Gromacs: Can we process the ss.xpm secondary structure file and save it in R?

[Cheng]

Dear Bio3D, The Gromacs command

gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns

will output the ss.xpm file (attached), which contains the secondary structures of individual residues throughout the simulation times.

I wonder, if there is an existing method to process this file and save it in R?

Thank you.

Yours sincerely Cheng

[Xinqiu Yao]

Hi Cheng,

Bio3D does not have function to directly deal with .xpm file. Note that the main focus of the package are analyses of structural biological data rather than comprehensive processing of all kinds of files generated by simulation software. In fact, it has very limited support of Gromacs. The reason is that for most files there are always ways to convert them from one format to another that is supported by Bio3D.

The file you attached seems to be a plain text file and can be easily parsed by using basic R functions, such as readLines(), strsplit(), etc. You can try to do it by yourself, or if you still have problems just let me know.

[Cheng]

thank you Xin-Qiu, I will write my own script.

[Cheng]

Just to share with you that the GromacsWrapper can do the thing https://github.com/Becksteinlab/GromacsWrapper/issues/125

Also, MDAnalysis is something like bio3d but use python. However, it could not be installed on Windows.

[Xinqiu Yao]

Thanks for sharing the tip, Cheng. It is really good to know.