[gmx-users] Force Field for Vacuum simulation

James Starlight jmsstarlight at gmail.com
Sun Jan 29 17:09:30 CET 2012

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 ?


2012/1/29 Justin A. Lemkul <jalemkul at 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
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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