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CHOLESTEROL flips after insane.py
- sreyoshi09
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8 years 4 weeks ago #5458
by sreyoshi09
CHOLESTEROL flips after insane.py was created by sreyoshi09
Hi,
I am working with an antimicrobial lipopeptide called Fengycin. I wanted to disperse the proteins in a bilayer with cholesterol and POPC. I had the protein gro file with the dispersed fengycins in it. Then I used insane to generate the bilayer using the following option:
./insane.py -f fengycins.gro -center -ring -o lipidified_feng1.gro -u POPC:4 -u CHOL:1 -l POPC:4 -l CHOL:1 -charge -10 -salt 0.10 -x 8.0 -y 8.0 -z 8.0 -dz 1.0 -d 1.0 -pbc cubic -sol PW
fengycin has a net charge of -1 and since I have -10 charge I wanted 10 NA+ more to make the system neutral. So I used the option -charge -10 and it worked. I had a system with the following:
FENGYCIN 10
POPC 130
CHOL 32
PW 1724
NA+ 18
CL- 8
The upper and lower leaflet differed in the number of POPC and CHOL since fengycin occupies only the upper leaflet but their relative concentration remains same.
Next I wanted to do energy minimization. So I used the following mdp file:
; VARIOUS PREPROCESSING OPTIONS =
title = BILAYER ASSEMBLY
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
define = -DFLEXIBLE
integrator = steep ; Run steepest descent energy minimization algorithm
dt = 0.001
nsteps = 100
nstcomm = 100
comm-grps = System
;OUTPUT CONTROL OPTIONS
nstxout = 50 ;
nstvout = 50
nstfout = 50
;Output frequency and precision for xtc file =
nstxout-compressed = 100
nstenergy = 100
compressed-x-precision = 100 ; Gromacs 5.0
energygrps = System
;NEIGHBOR SEARCHING PARAMETERS =
cutoff-scheme = group
epsilon-rf = 0
nstlist = 10
ns-type = grid
pbc = xyz
rlist = 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics
coulombtype = Shift
rcoulomb-switch = 0.0
rcoulomb = 1.2
epsilon-r = 2.5
vdwtype = Shift
rvdw-switch = 0.9
rvdw = 1.2
DispCorr = no
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = LINCS
continuation = no
lincs-order = 4
lincs-warnangle = 30
When I looked at the output gro file the Cholesterol has flipped to the lower leaflet. I don't know why this is happening.
I have done only POPC and Cholesterol in the same ratio without the fengycin. In that case Cholesterol doesn't flip.
How can I stop the cholesterol from flipping? I have tried position restraining the cholesterol but then the energy minimization fails.
Thanks
Sreyoshi
I am working with an antimicrobial lipopeptide called Fengycin. I wanted to disperse the proteins in a bilayer with cholesterol and POPC. I had the protein gro file with the dispersed fengycins in it. Then I used insane to generate the bilayer using the following option:
./insane.py -f fengycins.gro -center -ring -o lipidified_feng1.gro -u POPC:4 -u CHOL:1 -l POPC:4 -l CHOL:1 -charge -10 -salt 0.10 -x 8.0 -y 8.0 -z 8.0 -dz 1.0 -d 1.0 -pbc cubic -sol PW
fengycin has a net charge of -1 and since I have -10 charge I wanted 10 NA+ more to make the system neutral. So I used the option -charge -10 and it worked. I had a system with the following:
FENGYCIN 10
POPC 130
CHOL 32
PW 1724
NA+ 18
CL- 8
The upper and lower leaflet differed in the number of POPC and CHOL since fengycin occupies only the upper leaflet but their relative concentration remains same.
Next I wanted to do energy minimization. So I used the following mdp file:
; VARIOUS PREPROCESSING OPTIONS =
title = BILAYER ASSEMBLY
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
define = -DFLEXIBLE
integrator = steep ; Run steepest descent energy minimization algorithm
dt = 0.001
nsteps = 100
nstcomm = 100
comm-grps = System
;OUTPUT CONTROL OPTIONS
nstxout = 50 ;
nstvout = 50
nstfout = 50
;Output frequency and precision for xtc file =
nstxout-compressed = 100
nstenergy = 100
compressed-x-precision = 100 ; Gromacs 5.0
energygrps = System
;NEIGHBOR SEARCHING PARAMETERS =
cutoff-scheme = group
epsilon-rf = 0
nstlist = 10
ns-type = grid
pbc = xyz
rlist = 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics
coulombtype = Shift
rcoulomb-switch = 0.0
rcoulomb = 1.2
epsilon-r = 2.5
vdwtype = Shift
rvdw-switch = 0.9
rvdw = 1.2
DispCorr = no
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = LINCS
continuation = no
lincs-order = 4
lincs-warnangle = 30
When I looked at the output gro file the Cholesterol has flipped to the lower leaflet. I don't know why this is happening.
I have done only POPC and Cholesterol in the same ratio without the fengycin. In that case Cholesterol doesn't flip.
How can I stop the cholesterol from flipping? I have tried position restraining the cholesterol but then the energy minimization fails.
Thanks
Sreyoshi
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- peterkroon
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8 years 4 weeks ago #5460
by peterkroon
Replied by peterkroon on topic CHOLESTEROL flips after insane.py
Why shouldn't your cholesterol flip leaflets? Sounds perfectly normal to me...
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- tsjerk
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8 years 4 weeks ago #5462
by tsjerk
Replied by tsjerk on topic CHOLESTEROL flips after insane.py
I don't understand how cholesterol can flip during EM. Can you check the output from insane, possibly with pbc (genconf -nbox 2 2 2)? If it doesn't make sense, please send me the files. and I can have a look.
T.
T.
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- sreyoshi09
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8 years 3 weeks ago #5466
by sreyoshi09
Replied by sreyoshi09 on topic CHOLESTEROL flips after insane.py
I did genconf on the output from insane and I don't see any abnormality. How can I send you the files?
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- sreyoshi09
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8 years 3 weeks ago #5486
by sreyoshi09
Replied by sreyoshi09 on topic CHOLESTEROL flips after insane.py
Hi,
I found the problem in my simulation. I had a mixture of lipids and sterols. In the top file I was putting the total number of lipids and total number of cholesterol instead of specifying the lipids and sterols in each bilayer separately. So everytime I was running grompp my system would be rearranged with all cholesterol in the lower leaflet and POPC divided in two bilayers. I have fixed this issue.
I found the problem in my simulation. I had a mixture of lipids and sterols. In the top file I was putting the total number of lipids and total number of cholesterol instead of specifying the lipids and sterols in each bilayer separately. So everytime I was running grompp my system would be rearranged with all cholesterol in the lower leaflet and POPC divided in two bilayers. I have fixed this issue.
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