Hi, I just finished my energy minimization run on GROMACS 4.0.4 for my ligand/protein combination. I opened the minimized protein pdb and the original pdb in VMD to visualize, but saw that my minimized protein was outside the solvent box I had made. How should this be corrected? Below is what I specified for my commands:
editconf -bt octahedron -f BR6.pdb -o BR6.pdb -c -d 0.7 genbox -cp BR6.pdb -cs spc216.gro -o BR6_b4ion.pdb -p BR6.top Do I need to increase my -d value, and if so, to what? My protein is 244 residues..not too big. Also, is spc216 the right water model I should use? Thanks much in advance, Halie Shah
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