VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
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

https://salilab.org/modeller/manual/node33.html

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" <tuf90798_at_temple.edu> 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
>