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Questions and answers => MD simulations => Topic started by: rwmolt on February 19, 2016, 11:42:23 am

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Title: Analysis of Amber .mdcrd File
Post by: rwmolt on February 19, 2016, 11:42:23 am

Is there a way to analyze an Amber trajectory file (.mdcrd, in my case) using 3DNA? Other than to make a ton of PDB files from the trajectory using cpptraj, of course (ends up being a lot of "needless" I/O to make these from a trajectory and then analyze). How would one load in a parameter file to define a trajectory's atom labels?

Thank you for your time,

Title: Re: Analysis of Amber .mdcrd File
Post by: xiangjun on February 19, 2016, 01:16:22 pm

By design, the x3dna_ensemble Ruby script works on the standard MODEL/ENDMDL delineated PDB format, as for NMR ensemble structures in the RCSB PDB. MD-application specific binary formats are avoided on purpose. I'd assume each MD package comes with a utility to convert its binary format to the PDB ensemble format. You may need to try to find out if the x3dna_ensemble Ruby script is efficient enough for your purpose.

Alternatively, you may give do_x3dna (http://rjdkmr.github.io/do_x3dna/) a try. See quote below for what it is.

Quote

do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations. It uses 3DNA package to calculate several structural descriptors of DNA/RNA from the GROMACS MD trajectory. It executes 3DNA tools to calculate these descriptors and subsequently, extracts these output and saves in to external output files as a function of time.

HTH,

Xiang-Jun

Title: Re: Analysis of Amber .mdcrd File
Post by: sacky0003 on June 15, 2017, 11:47:47 am

Dear sir,

I am using AMBER package. I want to know is it possible to calculate Torsional angle wheel for average angles of segment of a bound and an unbound DNA from AMBER trajectory file (.mdcrd) ??

Thanks and regards.

saikat

Title: Re: Analysis of Amber .mdcrd File
Post by: xiangjun on June 15, 2017, 12:07:32 pm

3DNA starts from the standard MODEL/ENDMDL ensemble PDB format, as for NMR structures. It does not work directly from an AMBER trajectory file, or other specialized MD formats. However, it should be feasible to convert MD-specific formats to the standard PDB ensemble format. For torsional anlge calculations, you may want to try DSSR (which has the --nmr option).

Alternatively, you may try do_x3dna (https://github.com/rjdkmr/do_x3dna), or Curves+.

Xiang-Jun

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