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