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PMF of protein dimerization using MARTINI3 forcefield
- ayan95
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2 years 10 months ago #8958
by ayan95
PMF of protein dimerization using MARTINI3 forcefield was created by ayan95
Hi,
I was trying to reproduce the published dimerization energy value for GpA and EphA1 by using the MARTINI3 forcefield.
It seems like my results are deviating by a large number for both cases. I am not using the flexible protein model.
I am still not able to equilibrate the bilayer with the flexible model. It is giving linc error for a few protein beads.
Thanks,
Ayan
I was trying to reproduce the published dimerization energy value for GpA and EphA1 by using the MARTINI3 forcefield.
It seems like my results are deviating by a large number for both cases. I am not using the flexible protein model.
I am still not able to equilibrate the bilayer with the flexible model. It is giving linc error for a few protein beads.
Thanks,
Ayan
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- riccardo
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2 years 10 months ago #8961
by riccardo
Replied by riccardo on topic PMF of protein dimerization using MARTINI3 forcefield
Be sure to follow the same protocol as stated in
www.nature.com/articles/s41592-021-01098-3
and you should be OK.
How large is large?
What do you mean by flexible model?
How large is large?
What do you mean by flexible model?
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- ayan95
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2 years 10 months ago #8966
by ayan95
Replied by ayan95 on topic PMF of protein dimerization using MARTINI3 forcefield
I am using the same protocol as mentioned in the MARTINI3 paper, i.e., I am using the new-RF mdp file.
Q. How large is large?
The PMF depth of GpA is off by ~10 kJ/mol (I am getting more like MARTINI2 result) and EphA1 is off by 7 kJ/mol.
Q. What do you mean by flexible model?
In the martinize2 protein itp file. I see you guys included two options for sidechain parameter. One is flexible with sidechain beads interactions included in the bonded parameter. One like previous (#ifndef FLEXIBLE), sidechain beads are constrained.
Please let me know if I can share any files. Maybe through emails.
Thanks,
Ayan
Q. How large is large?
The PMF depth of GpA is off by ~10 kJ/mol (I am getting more like MARTINI2 result) and EphA1 is off by 7 kJ/mol.
Q. What do you mean by flexible model?
In the martinize2 protein itp file. I see you guys included two options for sidechain parameter. One is flexible with sidechain beads interactions included in the bonded parameter. One like previous (#ifndef FLEXIBLE), sidechain beads are constrained.
Please let me know if I can share any files. Maybe through emails.
Thanks,
Ayan
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