VMD-L Mailing List

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Thu Jul 26 2018 - 16:50:55 CDT

If you want control over the orientation of the two domains, you can try using chimera or pymol. You can move one domain with respect to another easily in those software. I don’t know if that functionality exists in vmd.

Dhiraj

Sent from my iPhone

> On Jul 26, 2018, at 4:01 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
> 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