[gmx-users] Force Field for Vacuum simulation

Peter C. Lai pcl at uab.edu
Mon Jan 30 08:35:50 CET 2012 

I am not sure of the actual interpretive value of such a methodology. 
Are you just trying to save computational time by not having to simulate 
an all atom bilayer? The solvent layer is going to contribute to the 
majority of the computation cost in the first place. As an example, the 
bilayer we are using for GPCR work consisting of 238 POPC molecules adds 
30552 atoms out of a total of 99547 atoms, In any case, people have been
conducting all-atom simulations of opsins since at least 2005 because
of the availability of computational resources. See: Lemaitre V., Yeagle, P.,
Watts, A. Biochemistry 2005, 44, 12667-12680 . So it is unlikely that 
any reviewers today will accept an opsin system simulated in anything but.

Perhaps a biphasic implicit solvent model would work better for you (unsure 
if gromacs can support an "exterior" dielectric and an interior dielectric).
There may also be some people using a coarse-grained bilayer with an all-atom
protein, but again, unless you have carefully determined the coupling
parameters between a MARTINI bilayer and an all-atom protein, there will
be doubts about the usefulness of such a system.

If you really must do without the bilayer, you might be able to get away
with using strong i,i+4 distance constraints within your TMs to preserve 
helical stability while the entire protein is solvated.


On 2012-01-30 10:50:35AM +0400, James Starlight wrote:
> 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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