[gmx-users] solvent box outside protein

Halie Shah haliepshah at gmail.com
Mon Mar 30 21:53:44 CEST 2009


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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