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Backward failed for CHOL molecules
- Smotta
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6 years 5 months ago #7414
by Smotta
Backward failed for CHOL molecules was created by Smotta
Hi,
I'm trying to backmap a Martini CG system composed of two proteins, within a membrane of POPC/CHOL 10:1. While the backmapping works with proteins only, it failed when I try to backmap the whole membrane. In particular I obtain an initial warning for cholesterols:
After that those warnings, the initram.py script launch energy minimizations completed and MD simulations, but at the first step of MD, the simulation stopped due to LINCS warnings. Even trying to increase minimization steps or reduce simulation timestep failed.
The problem appear to be related to CHOL molecules because removing them from the system the simulation initram pipeline works and the final structure (without cholesterols) looks fine.
The backmap of a single CHOL molecule was instead completed properly.
How can I resolve the problem?
PS: I used the charm36 forcefield, and the initram-v5 script for backmapping.
Thanks!
I'm trying to backmap a Martini CG system composed of two proteins, within a membrane of POPC/CHOL 10:1. While the backmapping works with proteins only, it failed when I try to backmap the whole membrane. In particular I obtain an initial warning for cholesterols:
Not all positions defined for [trans] operation:
[('C44', None), ('C47', None), ('C1', (8.931246084195303, 3.4044965661932687, 4.687000913633694)), ('O2', None)]
Not all positions defined for [trans] operation:
[('H45', None), ('C47', None), ('C1', (8.931246084195303, 3.4044965661932687, 4.687000913633694)), ('O2', None)]
Not all positions defined for [trans] operation:
[('H46', None), ('C47', None), ('C1', (8.931246084195303, 3.4044965661932687, 4.687000913633694)), ('O2', None)]After that those warnings, the initram.py script launch energy minimizations completed and MD simulations, but at the first step of MD, the simulation stopped due to LINCS warnings. Even trying to increase minimization steps or reduce simulation timestep failed.
The problem appear to be related to CHOL molecules because removing them from the system the simulation initram pipeline works and the final structure (without cholesterols) looks fine.
The backmap of a single CHOL molecule was instead completed properly.
How can I resolve the problem?
PS: I used the charm36 forcefield, and the initram-v5 script for backmapping.
Thanks!
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- riccardo
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6 years 5 months ago #7417
by riccardo
Replied by riccardo on topic Backward failed for CHOL molecules
Hi,
do you get the same warning when you try to backmap a single CHOL?
How big is your system?
do you get the same warning when you try to backmap a single CHOL?
How big is your system?
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- Smotta
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6 years 5 months ago #7418
by Smotta
Replied by Smotta on topic Backward failed for CHOL molecules
Yes, I get the same error when I backmap a single cholesterol molecule. My system us a 20×20 membrane POPC:CHOL 10:1 with 2 proteins embedded.
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- riccardo
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6 years 5 months ago #7419
by riccardo
Replied by riccardo on topic Backward failed for CHOL molecules
Looking through the forum, the error you get seems to be similar to this one:
www.cgmartini.nl/index.php/component/kun...-backward-py-mapping
(see the last three posts). Please let me know if this fixes it.
I suppose also you got the mapping file for chol from:
cgmartini.nl/index.php/force-field-param...r=Sterols&lipid=CHOL
www.cgmartini.nl/index.php/component/kun...-backward-py-mapping
(see the last three posts). Please let me know if this fixes it.
I suppose also you got the mapping file for chol from:
cgmartini.nl/index.php/force-field-param...r=Sterols&lipid=CHOL
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- Smotta
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6 years 3 weeks ago #7587
by Smotta
Replied by Smotta on topic Backward failed for CHOL molecules
Sorry for the delay in the response. I'm still stucked with the same problem. I have taken the cholesterol mapping file from the link you gave me, but the problem persist. When I try to backmap the cholesterol molecules alone, I obtain the same warning reported above, but after the minimization the MD simulations are stable. The problems regards the backmap of the whole system and starts from minimization:
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Any suggestion?
Thanks in advance
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Any suggestion?
Thanks in advance
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- riccardo
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6 years 2 weeks ago - 6 years 2 weeks ago #7590
by riccardo
Replied by riccardo on topic Backward failed for CHOL molecules
Backmapping for a single CHOL mol works, backmapping of everything else but CHOL works, together it does not..
Did you already try things like increasing the number of minimization steps (for either the bonded-only minimization (flag -em) and the nonbonded minimization (flag -nb))? E.g.
./initram.sh -f system.gro -o AA.gro -to charmm -p system_AA.top -em 1500 -nb 1500
or.. I am out of ideas. Make sure your target TOP contains the atomistic CHOL topology which corresponds to the CHOL mapping file you're using.
Does the 0-backward.gro of the CHOL-only backmapping look reasonable?
Did you already try things like increasing the number of minimization steps (for either the bonded-only minimization (flag -em) and the nonbonded minimization (flag -nb))? E.g.
./initram.sh -f system.gro -o AA.gro -to charmm -p system_AA.top -em 1500 -nb 1500
or.. I am out of ideas. Make sure your target TOP contains the atomistic CHOL topology which corresponds to the CHOL mapping file you're using.
Does the 0-backward.gro of the CHOL-only backmapping look reasonable?
Last edit: 6 years 2 weeks ago by riccardo.
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- Smotta
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6 years 2 weeks ago #7591
by Smotta
Replied by Smotta on topic Backward failed for CHOL molecules
I have finally found the problem. It seems that the atomistic topology for cholesterol molecule was not in agreement with the Martini mapping files. I have modified the atom names and order of atoms in the topology file according to what expected in the mapping files and it finally works!
Thanks for the support,
Stefano
Thanks for the support,
Stefano
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6 years 2 weeks ago #7592
by riccardo
Replied by riccardo on topic Backward failed for CHOL molecules
Awesome, cheers!
Riccardo
Riccardo
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5 years 8 months ago - 5 years 8 months ago #7748
by songhd
Replied by songhd on topic Backward failed for CHOL molecules
Stefano
I am also trying to convert the CHOL molecules from CG to AA but got an error message.
Could you or else share chol.itp file?
My error message is "No default Bond types, No default U-B types. No default Proper Dih. types"
My email : This email address is being protected from spambots. You need JavaScript enabled to view it.
thanks
Hyun
I am also trying to convert the CHOL molecules from CG to AA but got an error message.
Could you or else share chol.itp file?
My error message is "No default Bond types, No default U-B types. No default Proper Dih. types"
My email : This email address is being protected from spambots. You need JavaScript enabled to view it.
thanks
Hyun
Last edit: 5 years 8 months ago by songhd.
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