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 <sp...@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 <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 >> >> -- >> ==============================**__========== >> >> >> 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> >> > >> >> ==============================**__========== >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>> >> before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. 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