VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Dec 19 2018 - 17:27:58 CST

Hi Prabir,

Please keep this on the list, so that others can also impart wisdom where appropriate (and so that folks googling for answers later can find them). I think you aren't giving the force field enough credit. Long initial bonds can be minimized away pretty easily, so as long as your initial starting position is *close*, you should be fine. The way I'd set this up is to duplicate one monomer, rotate it by 60 degrees around your preferred axis, and merge them all into one file using atomselections and TopoTools. From there, psfgen would be your friend to make something you can simulate.

-Josh

On 2018-12-19 14:23:06-07:00 Prabir Khatua wrote:

Hi Josh,

Thank you very much for your reply. I have a protein which is an acyclic monomer. Now, I want to make hexamer
of this protein starting from this protein. The shape of hexamer will be a ring. I need to make a constant
distance between two specified residues of two adjacent monomers ( (1,2) (2,3) (3,4) (4,5) (5,6) and (6,1))
so that it forms a ring. Therefore, I need to translate the original protein and make
appropriate rotation. I need this structure to start the simulation. I hope the problem would be clear now to you.
Please let me know if you need to know anything else.

Sincerely,

Prabir

On Thu, Dec 20, 2018 at 12:23 AM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
Hi Prabir,

It isn't clear to me what you want to do, but I *think* you just want to simulate something akin to a cyclic peptide, right? Will you need to simulate the structure? If so, you'll need to become familiar with psfgen and the CHARMM force field. If not, what I've found to be the most straightforward is to just draw out the structure I want in Avogadro and use its minimization features to build the structure.

-Josh

On 2018-12-18 21:34:43-07:00 owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> wrote:

Hi,
I want to prepare a ring-like hexamer from a monomer where two atoms of the
adjacent monomers will be restricted within a certain distance. Can anyone please suggest me how to do it using vmd?
Thanks,
Prabir 

--
Prabir Khatua
Postdoctoral Research Associate
Department of Chemistry & Biochemistry
University of Oklahoma
Norman, Oklahoma 73019
U. S. A.
--
Prabir Khatua
Postdoctoral Research Associate
Department of Chemistry & Biochemistry
University of Oklahoma
Norman, Oklahoma 73019
U. S. A.