VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Jul 26 2018 - 19:33:48 CDT

VMD does have a very strong set of commands that can be used for structural
transformations ... provided they are known before hand. If you want a
more robust solution you will need something more than just "orient-ing",
like some form of post-edit optimization.

On Jul 27, 2018 05:50, "Dhiraj Srivastava" <dhirajks_at_gmail.com> wrote:

> 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
>>
>