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On January 17, 2011 at 1:20 PM "Justin A. Lemkul" <jalemkul@vt.edu> wrote:<br />
<br />
><br />
><br />
> TJ Mustard wrote:<br />
> ><br />
> ><br />
> > Hi all,<br />
> ><br />
> > <br />
> ><br />
> > I have been running alot of simulations on protein ligand interactions,<br />
> > and my settings/setup/mdp files worked great for one system. Then when<br />
> > we moved to a larger and more complicated system we started getting<br />
> > mdrun segmentation faults during "steep" energy minimization.  This<br />
> > happens on our cluster and on our iMacs.<br />
> ><br />
> > <br />
> ><br />
> > Any help would be appreciated. Also I can attach my mdp files.<br />
> ><br />
> > <br />
><br />
> There are a whole host of things that could be going wrong.  Without<br />
> substantially more information, including even more (like a thorough description<br />
> of what these systems are and the exact commands of what worked before), then<br />
> you won't get any useful advice.<br />
><br />
> -Justin<br />
>
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<p style="margin: 0px;">Ok, system 1 that worked is biotin and strepavidin in a water box, and the "larger" system is just rifampicin in a water box for hydration energies. Both ligands are being removed via FEP.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">As for commands they are identical as we have made a systematic script that sets up our systems.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">It is:</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><br />
pdb2gmx -f base.pdb -o base.gro -p base.top</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">===Here we put the ligand .gro and the protein "base" .gro together.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">editconf -bt cubic -f base.gro -o base.gro -c -d 3.5<br />
<br />
genbox -cp base.gro -cs spc216.gro -o base_b4ion.gro -p base.top</p>
<br />
<p style="margin: 0px;">grompp -f em.mdp -c base_b4ion.gro -p base.top -o base_b4ion.tpr -maxwarn 2<br />
<br />
genion -s base_b4ion.tpr -o base_b4em.gro -neutral -conc 0.01 -pname NA -nname CL -g base_ion.log -p base.top</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">==Here select SOL</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<br />
<br />
mdrun -v -s base_em.tpr -c base_after_em.gro -g emlog.log -cpo stat_em.cpt</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">===Segmentation fault occurs here.</p>
<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 -e pr.edr -c base_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt -dhdl dhdl-pr.xvg<br />
<br />
grompp -f md.mdp -c base_after_pr.gro -p base.top -o base_md.tpr<br />
<br />
mdrun -v -s base_md.tpr -o base_md.trr -c base_after_md.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dhdl dhdl-md.xvg<br />
<br />
grompp -f FEP.mdp -c base_after_md.gro -p base.top -o base_fep.tpr<br />
<br />
mdrun -v -s base_fep.tpr -o base_fep.trr -c base_after_fep.gro -g fep.log -e fep.edr -cpi state_fep.cpt -cpo state_fep.cpt -dhdl dhdl-fep.xvg</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I can include mdp files if that would help.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Thank you,</p>
<p style="margin: 0px;">TJ Mustard</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<div style="margin: 5px 0px 5px 0px;">
> ><br />
> > Thank you<br />
> ><br />
> > <br />
> ><br />
> > TJ Mustard<br />
> > Email: mustardt@onid.orst.edu<br />
> ><br />
><br />
> --<br />
> ========================================<br />
><br />
> Justin A. Lemkul<br />
> Ph.D. Candidate<br />
> ICTAS Doctoral Scholar<br />
> MILES-IGERT Trainee<br />
> Department of Biochemistry<br />
> Virginia Tech<br />
> Blacksburg, VA<br />
> jalemkul[at]vt.edu | (540) 231-9080<br />
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br />
><br />
> ========================================<br />
> --<br />
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>
</div>
<p style="margin: 0px;"> </p>
<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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