What force fields are used for the calculation of protein interaction with metal surfaces?

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Are there molecular mechanical Force Fields for nitro compounds?

I'm interested in the possibility of reproducing thermodynamic properties within 5%.

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Are there automatic force field generators/services comparable in quality to OPLS?

What do you think about SwissParam, MolMeccano, GAAMP?

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On what software start experiments on protein folding?

What is better for a beginner?

07 August 2015 7,062 3 View

Do the molecular-mechanical models with bond restraints an improvement of any properties except for the specific heat?

Sometimes people justify the imposition of restrictions on the length of the bonds the fact that in such way simulates a quantum mechanical effect of "freezing" of high-frequency oscillations.

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Can you recommend a good overview of halogen bonding?

Thanks.

11 December 2014 9,598 8 View

What is the accuracy of the models of proteins embedded into membrane?

Is there a model that can be regarded as the standard for comparison? Are the coordinates?

11 December 2014 528 2 View

Why Urey-Bradley term largely abandoned in modern force fields?

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Why in today's force fields do we not consider explicitly 1-3 van-der-Waals interactions?

Such interactions are explicitly considered in the force fields of the 70s.

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What quantum-chemical method is preferable to determine the dispersion interaction between the low-polar molecules?

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What force fields are used for modeling strongly polar compounds?

I'm interested in polar compounds in which there is a significant contribution of covalence, for example alkaline earth metal halides.

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Melchor Sanchez-Martinez

I agree with Prof. Coskuner.

Normally you have to take the standard existing force-fields like Amber, Gromos , OPLS or other more specific like MMFF or MM3 and parameterize the metal ligands if it is not done. Take into account that if you google it you could find a lot of metals and ligands coordinates and topologies parameterized for a lot of forcefields.

Furthermore recently an extension of the UFF to metal-organic frameworks has been appeared, may be is an easier starting point, but you should check it, I have never use it.

Carlo Tovar

MM+ is good alternative

Alexey Nikitin

MM+ is not able to calculate proteins.