[gmx-users] various issues when simulating cholesterol membrane

[Ayesha Fatima]

Dear All,
It has been a futile effort so far when I want to just simulate a simple
cholesterol membrane. I checked the mailing list. but some how my issues
was not really answered.
So after following a few answers and solutions here and there, i would like
to as a few questions  which i cannot solve even after following the
solutions posted.
1. My cholesterol membrane was prepared usingthe CHARMM Membrane BUilder,
hence it sed the xharmm forcefield. There is only 1 charmm forcefield in
Gromacs 2019 Charmm27. so, I downloaded the forcefield and parameter files
Slipids_2016 from the http://www.fos.su.se/~sasha/SLipids/. I used the non
bonded and bonded forcefield parameters given as there is a unique hydrogen
named H3' which is not found in other forcefields such as Gromos53A6 or
54A7.
Although when I used 54A7 parameterised cholesterol.itp from ATB server, i
got the error or naming mismatch which i thinks is because the number of
cholesterol atoms in the ATB file is only 31 while my pdb file has 74 atoms
per molecule and also the atom types are different.
If I use the normal charmm27 forcefield extended to BERGER lipids, error of
proper dihedrals, U-B atoms and i j parameters comes when it reads the
cholesterol.itp.
So when i will want to parametrise the protein, i will have issues or can i
use the same forcefield since the file does have the amino acid parameters
also?
Kindly suggest  what can be the correct way?
Thank you
Regards
Ayesha Fatima
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Re: [gmx-users] Protein ligand simulation

[Najamuddin Memon]

First of all take coordinates of ligand  from online available resources
mentioned in protocol of protein ligand simulation and exactly follow the
same you will get simulation run

Regards
Najam

On Sat, Sep 28, 2019, 2:38 PM DEEPANSHU SINGLA 
wrote:

> I am trying to learn protein ligand simulation. I tried to follow the steps
> for lysozyme using the GROMACS tutorial. I received the following error:
>
> *ERROR 1 {file jz4.itp, line 183]:*
> * No default Proper Dih. types*
>
>
> *ERROR 2 [file jz4.itp, line 194]:*
> * No default Proper Dih. types*
>
> *Fatal error: *
> *Syntax error -File forcefield.itp, line 10*
> *Last line resd:*
> *'{defaults]'*
> *Invalid order for directive defaults*
>
> Please help me resolve this error.
>
> Thanking you in advance.
>
> Deepanshu Singla
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[gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

Dear gromacs users,

Sorry for repeating my question.

I didn't receive any email so I couldn't reply and I missed

them.

I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis z increases.
My size box is 8.52807   8.52807  14.0.
And the pull distance is less than one-half the length of the box vector
along.pull distance is 6 nm.
After simulation my size box is 8.09025   8.09025  91.84508.

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane.

What should I do?

I would be very appreciated for your such kind helps.

My mdp file  :
title   = Umbrella pulling simulation
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 30 ; 600 ps

; Output parameters
nstlog  = 1000
nstxout = 500   ; every 1 ps
nstvout = 500
nstfout = 500
nstxtcout   = 500; every 1 ps
nstcalcenergy   = 500
nstenergy   = 500
; PME electrostatics parameters
coulombtype = pme
; Single-range cutoff scheme
cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
; Berendsen tempearture coupling is on in two groups
tcoupl  = nose-hoover
tc_grps = Protein_LIG TIP3_CLA DOPC
tau_t   = 1.01.0   1.0
ref_t   = 303.15 303.15 303.15
; Pressure coupling is on
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
refcoord_scaling= com
; Bond parameters
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = Protein_LIG TIP3_CLA DOPC
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz

; Pull code
pull= yes
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 2 ; two groups defining one reaction
coordinate
pull_group1_name= BILAYER
pull_group2_name= LIG
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_geometry= direction
pull_coord1_vec = 0 0 1
pull_coord1_groups  = 1 2
pull_coord1_start   = yes   ; define initial COM distance > 0
pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_nstxout= 500; every 1 ps
pull_nstfout= 500; every 1 ps

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[gmx-users] (no subject)

[Mahsa Rezaei]

Dear gromacs users,

Sorry for repeating my question.

I didn't receive any email so I couldn't reply and I missed

 them.

I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis z increases.
My size box is 8.52807   8.52807  14.0.
And the pull distance is less than one-half the length of the box vector
along.pull distance is 6 nm.
After simulation my size box is 8.09025   8.09025  91.84508.

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane.

What should I do?

I would be very appreciated for your such kind helps.

My mdp file  :
title   = Umbrella pulling simulation
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 30 ; 600 ps

; Output parameters
nstlog  = 1000
nstxout = 500   ; every 1 ps
nstvout = 500
nstfout = 500
nstxtcout   = 500; every 1 ps
nstcalcenergy   = 500
nstenergy   = 500
; PME electrostatics parameters
coulombtype = pme
; Single-range cutoff scheme
cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
; Berendsen tempearture coupling is on in two groups
tcoupl  = nose-hoover
tc_grps = Protein_LIG TIP3_CLA DOPC
tau_t   = 1.01.0   1.0
ref_t   = 303.15 303.15 303.15
; Pressure coupling is on
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
refcoord_scaling= com
; Bond parameters
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = Protein_LIG TIP3_CLA DOPC
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz

; Pull code
pull= yes
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 2 ; two groups defining one reaction
coordinate
pull_group1_name= BILAYER
pull_group2_name= LIG
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_geometry= direction
pull_coord1_vec = 0 0 1
pull_coord1_groups  = 1 2
pull_coord1_start   = yes   ; define initial COM distance > 0
pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_nstxout= 500; every 1 ps
pull_nstfout= 500; every 1 ps

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