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also for non-membrane proteins?
- meher
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14 years 6 days ago #352
by meher
also for non-membrane proteins? was created by meher
Hi
I've a quick question, are the protein force fields developed in martini also good for proteins that are not in membranes? I was trying to run a simulation with a protein in water with the standard parameters recommended in the martini tutorials and it collapses within a thousand steps into a entirely different structure.
Many thanks for in advance !
meher
I've a quick question, are the protein force fields developed in martini also good for proteins that are not in membranes? I was trying to run a simulation with a protein in water with the standard parameters recommended in the martini tutorials and it collapses within a thousand steps into a entirely different structure.
Many thanks for in advance !
meher
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- mara
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14 years 3 days ago #355
by mara
In principle the force field is just as applicable to soluble proteins than membrane proteins. Even though some CG proteins undergo unrealistically large conformational fluctuations (a problem that can be fixed to some extent by using a global elastic network, i.e. ElNeDyn in the Downloads->Tools section), a quick collapse of a protein structure is usually a tell-tale sign of a problematic starting structure rather than a problem in the model itself.
Did you follow the protocol out-lined in the tutorial? Minimise in vacuum, solvate, position restraint protein etc.
-martti-
Replied by mara on topic also for non-membrane proteins?
meher wrote: I've a quick question, are the protein force fields developed in martini also good for proteins that are not in membranes? I was trying to run a simulation with a protein in water with the standard parameters recommended in the martini tutorials and it collapses within a thousand steps into a entirely different structure.
In principle the force field is just as applicable to soluble proteins than membrane proteins. Even though some CG proteins undergo unrealistically large conformational fluctuations (a problem that can be fixed to some extent by using a global elastic network, i.e. ElNeDyn in the Downloads->Tools section), a quick collapse of a protein structure is usually a tell-tale sign of a problematic starting structure rather than a problem in the model itself.
Did you follow the protocol out-lined in the tutorial? Minimise in vacuum, solvate, position restraint protein etc.
-martti-
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- meher
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13 years 11 months ago #366
by meher
Replied by meher on topic also for non-membrane proteins?
I followed the procedure outlined in the tutorial example, but still it collapsed. I will try the elastic network approach. Thanks a lot for the suggestion
-meher
-meher
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