VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 19 2023 - 12:17:37 CDT

With a smallmolecule modulator of a protein, no problem in specifying "name
xyz" as the name of the atom of interest.

With the aminoacids of the protein, I am unable to specify an atom of just
one of the aminoacids - and only that one - which are in contact with the
small molecule. My poor knowledge of the tcl language may be responsible.

Actually, I am interested in the energy of residue-residue interaction.
However, H-bond interaction of the smallmolecule modulator with a water
molecule, when calculated from residue-residue interaction, gives too high
values for H-bonds. So that I am curious about the atom-atom interaction
energy for these and other cases.

Thanks
francesco pietra

On Wed, Apr 19, 2023 at 5:20 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> You should just be able to plug in standard vmd atom selection text. If
> you're having trouble, please give an example.
> Thanks,
> Peter
>
> On Wed, Apr 19, 2023 at 10:12 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hello
>>
>> With namdenergy plugin, how to select a specific atom of a given residue?
>> I thought to know the selection modes of vmd, but I am confused when it
>> deals of that plugin
>>
>> Thanks for advice
>> francesco pietra
>>
>