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Error when running initram.sh
- Romero
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9 years 5 months ago #4190
by Romero
Error when running initram.sh was created by Romero
Dear all,
I am trying to make the backward transformation of my coarse-grained system (which contains 1 protein, 300 DPPC and 7000 W, and run for 450 ns). I am trying with backward method. I have followed religiosly all the steps in the tutorial and have got some help from gromacs tutorial to make the atomistic topology file.
I have got the atomistic topology file in which i have included itp files for DPPC (i have also compare it with the one in the example and it seems it is alright), I have got the cg structure file.
However I keep getting this:
[]
Traceback (most recent call last):
File "/home/raquel/ACADWORK/ATOMISTIC/BACKWARD/GBA/GBA-ATOM-11/backward.py", line 821, in <module>
raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: ALA
What can I do? Help me please!
I am trying to make the backward transformation of my coarse-grained system (which contains 1 protein, 300 DPPC and 7000 W, and run for 450 ns). I am trying with backward method. I have followed religiosly all the steps in the tutorial and have got some help from gromacs tutorial to make the atomistic topology file.
I have got the atomistic topology file in which i have included itp files for DPPC (i have also compare it with the one in the example and it seems it is alright), I have got the cg structure file.
However I keep getting this:
[]
Traceback (most recent call last):
File "/home/raquel/ACADWORK/ATOMISTIC/BACKWARD/GBA/GBA-ATOM-11/backward.py", line 821, in <module>
raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: ALA
What can I do? Help me please!
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- Romero
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9 years 5 months ago #4191
by Romero
Replied by Romero on topic Error when running initram.sh
PS I am using Gromacs 4.6.2 and I have tried with both Gromos43a1 and Gromos53a6.
Thanks
Thanks
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- Vytautasrask
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8 years 11 months ago #4545
by Vytautasrask
Replied by Vytautasrask on topic Error when running initram.sh
I am trying to make the backward transformation and get almost identical error except Unknown residue: ARG.
I tried same on system without protein too then I get similar error again, this time about DPPC.
I tried same on system without protein too then I get similar error again, this time about DPPC.
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- tsjerk
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8 years 11 months ago #4546
by tsjerk
Replied by tsjerk on topic Error when running initram.sh
Can you post more information? What is in your system and what command line did you use to run? Then what output did you get in the terminal?
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- Vytautasrask
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8 years 11 months ago #4547
by Vytautasrask
Replied by Vytautasrask on topic Error when running initram.sh
I found post in mailing list and did:
Now it complains only about my custom built lipids. I think that is normal../initram.sh -f insane.gro -p topol.top -to gromos
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8 years 11 months ago #4548
by Vytautasrask
Replied by Vytautasrask on topic Error when running initram.sh
Now I get:
From where I can get it?
I give same topol.top file I use for my Martini simulations. This one:Fatal error:
No such moleculetype SOL
Or I should provide other topology file to -p flag?#include "martini_v2.2P.itp"
#include "martini_v2.0_lipids.itp"
#include "martini_v2.0_ions.itp"
#include "Protein.itp"
#define RUBBER_BANDS
[ system ]
NORMAL
[ molecules ]
; X: 15.000 (19 lipids) Y: 10.000 (13 lipids)
; 243 lipids in upper leaflet, 247 lipids in lower leaflet
; NDX Solute 1 38
; Charge of protein: 5.000000
; NDX Membrane 39 5945
; Charge of membrane: -63.000000
; Total charge: -58.000000
; NDX Solvent 5946 27221
; NDX System 1 27221
Protein 1
DPPC 96
POPC 74
DOPC 42
POPS 31
DPPC 97
POPC 75
DOPC 42
POPS 32
PW 6820
NA+ 105
CL- 45
So not that one I pasted above?-p Input atomistic target topology
From where I can get it?
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- tsjerk
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8 years 11 months ago #4549
by tsjerk
Replied by tsjerk on topic Error when running initram.sh
The atomistic target topology is required to let the program know what you want to get out. You will certainly also need it to run the subsequent atomistic simulations.
The protein topology can be generated with pdb2gmx from the original PDB file. You'll need to have atomistic topologies for the lipids, #include them in the atomistic .top file and add the names and numbers under [ system ], just like the list in the coarse grained one you have. The water and ions you can leave out, as these are generated automatically, except that you do need to #include "spc.itp" and "ions.itp".
The protein topology can be generated with pdb2gmx from the original PDB file. You'll need to have atomistic topologies for the lipids, #include them in the atomistic .top file and add the names and numbers under [ system ], just like the list in the coarse grained one you have. The water and ions you can leave out, as these are generated automatically, except that you do need to #include "spc.itp" and "ions.itp".
