True, insane is originally made for Martini, but I *think* it should work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
I don't have any experience with charmm-gui myself, so I can't help you
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"
> ; 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
> ; Include topology for ions
> #include "charmm36-jul2017.ff/ions.itp"
> #include "POT.itp"
> [ system ]
> ; Name
> [ 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
> Hi Alex,
> Try either insane.py, or charmm-gui. I can't provide links, since I'm on my
> 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.
> 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
> > 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
> > domains.
> > the forcefield is CHARMM36, lipid type - POPG.
> > I tried Membrane builder, but couldn't orient the plane of the membrane
> > changing XYZ principles many times in different combinations.. Thus I
> > 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
> > 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
> > simple python scripting and got a pretty protein in the center of rare
> > molecules, which looks reliable enough) I started to compact the bilayer
> > 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,
> > 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
> > 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
> > 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*
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