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Elnedyn and backbone RMSD
- Luca
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8 years 3 weeks ago #5469
by Luca
Elnedyn and backbone RMSD was created by Luca
Does the ElNeDyn affect the RMSD of the protein backbone?
Because i want to use the ElNeDyn on a protein to see its stability but i fear that what i see it's not the stability of the protein but the effect of ElNeDyn restraints on the backbone.
Looking at ElNeDyn tutorial the difference in RMSD with ElNeDyn look massive in comparison with standard Martini.
Because i want to use the ElNeDyn on a protein to see its stability but i fear that what i see it's not the stability of the protein but the effect of ElNeDyn restraints on the backbone.
Looking at ElNeDyn tutorial the difference in RMSD with ElNeDyn look massive in comparison with standard Martini.
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- helgi
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8 years 3 weeks ago #5471
by helgi
Replied by helgi on topic Elnedyn and backbone RMSD
I am not sure if I get your question correctly, but yes using ElNeDyn will “mostly” fix the structure of your protein and therefore limit the RMSD. Most proteins in Martini are not stable without some sort of elastic network to keep their structure therefore if you want to study protein stability Martini is probably not the best choice.
The RMSD with ElNeDyn is better explained in the ElNeDyn paper:
X. Periole, M. Cavalli, S.J. Marrink, M. Ceruso. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics and intermolecular recognition. J. Chem. Th. Comp., 5:2531-2543, 2009.
Cheers,
- Helgi
The RMSD with ElNeDyn is better explained in the ElNeDyn paper:
X. Periole, M. Cavalli, S.J. Marrink, M. Ceruso. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics and intermolecular recognition. J. Chem. Th. Comp., 5:2531-2543, 2009.
Cheers,
- Helgi
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- Luca
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8 years 3 weeks ago #5473
by Luca
Replied by Luca on topic Elnedyn and backbone RMSD
Thank you for your answer, you got my question right.
So you are saying that if my protein is not really stable the best choice is use the elnedyn to keep the structure.
But i ran 2 simulations of the same transmembrane protein with classic Martini in 2 different membranes (that's why i'm using CG Martini) and i had 2 backbone RMSD with average running RMSD of 0,185nm and 0,175nm that look stable to me (even with the .gro file visualization with VMD).
It would be great for me if ElNeDyn can give me more stability to show if there's a different trend in the Backbone RMSD to indicate a more stable protein. What i dont want is that using ElNeDyn will make me loose that difference in trend that will make the result look the same.
i hope i explained myself right :P
So you are saying that if my protein is not really stable the best choice is use the elnedyn to keep the structure.
But i ran 2 simulations of the same transmembrane protein with classic Martini in 2 different membranes (that's why i'm using CG Martini) and i had 2 backbone RMSD with average running RMSD of 0,185nm and 0,175nm that look stable to me (even with the .gro file visualization with VMD).
It would be great for me if ElNeDyn can give me more stability to show if there's a different trend in the Backbone RMSD to indicate a more stable protein. What i dont want is that using ElNeDyn will make me loose that difference in trend that will make the result look the same.
i hope i explained myself right :P
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- helgi
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8 years 3 weeks ago #5479
by helgi
Replied by helgi on topic Elnedyn and backbone RMSD
I think I now understand you question but sadly it’s really hard to say anything without carefully looking at the specific protein / system in question.
ElNeDyn, or adding a elastic network, will stabilize your protein overall structure but it can also over stabilize e.g. link together parts of your protein that potentially could separate. You can solve this by selectively adding the elastic network (or removing some unwanted elastic bonds) but to know what should be able to move and what not requires a lot of knowledge about your system and preferable experimental and/or atomistic reference data.
ElNeDyn, or adding a elastic network, will stabilize your protein overall structure but it can also over stabilize e.g. link together parts of your protein that potentially could separate. You can solve this by selectively adding the elastic network (or removing some unwanted elastic bonds) but to know what should be able to move and what not requires a lot of knowledge about your system and preferable experimental and/or atomistic reference data.
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- Luca
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8 years 3 weeks ago #5482
by Luca
Replied by Luca on topic Elnedyn and backbone RMSD
I don't know what bond to remove, i guess i will go with normal martini because i have a stable system.
Thank you for your time :)
Thank you for your time :)
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