[gmx-users] Bonds between New residues and Terminals

[Justin A. Lemkul]

On 5/25/12 5:43 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> My surface is made of 4 types of residues created on my own. They are placed
> within they vdwradii away from each other. I want to keep the surface rigid and
> allow it to move into only one direction (freezgrps, freezdim). Each residue is
> made of one atom. The best option would be to create bonds between or apply
> distnce restraints e.g. using cutoff of 1nm.
>
> How can I create bonds between them? Shall I specify in my aminoacids.rtp the
> possibilities of each of them to create bonds with any 3 others? Then to add
> proper lines to specbond.dat?
> I want two of them to create extra bond with my protein terminals. How to do
> this using bonds? Or would you suggest distance restraints?
>

The nature of the model depends on how you want to treat them.  Distance 
restraints are harmonic potentials that can be set up with arbitrary 
flexibility.  Bonds can be harmonic or rigid, depending on the use of 
constraints.  The manner that makes the most sense for what you hope to achieve 
should prevail.

As for creating the topology, you can only use pdb2gmx to create a linear 
sequence of bonded residues.  Thus, you can't specify all possible bonds within 
the .rtp file; the majority of the work comes in creating suitable entries in 
specbond.dat.  There are a number of discussions in the list archive about doing 
so, usually in the context of silica-type species.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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