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<p style="margin: 0px;">Downloaded a pdb from pdb.org (1HNX) and stripped the PCY ligand and plugged it into pdb2gmx using AMBER03 and TIP3P (GROMACS 4.5). Ran through the rest of my process and I am having some issues.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Here is my flow of commands:</p>
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<p style="margin: 0px;">pdb2gmx -f "$base".pdb -o "$base".gro -p "$base".top</p>
<p style="margin: 0px;">I use AMBER03 and TIP3P</p>
<p style="margin: 0px;"> </p>
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<p style="margin: 0px;">editconf -bt cubic -f "$base".gro -o "$base".gro -c -d 1.5</p>
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<p style="margin: 0px;">genbox -cp "$base".gro -cs spc216.gro -o "$base"_b4ion.gro -p "$base".top<br />
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grompp -f em.mdp -c "$base"_b4ion.gro -p "$base".top -o "$base"_b4ion.tpr<br />
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genion -s "$base"_b4ion.tpr -o "$base"_b4em.gro -neutral -conc 0.001 -pname NA -nname CL -g "$base"_ion.log -p "$base".top</p>
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<p style="margin: 0px;">Here I have some issues too, but it is intermittent. I have a charge of -563 but genion wants to add 580+ NA and one if any CL giving me a possitive charge in the system. My thought is that -neutral would give me a neutral system?</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">grompp -f em.mdp -c "$base"_b4em.gro -p "$base".top -o "$base"_em.tpr</p>
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<p style="margin: 0px;">mdrun -v -s "$base"_em.tpr -c "$base"_after_em.gro -g emlog.log</p>
<p style="margin: 0px;">I have set this up to be very thorough and it can run for 1000+ steps. My problem is it never gives me a good Fmax. I am always above 1e-4.</p>
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<p style="margin: 0px;"><br />
grompp -f pr.mdp -c "$base"_after_em.gro -p "$base".top -o "$base"_pr.tpr<br />
<br />
mdrun -v -s "$base"_pr.tpr -o "$base"_pr.trr -e pr.edr -c "$base"_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt</p>
<p style="margin: 0px;">This is where I always fail. First I get pressure errors and LINCS errors. I don't know how to minimize my system any farther, and therefor continue my jobs.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">grompp -f md.mdp -c "$base"_after_pr.gro -p "$base".top -o "$base"_md.tpr<br />
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mdrun -v -s "$base"_md.tpr -o "$base"_md.trr -c "$base"_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt</p>
<p style="margin: 0px;">I NEVER get to here....</p>
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<p style="margin: 0px;">I have stripped the MG and ZN. I have removed a significant portion of the protein/rna to limit its size. I have ran it at 1 fs, 2 fs, 4 fs. I have ran it with -heavyh. And I have tried every AMBER force field available in GROMACS 4.5.</p>
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<p style="margin: 0px;">Any help would be much appreciated.</p>
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<p style="margin: 0px;"><span></span></p>
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<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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