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.
Here is my flow of commands:
pdb2gmx -f "$base".pdb -o "$base".gro -p "$base".top
I use AMBER03 and TIP3P
editconf -bt cubic -f "$base".gro -o "$base".gro -c -d 1.5
genbox -cp "$base".gro -cs spc216.gro -o "$base"_b4ion.gro -p "$base".top
grompp -f em.mdp -c "$base"_b4ion.gro -p "$base".top -o "$base"_b4ion.tpr
genion -s "$base"_b4ion.tpr -o "$base"_b4em.gro -neutral -conc 0.001 -pname NA -nname CL -g "$base"_ion.log -p "$base".top
Here I have some issues too, but it is intermittent. I have a charge of -563 but genion wants to add 580+ NA and one if any CL giving me a possitive charge in the system. My thought is that -neutral would give me a neutral system?
grompp -f em.mdp -c "$base"_b4em.gro -p "$base".top -o "$base"_em.tpr
mdrun -v -s "$base"_em.tpr -c "$base"_after_em.gro -g emlog.log
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.
grompp -f pr.mdp -c "$base"_after_em.gro -p "$base".top -o "$base"_pr.tpr
mdrun -v -s "$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
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.
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_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt
I NEVER get to here....
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.
Any help would be much appreciated.
TJ Mustard
Email: musta...@onid.orst.edu
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
