True, insane is originally made for Martini, but I *think* it should work for atomistic as well. Otherwise, make the Martini system with insane, simulate for a short while, and then convert it to atomistic with backward.py.
I don't have any experience with charmm-gui myself, so I can't help you further there. Peter On 19 Feb 2018 02:15, "alex rayevsky" <rayevsk...@gmail.com> wrote: > Dear Peter, thank You for responce! > > I've already prepared toplogy file, here is a content: > '''' > ; Include forcefield parameters > #include "charmm36-jul2017.ff/forcefield.itp" > #include "/home/dikov/alex/WORK/lipid/charmm36.itp" > #include "LIG.itp" > > ; Include chain topologies > > #include "topol_Protein_chain_A.itp" > #include "topol_Protein_chain_A2.itp" > #include "topol_Other_chain_A3.itp" > #include "topol_Protein_chain_B.itp" > #include "topol_Protein_chain_B2.itp" > #include "topol_Protein_chain_C.itp" > #include "topol_Protein_chain_C2.itp" > #include "topol_Protein_chain_D.itp" > #include "topol_Protein_chain_D2.itp" > > ; Strong position restraints for InflateGRO > #ifdef STRONG_POSRES > #include "strong_posre.itp" > #endif > > ; Include POPG chain topology > #include "POPG.itp" > > ; Include water topology > #include "/home/dikov/alex/WORK/lipid/TIP3.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > > #endif > > ; Include topology for ions > #include "charmm36-jul2017.ff/ions.itp" > #include "POT.itp" > > [ system ] > ; Name > Protein > > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Protein_chain_A2 1 > Other_chain_A3 1 > Protein_chain_B 1 > Protein_chain_B2 1 > Protein_chain_C 1 > Protein_chain_C2 1 > Protein_chain_D 1 > Protein_chain_D2 1 > LIG 1 > POT 118 > POPG 96 > ''' > > Insane script is for Martini, am I right? Charmm-gui was very confusing and > hard to generate orientation. > However, if no ohter suggestions available, I'll try Your's! > Thank You!! > >>>> > _______ > > Kroon, P.C. Sun, 18 Feb 2018 15:52:30 -0800 > <https://www.mail-archive.com/search?l=gromacs.org_gmx- > us...@maillist.sys.kth.se&q=date:20180218> > > Hi Alex, > > Try either insane.py, or charmm-gui. I can't provide links, since I'm on my > phone. > > You may need to generate the topology (itp) of the protein, which you can > do with calling pdb2gmx on just the protein. You should have a topology > (itp) of your favourite lipid. > > Peter > > > > > > > > > 2018-02-17 0:56 GMT+02:00 alex rayevsky <rayevsk...@gmail.com>: > > > Hi all! > > > > I have a question concerning immersion of the ion channel (four subunits > > with extracellular domains and a bundles of helixes) into the lipid > > bilayer. 6 years ago I used some tutorial or mailing lists, which > described > > the way from KALP15 tutor. With CCR5 model there were no problems at all. > > Now I have a not 'cylindric' protein with a complex shape and > overhanging > > domains. > > the forcefield is CHARMM36, lipid type - POPG. > > > > I tried Membrane builder, but couldn't orient the plane of the membrane > by > > changing XYZ principles many times in different combinations.. Thus I > used > > a slightly modified KALP15 method (other .itps, lipids and water > > molecules). First of all after pdb2gmx for protein a series of > > topologies were generated with identifiers in the name, as it was > assigned > > in each chain. However editconf produced a new pdb from the outpu gro > > without any ID or terminators for the chains, in Pymol it is represented > > with a tetramer entirely highlithing if a single chain is selected (maybe > > it is a reason of faults at later stages). > > > > Well, it works fine until the perl script execution. Beside some problems > > with the output (system_inflated.gro was corrupted, but I repaired it > with > > simple python scripting and got a pretty protein in the center of rare > > molecules, which looks reliable enough) I started to compact the bilayer > to > > rich the lipid area of ~53A^2. I finished it on the 13 stage of perl > > execution - the distance between nearest lipids was about 16A, however, > the > > layer was really holey. At the same time the protein was not surrounded > > from all sides. But if I try to put lipids closely one to other, they are > > simultaneously penetrate the protein body. > > > > Is it the correct method for such kind of simmulations? Could I increase > > the number of POPG molecules after getting inflated.gro file with scaled > up > > bilayer (the initial step for tightning) before scaling iterations? I can > > do it manually by copy of the layer (all lipid coordinates) and its > > rotation around Y axis in any soft to enlarge the number of molecules in > > the cell (even 200 mols is more than 128). Of course I will make changes > in > > a topology file. It seems, that I will obtain a fully wrapped protein > > without anxiety about clashes or presure in cavities... > > > > What do You think? Thank You in advance! > > > > > > > > *Nemo me impune lacessit* > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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