VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Aug 09 2017 - 14:27:48 CDT

Electrostatic interactions are charge dependant. Any two things that will
have a charge will interact.

You need to decide what distance you want to use as cutoff and based on
that calculate interactions between charged particles.

The interactions will be computed as energies. Is that what you are after?
>From the subject it sounds like you are not interested in energies but
rather the number of hydrogen bonds. Is that the case?

In either case you will have to make selection groups of your atoms and
then use the NAMD energy plugin for example to calculate the energies
between those selection. If you want the number of hydrogen bonds you can
use the hbond plugin for those selection groups.

Hope this helps.

On Aug 10, 2017 6:56 AM, "Rabeta Yeasmin" <rabetayeasmin_at_gmail.com> wrote:

> Dear VMD Users,
>
> I want to find out which atoms have electrostatic interaction of a
> protein-lipid system. I am wondering if you can suggest me how can I do
> this.
>
> Thanks.
>
> Regards
> Rabeta Yeasmin
>