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Problems with reverse transformation
- Carla
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13 years 8 months ago #399
by Carla
Problems with reverse transformation was created by Carla
Hi,
I performed the reverse transformation following the tutorial (making the mapping, adjusting the same number of FG_W and performing the 4 annealing simulations) but the final structure doesn't have the secondary structures just a few helices.
Have I done something wrong? Here is the image of my protein after the last annealing (the optional one) and below is the MDP.
img514.imageshack.us/img514/2282/proteinsa04.png
cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 60000
nstcomm = 0
nstxout = 10000
nstvout = 10000
nstfout = 10000
nstlog = 10000
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
nstlist = 10
energygrps = Protein FG_W
ns_type = grid
rlist = 0.9
coulombtype = Generalized-Reaction-Field
epsilon_rf = 62
rcoulomb = 1.5
rvdw = 1.0
Tcoupl = nose-hoover
tc-grps = Protein FG_W
ref_t = 320 320
tau_t = 0.1 0.1
Pcoupl = no
table_extension = 1.3
dihre = simple ; Some dihedrals are restrained for instance peptide bonds are set to trans conformation.
dihre_fc = 500
dihre_tau = 0.0
nstdihreout = 50
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
andersen_seed = 815131
annealing = single single
annealing_npoints = 2 2
annealing_time = 0 100 0 100 ; CHANGE HERE -annealing control points for each group
annealing_temp = 1300 300 400 300 ; list of temperatures at control points for each group
gen_vel = yes
gen_temp = 1300
gen_seed = 473529
lincs_warnangle = 100
I performed the reverse transformation following the tutorial (making the mapping, adjusting the same number of FG_W and performing the 4 annealing simulations) but the final structure doesn't have the secondary structures just a few helices.
Have I done something wrong? Here is the image of my protein after the last annealing (the optional one) and below is the MDP.
img514.imageshack.us/img514/2282/proteinsa04.png
cpp = /lib/cpp
constraints = none
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 60000
nstcomm = 0
nstxout = 10000
nstvout = 10000
nstfout = 10000
nstlog = 10000
nstenergy = 100
nstxtcout = 100
xtc_precision = 1000
nstlist = 10
energygrps = Protein FG_W
ns_type = grid
rlist = 0.9
coulombtype = Generalized-Reaction-Field
epsilon_rf = 62
rcoulomb = 1.5
rvdw = 1.0
Tcoupl = nose-hoover
tc-grps = Protein FG_W
ref_t = 320 320
tau_t = 0.1 0.1
Pcoupl = no
table_extension = 1.3
dihre = simple ; Some dihedrals are restrained for instance peptide bonds are set to trans conformation.
dihre_fc = 500
dihre_tau = 0.0
nstdihreout = 50
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
andersen_seed = 815131
annealing = single single
annealing_npoints = 2 2
annealing_time = 0 100 0 100 ; CHANGE HERE -annealing control points for each group
annealing_temp = 1300 300 400 300 ; list of temperatures at control points for each group
gen_vel = yes
gen_temp = 1300
gen_seed = 473529
lincs_warnangle = 100
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- andrzej
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13 years 8 months ago #400
by andrzej
Replied by andrzej on topic Problems with reverse transformation
The protein structure You want to transform back is taken from CG Martini simulation , wright ? Did You check the structural changes on the coarse grained level (RMSD), maybe there is some unrealistic events during the run. Which atomistic forcefield do You use ?
Andrzej
Andrzej
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- Carla
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13 years 8 months ago #401
by Carla
Replied by Carla on topic Problems with reverse transformation
I checked the RMSD and there were none unrealistic events during my simulations. The atomistic forcefield I used for reverse CG is 53a6 with mapping.
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- andrzej
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13 years 8 months ago #402
by andrzej
Replied by andrzej on topic Problems with reverse transformation
In the 53a6 there is a problem with backbone dihedral angles, i.e helices are not stable and unfold. There is correction for the backbone dihedral angles from Alan Marks group flying around, we use it in Groningen, i dont know if it is already published, if not i may try to send You the file. The 43a2 or Amber is much more stable in this respect. During the reverse transformation unfolding will be much more pronounced because the dihedrals will equilibrate in the minimal configurations, which are not the ones for the helix.
Second thing, did You use the dihedral constraints generated with g_dihfix , to constraint backbone dihedrals ?
Andrzej
Second thing, did You use the dihedral constraints generated with g_dihfix , to constraint backbone dihedrals ?
Andrzej
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- Carla
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13 years 8 months ago #403
by Carla
Replied by Carla on topic Problems with reverse transformation
I did not use the dihedral constraints. Do you think my problem is because of that?
What do you suggest me: try to use the constraints or change the forcefield (to 43a2) first? In the website of professor Alan Mark I did not find the correction for the 53a6. Maybe it's not available/published yet.
Carla
What do you suggest me: try to use the constraints or change the forcefield (to 43a2) first? In the website of professor Alan Mark I did not find the correction for the 53a6. Maybe it's not available/published yet.
Carla
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- andrzej
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13 years 8 months ago #405
by andrzej
Replied by andrzej on topic Problems with reverse transformation
Constraints, with g_dihfix You generate constraints for dihedrals with high barriers, the ones that in normal temperature occupy only one minimum, even if there is more available, namely the barrier is too high to jump, like for peptide bond. If there is no constraints, because in the procedure You start from random positions, all minimums will be occupied, which is not what You want.
A
A
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- Carla
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13 years 6 months ago #426
by Carla
Replied by Carla on topic Problems with reverse transformation
Sorry for taking too long to answer.
I performed the transformation in 53a6 again with g_dihfix and performed another one in 43a2 with g_dihfix, but none of them worked. I get almost the same result as previous.
What should I do? Could the g_dihfix with "-fc 10" not be enough for my protein? Should I change this value?
I performed the transformation in 53a6 again with g_dihfix and performed another one in 43a2 with g_dihfix, but none of them worked. I get almost the same result as previous.
What should I do? Could the g_dihfix with "-fc 10" not be enough for my protein? Should I change this value?
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- andrzej
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13 years 6 months ago #428
by andrzej
Replied by andrzej on topic Problems with reverse transformation
I cannot give You straight answer from what You write, so if You want I can check the input files ( This email address is being protected from spambots. You need JavaScript enabled to view it. ), to see if there are any mistakes.
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