Hello!
How can I calculate radius of gyration for the proteins using .gro files.
We use .tpr and .xtc files to calculate R of G but right now I need to use my .gro files.
Thank you.
you can use gro files instead of xtc file
http://manual.gromacs.org/archive/4.6.5/online/g_gyrate.html
Thank you Kolattukudy,
And what can I use instead of tpr files?
Because as you see:
gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg
I need one .tpr and one .xtc.
But I cannot use my .tpr file.
Thank you.
Why can't you use your .tpr file?
Both -s and -f accept .gro files (see the help text). Whether or not you get a proper result is another matter; you need to get a center of mass as part of that calculation, and with only a coordinate file, the masses may not be correct. With a .tpr file, they will be.
You may have generated your gro file from a run, that is using a tpr file OR you have a gro file from somewhere but you should still be able to create the tpr file knowing the topology.
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