Talk:AMBER

Untitled

Mjhsieh:

Potential topic in this entry

the contents in the package

the evolution of the force field

Anthracene:

I'm listed as one of the authors of AMBER, so I'm designating myself an expert. :) I've clarified and expanded the force field section and put in a brief summary of the software.

I hope no one is offended that I removed the reference to folding at home. In my opinion (working in the field) the use of the AMBER ff by the Pande group isn't really any more notable than its use by many other people. I'm willing to change my mind on this, though. Anthracene 07:05, 12 February 2006 (UTC)

AMBER (file format) needed

A new page AMBER (file format) is needed, which should cross link to Chemical file format and use also the proper [[Category:Chemical file format]] category. JKW 16:05, 8 April 2006 (UTC)

I'm not sure what the content of this new page would be, since there are multiple AMBER file formats, as described here: AMBER file formats. You want all of these to be described, or is there one in particular that you mean by AMBER file format (perhaps the topology file format)? --Anthracene 23:47, 21 April 2006 (UTC)

If there are multiple file formats, then all should be mentioned and a proper short description and a link-out should be generated. This problem is well know, also for other chemical file formats, like the Chemical table file formats. And exactly this is the reason why we need another page for this. JKW 10:41, 22 April 2006 (UTC)

Initial AMBER (file format) page created, feel free to extend it. JKW 10:56, 22 April 2006 (UTC)

Image

The image actually used MM2 but I don't think there is a visible difference. Bensaccount 19:46, 20 February 2007 (UTC)

Author

I don't think the authors isn't necessary to be listed in wiki. Or at least, I think they should be listed on the Software section, not in the introduction. What do you think about that? Lý Minh Nhật (talk) 03:56, 24 May 2014 (UTC)

Improper Dihedral

Does the potential energy function of Amber Focefield have improper dihedral term? — Preceding unsigned comment added by 108.236.198.181 (talk) 14:13, 25 February 2015 (UTC)

External links modified

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force field terms should define what the variables mean

e.g. in the non-bonded terms f sub ij is not defined. I imagine it is a factor that is 0 for 1-3 bonded atoms, and possibly 0.5 for 1-4 interactions, and 1.0 for other atom-atom interactions.

rij 0 = (r i + r sub j) for two atoms interacting eij = sqrt( ei * ej ) for the two atoms interacting

1/4pie0 = 332.0637 kcal/mol-coulomb 2601:47:477E:43C0:70F3:9D1D:3893:A567 (talk) 13:06, 1 November 2024 (UTC)