My appologies I have errors all over this.
On September 11, 2010 at 12:44 AM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
>
>
> TJ Mustard wrote:
> >
> >
> > 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 "$base".top
> >
> > I use AMBER03 and TIP3P
> >
> >
>
> You should have failed right here. 1HNX has missing atoms in a THR residue, so
> pdb2gmx would otherwise exit with a fatal error (I know because I tried). I
> assume this means you have re-built the appropriate sidechain atoms? If so, how
> did you do it? Did you obtain a sensible .pdb file as output from whatever
> process you used?
>
>
> TJ Mustard wrote:
> >
> >
> > Downloaded a pdb from pdb.org (1HNX) and stripped the PCY ligand and
> > plugged it into pdb2gmx using AMBER03 and TIP3P (GROMACS 4.5). Ran
> > through the rest of my process and I am having some issues.
> >
> >
> >
> > Here is my flow of commands:
> >
> >
> >
> > pdb2gmx -f "$base".pdb -o "$base".gro -p "$base".top
> >
> > I use AMBER03 and TIP3P
> >
> >
>
> You should have failed right here. 1HNX has missing atoms in a THR residue, so
> pdb2gmx would otherwise exit with a fatal error (I know because I tried). I
> assume this means you have re-built the appropriate sidechain atoms? If so, how
> did you do it? Did you obtain a sensible .pdb file as output from whatever
> process you used?
I would import into swiss pdb to fix the sidechanes and nomenclature. Then I would manually edit out the first phosphorus and its oxygens on both chain a and x. Then I would rename any atoms (ie OP1 - O1P or C* - C').
> > >
> >
> >
> > 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?
> >
> >
>
> Unfortunately, genion doesn't deal well with large numbers for some reason. If
> you know how many ions you need to neutralize, do it manually with -np or -nn.
>
> Also of interest: how did you get this net charge? When I processed 1HNX (after
> re-building missing atoms, I have a charge in excess of -1000.
> >
> >
> > 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?
> >
> >
>
> Unfortunately, genion doesn't deal well with large numbers for some reason. If
> you know how many ions you need to neutralize, do it manually with -np or -nn.
>
> Also of interest: how did you get this net charge? When I processed 1HNX (after
> re-building missing atoms, I have a charge in excess of -1000.
Sorry for this exact run I was using a truncated pdb to limit atom numbers. It is over 1000 for the whole ribosome subunit. I have been doing it manually when genion is wrong.
> > >
> >
> >
> > grompp -f em.mdp -c "$base"_b4em.gro -p "$base".top -o "$base"_em.tpr
> >
> >
> >
> > mdrun -v -s "$base"_em.tpr -c "$base"_after_em.gro -g emlog.log
> >
> > I have set this up to be very thorough and it can run for 1000+ steps.
> > My problem is it never gives me a good Fmax. I am always above 1e-4.
> >
>
> An Fmax of 0.0001 is extremely stringent and unlikely to be produced for most
> systems in the absence of exhaustive EM using double precision. Such
> minimization is usually unnecessary for most systems, unless you're doing normal
> modes. The fact that you are "above" 0.0001 is thus unsurprising. How far
> above are you? Hard numbers, please, and do remind everyone of what your EM
> settings are.
> >
> >
> > grompp -f em.mdp -c "$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.
> >
>
> An Fmax of 0.0001 is extremely stringent and unlikely to be produced for most
> systems in the absence of exhaustive EM using double precision. Such
> minimization is usually unnecessary for most systems, unless you're doing normal
> modes. The fact that you are "above" 0.0001 is thus unsurprising. How far
> above are you? Hard numbers, please, and do remind everyone of what your EM
> settings are.
Sorry my energies would never get below 1e4 or 10000.
EM output
Potential Energy = -2.4193396e+07 Maximum force = 2.2069838e+04 on atom 18961 Norm of force = 3.3190449e+01
EM Settings:
define = -DPOSRES_WATER
integrator = steep
nsteps = 10000
nstcomm = 1
emtol = 200
emstep = 0.0001
nstcgsteep = 10
ns-type = Grid
rlist = 0.9
coulombtype = PME
rcoulomb-switch = 0
rcoulomb-switch = 0
pme_order = 6
optimize_fft = yes
PR output (2 fs steps)
No previous checkpoint file present, assuming this is a new run.
Getting Loaded...
Reading file 1HNX-15_pr.tpr, VERSION 4.5 (single precision)
Starting 2 threads
Loaded with Money
Making 1D domain decomposition 2 x 1 x 1
starting mdrun 'Protein in water'
100 steps, 0.2 ps.
step 0
Step 21 Warning: pressure scaling more than 1%, mu: 0.98428 0.98428 0.98428
Step 21 Warning: pressure scaling more than 1%, mu: 0.98428 0.98428 0.98428
Step 31 Warning: pressure scaling more than 1%, mu: 1.0315 1.0315 1.0315
Step 31 Warning: pressure scaling more than 1%, mu: 1.0315 1.0315 1.0315
Step 41 Warning: pressure scaling more than 1%, mu: 0.940629 0.940629 0.940629
Step 41 Warning: pressure scaling more than 1%, mu: 0.940629 0.940629 0.940629
Step 51 Warning: pressure scaling more than 1%, mu: 1.1314 1.1314 1.1314
Step 51 Warning: pressure scaling more than 1%, mu: 1.1314 1.1314 1.1314
Step 61 Warning: pressure scaling more than 1%, mu: 0.789849 0.789849 0.789849
Step 61 Warning: pressure scaling more than 1%, mu: 0.789849 0.789849 0.789849
step 63: Water molecule starting at atom 740268 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 63: Water molecule starting at atom 950013 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
> > In assessing the inability to minimize, you should look at the atom on which the
> maximum force resides. It is likely one of the first to be destabilized during
> any subsequent MD. What atoms are around it that might be pushing on it? Is
> there any nonsensical geometry that may be present?
>
> What also might be substantially more beneficial would be to minimize in vacuo
> before going through all the effort of adding solvent and ions and thus just
> slowing your whole process down by adding tons more atoms to an already enormous
> system. If that doesn't work, minimize each chain separately (painstaking, I
> know) in vacuo to see where the problem(s) may lie.
>
> -Justin
The in vacuo I will do. Painstaking is nothing if this will work.
> > >
> >
> >
> >
> >
> > 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
> >
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> 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
>
I am also running to jobs with PR (-DPOSRES mdrun) settings of 1 fs and tau_p and parrinelo-Rahman p coupling.
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
