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General discussions (Q&As) / basepair centers
« on: April 28, 2020, 06:10:00 pm »
Hi everyone,
I hope you are all doing ok on these crazy days.
I have performed some molecular dynamics simulations for a DNA-protein system. I am trying to understand the results by analyzing the DNA's structure before and after the protein binds. In particular I'm trying to calculate a parameter called the crookedness (beta) of the DNA which is defined as cosine(beta) = x / y , where x is the end-to-end distance of the molecule and y is the sum of the individual base-pair-center distance (PHYSICAL REVIEW LETTERS 122, 048102 (2019)). Reading the x3dna documentation I've found that the distance between two consecutive base-pair centers is equal to the square root of (shift^2 + slide² + rise^2), nevertheless I still need to calculate the end-to-end distance of the entire DNA (or the centers for the corresponding basepairs). Can anyone please help me to obtain this information with x3dna? I have already run x3dna_ensemble analyze for a list of MD snapshots and can run x3dna_ensemble extract stuff but do not know where to find the information for the coordinates of the basepairs.
Best regards.
Daniel
I hope you are all doing ok on these crazy days.
I have performed some molecular dynamics simulations for a DNA-protein system. I am trying to understand the results by analyzing the DNA's structure before and after the protein binds. In particular I'm trying to calculate a parameter called the crookedness (beta) of the DNA which is defined as cosine(beta) = x / y , where x is the end-to-end distance of the molecule and y is the sum of the individual base-pair-center distance (PHYSICAL REVIEW LETTERS 122, 048102 (2019)). Reading the x3dna documentation I've found that the distance between two consecutive base-pair centers is equal to the square root of (shift^2 + slide² + rise^2), nevertheless I still need to calculate the end-to-end distance of the entire DNA (or the centers for the corresponding basepairs). Can anyone please help me to obtain this information with x3dna? I have already run x3dna_ensemble analyze for a list of MD snapshots and can run x3dna_ensemble extract stuff but do not know where to find the information for the coordinates of the basepairs.
Best regards.
Daniel