i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following
gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx
but i am getting the error
Range checking error (possible bug):
The provided structure file only contains 10 coordinates, but coordinate index
147 was requested for fitting. Make sure to update structure files and index
files if you store only a part of your system.
how should i prepare the md.tpr file for only c-alpha atom
To perform PCA analysis on the C-alpha atoms of a protein using GROMACS, you need to prepare the necessary files and use the appropriate commands. Here are the steps you can follow:
It is important to note that the error you encountered may be due to an issue with the structure file or index file. Make sure that your structure file contains all the necessary coordinates and that the index file correctly selects the C-alpha atoms.For further guidance and troubleshooting, you may find it helpful to consult the GROMACS documentation, user forums, or research papers that discuss PCA analysis in GROMACS.
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