On 2012-01-29 17:09, James Starlight wrote:
Hi, Justin.
Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr
Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As
the consequence the mature chromophore has cyclised structure wich named
as the CRO residue in PDB structure.
I've made for this CRO residue topology via PRODG server for GROMOS ff.
Than I've imported that new chromophore.top into the topology.top of my
structure in accordance to your tutorial.
Finally I've merged CRO.gro and protein.gro ( I've cut CRO from the pdb
for creation of the topoogy for my protein via pdb2gmx)
Than I've done minimisation and chromophore have been diffused from my
protein :) It seems that I must add covalent bond between CRO and
protein into the topology. But how I could do it for my multi topology
file ?
You need to add the bonds angles etc. The easiest way would be to make a
special bond (specbond.dat file). You need an rtp entry for your cro
group as well. Then pdb2gmx makes the necessary bonds.
Of course you can make all the bonds, angles, diehdrals and pairs
manually as well, but that is tedious and error prone.
James
2012/1/29 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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