Re: [gmx-users] ion channel in lipid bilayer

2018-02-19 Thread Kroon, P.C. 
True, insane is originally made for Martini, but I *think* it should work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"  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   fcxfcyfcz
>11   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_A21
> Other_chain_A3  1
> Protein_chain_B 1
> Protein_chain_B21
> Protein_chain_C 1
> Protein_chain_C21
> Protein_chain_D 1
> Protein_chain_D21
> LIG 1
> POT 118
> POPG96
> '''
>
> 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
>  us...@maillist.sys.kth.se=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 :
>
> > 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,

Re: [gmx-users] ion channel in lipid bilayer

2018-02-19 Thread alex rayevsky 
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   fcxfcyfcz
   11   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_A21
Other_chain_A3  1
Protein_chain_B 1
Protein_chain_B21
Protein_chain_C 1
Protein_chain_C21
Protein_chain_D 1
Protein_chain_D21
LIG 1
POT 118
POPG96
'''

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
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 :

> 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*
>
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