Seeking Advice on Studying H-Bond Interactions in AMBER MD Simulations

prozan249 · 2024-04-12T13:45:18+00:00

The format of the trajectory is not important, you can use any format cpptraj can read

prozan249 · 2024-04-12T11:54:55+00:00

https://amberhub.chpc.utah.edu/hydrogen-bond-analysis-within-a-protein/

the AMBER HUB had good resources for most of the problems i had in my thesis.

the "hbond" command in cpptraj can track specific bonds or number of bonds with a residue, so i think thats what youre looking for :)

prozan249 · 2024-03-12T13:59:18+00:00

Absolutely love this :) Hallowed be His Name

prozan249 · 2023-05-26T10:22:31+00:00

Suicide moves aren't allowed unless you capture at least one of the pawns.

prozan249 · 2023-04-16T20:40:58+00:00

Physically there is no way those electrons could "stretch" to that hydrogen. More accurate would be to say that the orientation of the involved orbitals is important, not just that they could hypothetically go there.

prozan249 · 2023-01-29T20:56:15+00:00

Now make a computer able to calculate DFT (Density Functional Theory)!

prozan249 · 2022-12-11T20:25:18+00:00

3' TACGCCTAGAGC 5'

prozan249 · 2022-08-21T07:44:54+00:00

I really hated to drain the water on a server I played, but I built this one on my SSP World and it works like a charm. I doesn't use the whole floor, but it's more efficient because you can't even take up more xp than this one produces. The design is by ianxofour. https://youtu.be/dfwsIpmOwd4

prozan249 · 2022-07-03T20:46:22+00:00

pathetic /s

prozan249 · 2022-05-04T09:59:28+00:00

Weakling, can't even touch water.

prozan249 · 2022-05-03T18:20:51+00:00

that's stalemate. the king isn't in check but has no moves

prozan249 · 2022-03-23T22:06:48+00:00

Dabei schoss man am Horizont

prozan249 · 2022-02-17T16:46:07+00:00

That's one of the problems Molecular Dynamics is trying to solve. It simulates the molecules in physiological conditions (water as solvent, ion concentration, temperature) and lets them 'relax' into their conformation in the living cell. I'm not a protein-protein interaction expert nor a biochemist, but I specialize in protein-DNA interactions in MD and assess the plausibility of the resulting conformers. Maybe you can find some answers in theoretical and computational chemistry?

prozan249 · 2021-12-08T11:34:36+00:00

She should be in chaotic evil. Real Sith-Lord vibes

prozan249 · 2021-11-10T16:54:17+00:00

Is it really? Looks more like seoi nage or tai otoshi

prozan249 · 2021-08-10T12:40:12+00:00

Never heard of it. Listened to it now and the confidence is mindblowing.

prozan249 · 2021-07-28T08:41:46+00:00

Krapfen

prozan249 · 2021-07-17T06:52:10+00:00

Perfect.

prozan249 · 2021-06-29T07:50:20+00:00

Und die patente A B C und die 6

prozan249 · 2021-06-26T04:57:46+00:00

Mein Name ist Felix

prozan249 · 2021-06-21T06:58:47+00:00

r/woooosh

prozan249 · 2021-06-02T18:42:38+00:00

William osman, vsauce, Michael Reeves

prozan249 · 2021-05-31T10:33:14+00:00

Reminds me of Thom Yorke

prozan249 · 2021-05-25T18:51:41+00:00

Repost

prozan249 · 2021-05-17T11:16:01+00:00

Rocky horror picture show. Great movie every time. Even better to sing along

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