FDATools Installation about gromacs-fda HOT 4 CLOSED

Hi Khushboo,

the FDAtools are obsolete and were replace by the GROMACS analysis tools, descriped in the FDA manual chapter 5. The packages in fda-archive are only provided for backward compatibility reasons and will not be supported anymore. Therefore, I highly recommend to use the new FDA version and analysis tools. However, if you still interested in using the old FDAtools you have to install it as described at fda-archive/README.md typing R CMD INSTALL FDAtools_1.0.tar.gz outside the R console.

Best regards,
Bernd

from gromacs-fda.

Thank you so much for your constant help, Bernd.
Since I was having a tough time installing newer versions of FDA, TRFDA, and FDATools on my university cluster I had to settle for an older version. Right now, I am in the last of FDA, which is generating residue and atom graph. While running atomGraph command needed to generate network representation of the force propagation within my protein I am receiving an error. Below are commands that I ran for utilizing the atomGraph function.
$ module load gromacs/fda
$ R
$ library(FDAtools)
$atomGraph(prod_50ns.pdb, as.matrix(scalar_avg.fm), cutoff=5, file="test_graph.pdb")
Error in atomGraph(prod_50ns.pdb, scalar_avg.fm, cutoff = 5, file = "test_graph.pdb") :
object 'scalar_avg.fm' not found

I am not sure why is it unable to find the file/s even if I am in the directory where the files are located, unless the syntax is wrong or I am missing something. Could you please guide me to the manual or documentation that discuss the syntax for utilizing the modules within FDAtools? I got the above atomGraph syntax from this link, https://rdrr.io/github/tectronics/force-distribution-analysis.r-libs/man/atomGraph.html).

Please advise.
Thanks,
Khushboo

from gromacs-fda.

Hi Khushboo,

I stlll strongly recommend an upgrade to the newest FDA version and analysis tools. Its better to spend your time into the installation of the new version than to learn the usage of the old tools. I am also not very helpful since I worked only with the new TRFDA version. The only hint I can give is that the filename 'scalar_avg.fm' is not an object. You should first read the file into a data object using 'data(scalar_avg)' and use than the data object with 'as.matrix(scalar_fm)', as described in the example atomGraph documentation you found at R docs.

Best regards,
Bernd

from gromacs-fda.

Please reopen the issue or create a new one in case of more questions.

from gromacs-fda.