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Messages - drknnetz

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MD simulations / Re: A-Form B-Form RNA/DNA
« on: August 12, 2015, 07:25:42 pm »
I was basically trying to determine what parameters were used when the software determines A form or B form so I could validate the results from the program to my MD simulations. I will read the paper, thanks for the reference. You are very prompt and helpful!

MD simulations / A-Form B-Form RNA/DNA
« on: August 12, 2015, 05:23:29 pm »
Does anyone know where to find the specifics as to how x3dna paramaterizes whether the RNA is in A form and the DNA is in B form? What coordinates does it use in the DNA molecule or RNA molecule?

Feature requests / Re: Trajectory over time
« on: August 12, 2015, 05:20:55 pm »
Thanks for the response, I used the ruby script and it was great. Trying to figure out a way to edit it to work for the dssr but no luck yet. I also found it useful to compile the trajectory into an output pdb file with "time stamps" of the simulation for each step. So basically my one pdb file has 500 time stamps in it and I am using scripts to analyze those. That may work for others in similar fashion. I'm still a pretty weak programmer though, so it is taking some doing.

Feature requests / Trajectory over time
« on: August 11, 2015, 02:43:31 pm »
Hello all, I am brand new to using dssr and x3DNA. I started yesterday and it seems like a pretty awesome download so thanks for creating this! I was wondering if there is anything in the works for analyzing an entire trajectory? I know this current dssr analyzes pdb files and not an mdcrd file so I'm sure there is a lot more that goes into it. I was just wondering if there was anything in the works.

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.