From: Ashar Malik (
Date: Thu Jul 26 2018 - 16:01:55 CDT

In other words (if I understand this correctly), you have structures from
two domains connected by a linker protein??. I am not sure I am aware of a
package within vmd which does this, how ever since this sounds like a
typical model building problem, have you thought about considering the use
of modeller? E.g. here

The exercise will vary depending on your exact problem.

Feel free to write back if you have further questions.

On Jul 27, 2018 03:22, "Nick Palmer" <> wrote:

> Hello,
> I am attempting to fuse two proteins to the N and C terminus of a linker
> protein to run in further simulations. I know I can link them with a patch
> when creating a psf file, but I would like to know the best way to orient
> the proteins in a reasonable position before I link them.
> Thank you in advance!
> --
> Nicholas J. Palmer