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Reverse transformation- pdb2gmx error
- c.poojari
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12 years 1 month ago #920
by c.poojari
Reverse transformation- pdb2gmx error was created by c.poojari
Hi,
I was successfully able to coarse grain, self assembly of helix structure within the bilayer.
Now i want to convert this CG structure to fine grained structure. I went through the tutorial for reverse transformation and tried the first step:
pdb2gmx -f *.gro -missing
When prompted, i choose GROMOS96 53a6 force field with MAPPING option.
Now i get a error message as such:
Fatal error:
Atom BB in residue MET 1 not found in rtp entry with 9 atoms while sorting atoms
Looking into rtp file, they dont have CG atoms in it.
Please can I know how do i fix this error..
Kind Regards,
Chetan.
I was successfully able to coarse grain, self assembly of helix structure within the bilayer.
Now i want to convert this CG structure to fine grained structure. I went through the tutorial for reverse transformation and tried the first step:
pdb2gmx -f *.gro -missing
When prompted, i choose GROMOS96 53a6 force field with MAPPING option.
Now i get a error message as such:
Fatal error:
Atom BB in residue MET 1 not found in rtp entry with 9 atoms while sorting atoms
Looking into rtp file, they dont have CG atoms in it.
Please can I know how do i fix this error..
Kind Regards,
Chetan.
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- andrzej
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12 years 1 month ago #924
by andrzej
Replied by andrzej on topic Reverse transformation- pdb2gmx error
Hey,
did you use coarse grained file as pdb2gmx input ? It should be the atomistic one.
Andrzej
did you use coarse grained file as pdb2gmx input ? It should be the atomistic one.
Andrzej
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- c.poojari
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12 years 2 weeks ago #934
by c.poojari
Replied by c.poojari on topic Reverse transformation- pdb2gmx error
Dear Andrzej,
Yes i had used coarse grained str., after using atomistic it worked fine.
I have another question regarding reconstruction simulation.
Before releasing restraints, my mdp parameters for reconstruction
simulation are;
Restrained SA:
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
For Release of restraints,
cap_force = 15000
cap_a = 100
fc_restr = 0
r_CGW = 0.21
fc_restrW = 0
rel_steps = 5000
rel_water = yes
i will be setting rel_steps to 5000,
Should i set rel_water = yes, and set fc_restr = 0, fc_restrW = 0 ??
Kind Regards,
Chetan.
Yes i had used coarse grained str., after using atomistic it worked fine.
I have another question regarding reconstruction simulation.
Before releasing restraints, my mdp parameters for reconstruction
simulation are;
Restrained SA:
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
For Release of restraints,
cap_force = 15000
cap_a = 100
fc_restr = 0
r_CGW = 0.21
fc_restrW = 0
rel_steps = 5000
rel_water = yes
i will be setting rel_steps to 5000,
Should i set rel_water = yes, and set fc_restr = 0, fc_restrW = 0 ??
Kind Regards,
Chetan.
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- xavier
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11 years 11 months ago #942
by xavier
Sorry for the delay in answering but we had a problem with the server ...
did you manage to fix the problem you had?
XAvier.
Replied by xavier on topic Reverse transformation- pdb2gmx error
c.poojari wrote: Dear Andrzej,
Yes i had used coarse grained str., after using atomistic it worked fine.
I have another question regarding reconstruction simulation.
Before releasing restraints, my mdp parameters for reconstruction
simulation are;
Restrained SA:
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
For Release of restraints,
cap_force = 15000
cap_a = 100
fc_restr = 0
r_CGW = 0.21
fc_restrW = 0
rel_steps = 5000
rel_water = yes
i will be setting rel_steps to 5000,
Should i set rel_water = yes, and set fc_restr = 0, fc_restrW = 0 ??
Kind Regards,
Chetan.
Sorry for the delay in answering but we had a problem with the server ...
did you manage to fix the problem you had?
XAvier.
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- c.poojari
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11 years 11 months ago #945
by c.poojari
Replied by c.poojari on topic Reverse transformation- pdb2gmx error
Hi Xavier,
I am still stuck with it.
Regards,
Chetan
I am still stuck with it.
Regards,
Chetan
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- xavier
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11 years 11 months ago #946
by xavier
Replied by xavier on topic Reverse transformation- pdb2gmx error
Ok let's try to fix your problem. Could you summarize the problem and what you might have tried on the mean time.
XAvier.
XAvier.
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- c.poojari
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11 years 11 months ago #962
by c.poojari
Replied by c.poojari on topic Reverse transformation- pdb2gmx error
Hi Xavier,
I am running protein-membrane reverse transformation simulation.
I ran restrained simulated annealing with below parameters, run completed successfully. I ran this at 1 fs time step for 40 ps.
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
Now for release of restraints, i have used the following parameters. Even this run completed without any errors. I ran this at 1 fs time step for 40 ps.
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 5000
rel_water = no
In total i ran reverse tranformation for 80 ps. Please can i know if my settings for release of restraints is alright or should i be setting rel_water= yes.
Kind Regards,
Chetan.
I am running protein-membrane reverse transformation simulation.
I ran restrained simulated annealing with below parameters, run completed successfully. I ran this at 1 fs time step for 40 ps.
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 0
rel_water = no
Now for release of restraints, i have used the following parameters. Even this run completed without any errors. I ran this at 1 fs time step for 40 ps.
cap_force = 15000
cap_a = 100
fc_restr = 12000
r_CGW = 0.21
fc_restrW = 400
rel_steps = 5000
rel_water = no
In total i ran reverse tranformation for 80 ps. Please can i know if my settings for release of restraints is alright or should i be setting rel_water= yes.
Kind Regards,
Chetan.
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