VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Tue Dec 12 2017 - 01:13:10 CST

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
>