I have done two 100 ns simulations for comparing native and glycosated proteins.
Now for computing the cavities, channels, voids,… in two proteins using mole2 package, i need to pdb files. My problem is i dont know whats the most appropriate pdb file for loading in the mole2 program. can i use the md.gro of the last frame of simulation and convert it to pdf file ?
gmx editconf -f md.gro -o output.pdb
or should i use the avearge of trajectoris?
gmx rmsf -f md.trr -s md.tpr -o rmsf.xvg -ox average.pdb
or i have to compute global energy minimum at any point during the trajectory.??
if you know better method for copmuting tne cavities, channels, voids,. i would be glad advise me?