[gmx-users] Force Field for Vacuum simulation

James Starlight jmsstarlight at gmail.com
Mon Jan 30 07:50:35 CET 2012 

David, Justin

Thanks again for help!


I have just few questions about in vacum sumulation of membrane proteins.


I want to simulate GPCR receptor wich have big transmembrane ( helix)
domain and some connecting loop regions wich are exposed to the solvent.

As I understood in classical vacum simulation all charges must be redused
to avoid its collapse.

I want to build biphastic system water-vacum-water where loops would be in
water and TM helixes in vacum region.

Something like this I've read in old publications about simulation of
bacteriorhodopsin http://ukpmc.ac.uk/abstract/MED/10412722


1- Could you tell me where I could found possible algorithm about builing
of such water-vacum-water system?

2- Also I'd like to specify what should I do with the charges residues. I'd
like to use AMBER-like or OPLS ff for such simulation As I understood I
must neitralize only charges in TM helices and keep residues in LOOP
intact. Might this aproache be correct?


James

2012/1/29 David van der Spoel <spoel at xray.bmc.uu.se>

> 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 <jalemkul at vt.edu <mailto: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
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>>    ==============================**__==========
>>
>>
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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