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<p><br></p>
<p><br></p>
<p><span class=rvts7>I guess this procedure should work, so this might be a bug.</span></p>
<p><span class=rvts7>But you are making things much more complicated than needed.</span></p>
<p><span class=rvts7>You can skip the first two steps and just use the -box option of genbox instead of -cp.</span></p>
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<p><span class=rvts7>Berk.</span></p>
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<p><br></p>
<p><br></p>
<p>OK. </p>
<p>genbox -cs spc216.pdb -box 3 3 3.</p>
<p>It outputs:</p>
<p> Option Type Value Description</p>
<p>------------------------------------------------------</p>
<p> -[no]h bool no Print help info and quit</p>
<p> -[no]X bool no Use dialog box GUI to edit command line options</p>
<p> -nice int 19 Set the nicelevel</p>
<p> -box vector 3 3 3 box size</p>
<p> -nmol int 0 no of extra molecules to insert</p>
<p> -try int 10 try inserting -nmol*-try times</p>
<p> -seed int 1997 random generator seed</p>
<p> -vdwd real 0.105 default vdwaals distance</p>
<p> -shell real 0 thickness of optional water layer around solute</p>
<p> -maxsol int 0 maximum number of solvent molecules to add if</p>
<p> they fit in the box. If zero (default) this is</p>
<p> ignored</p>
<p><br></p>
<p>WARNING: masses will be determined based on residue and atom names,</p>
<p> this can deviate from the real mass of the atom type</p>
<p>In case you use free energy of solvation predictions:</p>
<p><br></p>
<p>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++</p>
<p>D. Eisenberg and A. D. McLachlan</p>
<p>Solvation energy in protein folding and binding</p>
<p>Nature 319 (1986) pp. 199-203</p>
<p>-------- -------- --- Thank You --- -------- --------</p>
<p><br></p>
<p>Opening library file /usr/share/gromacs/top/aminoacids.dat</p>
<p>Opening library file /usr/share/gromacs/top/atommass.dat</p>
<p>Opening library file /usr/share/gromacs/top/vdwradii.dat</p>
<p>Opening library file /usr/share/gromacs/top/dgsolv.dat</p>
<p>#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7</p>
<p>Reading solvent configuration</p>
<p>""</p>
<p>solvent configuration contains 648 atoms in 216 residues</p>
<p><br></p>
<p>And hangs up. </p>
<p>:(</p>
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