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- nivedita
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8 years 9 months ago #4687
by nivedita
Replied by nivedita on topic Error when running initram.sh
Hi tsjerk,
When im running the command:./initram.sh -f md.gro -p topol.top -to gromos -p system.top with little modification in initram.sh is shows following stuff:
NOTE 1 : You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Largest charge group radii for Van der Waals: 0.254, 0.254 nm Largest charge group radii for Coulomb: 0.254, 0.254 nm This run will generate roughly 86 Mb of data Steepest Descents converged to machine precision in 407 steps, but did not reach the requested Fmax < 10. Potential Energy = -6.4093130e+06 Maximum force = 4.4133960e+03 on atom 460 Norm of force = 3.9089390e+01 but apart from this it is running very well. Fmax <10 is not reached but the steepest descent is converged my doubt is that it will create any problem, Should i ignore this? because after getting backmapped.gro file again i have to do minimization, equilibration and final production run (20ns).[file 2-EM.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
Largest charge group radii for Van der Waals: 0.254, 0.254 nm
Largest charge group radii for Coulomb: 0.254, 0.254 nm
This run will generate roughly 86 Mb of data
Steepest Descents converged to machine precision in 407 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -6.4093130e+06
Maximum force = 4.4133960e+03 on atom 460
Norm of force = 3.9089390e+01
but apart from this it is running very well. Fmax <10 is not reached but the steepest descent is converged my doubt is that it will create any problem, Should i ignore this? because after getting backmapped.gro file again i have to do minimization, equilibration and final production run (20ns).
When im running the command:./initram.sh -f md.gro -p topol.top -to gromos -p system.top with little modification in initram.sh is shows following stuff:
NOTE 1 : You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Largest charge group radii for Van der Waals: 0.254, 0.254 nm Largest charge group radii for Coulomb: 0.254, 0.254 nm This run will generate roughly 86 Mb of data Steepest Descents converged to machine precision in 407 steps, but did not reach the requested Fmax < 10. Potential Energy = -6.4093130e+06 Maximum force = 4.4133960e+03 on atom 460 Norm of force = 3.9089390e+01 but apart from this it is running very well. Fmax <10 is not reached but the steepest descent is converged my doubt is that it will create any problem, Should i ignore this? because after getting backmapped.gro file again i have to do minimization, equilibration and final production run (20ns).[file 2-EM.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
Largest charge group radii for Van der Waals: 0.254, 0.254 nm
Largest charge group radii for Coulomb: 0.254, 0.254 nm
This run will generate roughly 86 Mb of data
Steepest Descents converged to machine precision in 407 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -6.4093130e+06
Maximum force = 4.4133960e+03 on atom 460
Norm of force = 3.9089390e+01
but apart from this it is running very well. Fmax <10 is not reached but the steepest descent is converged my doubt is that it will create any problem, Should i ignore this? because after getting backmapped.gro file again i have to do minimization, equilibration and final production run (20ns).
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- tsjerk
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8 years 9 months ago #4688
by tsjerk
Replied by tsjerk on topic Error when running initram.sh
initram.sh uses pretty simple schemes to quickly relax the configuration. The purpose is to generate a structure that is reasonable and that can be used for further (refinement) simulations. initram.sh has an option -mdp that allows providing your own mdp files, which will be used after the initial relaxation. The advice is to first add a short equilibration (~0.1 ns) run under production conditions (NpT) with a reduced time step and after that start the production run:
initram.sh -f ... -p ... -o ... -from ... -to ... -mdp equilibrate.mdp -mdp production.mdp
initram.sh -f ... -p ... -o ... -from ... -to ... -mdp equilibrate.mdp -mdp production.mdp
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- nivedita
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8 years 9 months ago - 8 years 9 months ago #4692
by nivedita
Replied by nivedita on topic Error when running initram.sh
Hi tsjerk,
When im using the default initram.sh file along with im keeping the trash file to check that the structure is converged or not. so i found that than em1.log and em2.log shows:
Steepest Descents did not converge to Fmax < 10 in 501 steps.
Potential Energy = -4.9557420e+06
but rest of the things like nvt(300K) at 0.2 0.5 1.0 and 2.0 fs are completed so should i ignore the energy convergence steps? if yes than after getting backmapping.gro structure i can further run minimization.
When im using the default initram.sh file along with im keeping the trash file to check that the structure is converged or not. so i found that than em1.log and em2.log shows:
Steepest Descents did not converge to Fmax < 10 in 501 steps.
Potential Energy = -4.9557420e+06
but rest of the things like nvt(300K) at 0.2 0.5 1.0 and 2.0 fs are completed so should i ignore the energy convergence steps? if yes than after getting backmapping.gro structure i can further run minimization.
Last edit: 8 years 9 months ago by nivedita. Reason: make it clear
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- tsjerk
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8 years 9 months ago #4696
by tsjerk
Replied by tsjerk on topic Error when running initram.sh
That's not a problem. Please check the Gromacs user list on more background information regarding energy minimization.
The structure that comes out of backward/initram is already relaxed. You don't need to energy minimize. Just start a short run under your production simulation conditions, possibly with a reduced time step and maybe using Berendsen pressure coupling for better convergence. Then after that you can go straight to production.
The structure that comes out of backward/initram is already relaxed. You don't need to energy minimize. Just start a short run under your production simulation conditions, possibly with a reduced time step and maybe using Berendsen pressure coupling for better convergence. Then after that you can go straight to production.
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