[gmx-users] Force Field for Vacuum simulation

[Justin A. Lemkul]

James Starlight wrote:
> Hi David!
> 
> Thanks for reference I'll study it carefully.
> 
> 
> I have some general question about the vacuum simulation
> 
> 1- I've found that common GROMOS fields are not suitable for the
> vacuum simulation because of its implementation for condensed phase .
> But In some referencces I've found that people use 53.6 ff for the in
> vacuum simulation. In addition Ive done minimisation and equilibration
> in that ff in vacuum and my system have not been collapse :) Is there
> any wy to adopt this ff for the in vacum ?
> 
> 2- I have uncommon onject for simulation. It's GFP protein where
> chromophore group ( like ligand) is covalent bonded to the backbone of
> this protein. As I've understood in Justins tutorial there are no any
> covalent bonds between protein and ligand. But how I could make this
> bond if I operate with TWO topology files ( one for chromophore and
> another for protein itself) ? I've done all steps in accordance to
> Justins tutorial but on the minimisation step my chromphore dissuse
> out of the protein interior because of absent of backbone group.
> 

The GFP chromophore is part of the backbone of the protein, is it not?

The tutorial I have for a protein-ligand complex should not be taken to mean 
that all non-protein entities are physically separate entities.  Plenty of 
cofactors, chromophores, and the like are covalently attached to the protein.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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