[gmx-users] Force Field for Vacuum simulation
jmsstarlight at gmail.com
Mon Jan 30 07:50:35 CET 2012
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
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?
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.
>> 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
>> in that ff in vacuum and my system have not been collapse :) Is
>> 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
>> 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 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
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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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