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I have developed a 3DNA wrapper in C language, which uses GROMACS library to read GROMACS format trajectory, topology and index file. This wrapper dumps frame-wise data to several text files. I guess, this tool will work for any format of MD trajectory such as AMBER, NAMD and CHARMM, but it is yet to be tested.I appreciate your effort in building a 3DNA wrapper for the analysis of GROMACS MD trajectories. It'd be great if you can test and verify that it works for "MD trajectory such as AMBER, NAMD and CHARMM".
Additionally, I am developing Python APIs to analyze the vast amount of data obtained from the wrapper. It includes many useful methods to analyze properties of the DNA. One can analyze the changes in DNA upon binding to protein. Also, it can be used to calculate elastic properties of the DNA. Moreover, I have implemented few methods to analyze bending motions of helical axis.If done right, a Python API on top of the wrapper will make the results of MD simulations readily accessible to a much larger community. I'd suggest you start from a small selection of key parameters, and build your tool incrementally.
I have a query. Since I am using C language for wrapper, may I get C APIs/library of 3DNA such that I can use directly these APIs in wrapper. Currently, I use find_pair and analyze executable binary. When I use wrapper for ~30,000 frames containing 60 BP DNA, it takes a while to complete and I want to speed up this calculation.3DNA is composed of a few standalone commandline tools, and does not include a C APIs/library. However, I'd like to help you out where appropriate. Do you really need to run find_pair for each frame? See the output from running "x3dna_ensemble analyze -h". How long it takes approximately for running a MD simulation vs analyzing it?
I would like to release this tool through GitHub, however I am not sure that this work alone is of publication level. Please let me know, what would be your suggestion.GitHub seems a good option. As for publishing such work, did you know the paper "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data (http://pubs.acs.org/doi/abs/10.1021/ct400341p)" by Daniel Roe and Thomas Cheatham?
It'd be great if you can test and verify that it works for "MD trajectory such as AMBER, NAMD and CHARMM".
If done right, a Python API on top of the wrapper will make the results of MD simulations readily accessible to a much larger community. I'd suggest you start from a small selection of key parameters, and build your tool incrementally.
3DNA is composed of a few standalone commandline tools, and does not include a C APIs/library. However, I'd like to help you out where appropriate.
Do you really need to run find_pair for each frame? See the output from running "x3dna_ensemble analyze -h".
GitHub seems a good option. As for publishing such work, did you know the paper "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data (http://pubs.acs.org/doi/abs/10.1021/ct400341p)" by Daniel Roe and Thomas Cheatham?
I was thinking that if I will able to pass coordinates and base-pair information directly to some C functions present in analyze, which in results would return all calculated parameters. At least, I can avoid writing and reading intermediate PDB files, and this process will speedup the wrapper execution.
I have implemented two type of calculations. In first type, find_pair executes only once at the start, and then same base-pairs information is used for whole calculation. However, during simulations, new base-pair may form and old may break, particularly in RNA. Therefore in second type, find_pair executes at every frame, and output files are generated such that, one can easily able to get how base-pairs are forming and breaking.
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University