diff --git a/wiki/pages/model.html b/wiki/pages/model.html index 01086424eacd9346d6564256244de2dd68683045..5fd81832f1d3e91e085f74691e9b3afff2080e09 100644 --- a/wiki/pages/model.html +++ b/wiki/pages/model.html @@ -713,7 +713,7 @@ out=muscure.pdbqt</div> receptor <code>MOR_processed.gro</code> into a single system <code>complex.gro</code>. </li> <pre><code>gmx editconf -f mus_ini.pdb -o mus.gro - gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0</code></pre> +gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0</code></pre> <li>Solvate the system in solvent (such as water). From <code>topol.top</code>, it is known that the net charge is 9; add counterions to neutralize the system.</li> @@ -804,8 +804,7 @@ dit xvg_show -f temperature.xvg</code></pre> </ul> <pre><code>gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr - gmx mdrun -deffnm md_0_10 - </code></pre> +gmx mdrun -deffnm md_0_10</code></pre> <div class="image-container"> <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/mds.png" alt="MDS" class="shadowed-image" style="width: 100%; max-width: 1000px;">