<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
<title></title>
</head>
<body>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">My appologies I have errors all over this. <span></span></p>
<div style="margin: 5px 0px;">
On September 11, 2010 at 12:44 AM "Justin A. Lemkul" <jalemkul@vt.edu> wrote:<br />
<br />
><br />
><br />
> TJ Mustard wrote:<br />
> ><br />
> ><br />
> > Downloaded a pdb from pdb.org (1HNX) and stripped the PCY ligand and<br />
> > plugged it into pdb2gmx using AMBER03 and TIP3P (GROMACS 4.5). Ran<br />
> > through the rest of my process and I am having some issues.<br />
> ><br />
> > <br />
> ><br />
> > Here is my flow of commands:<br />
> ><br />
> > <br />
> ><br />
> > pdb2gmx -f "$base".pdb -o "$base".gro -p "$base".top<br />
> ><br />
> > I use AMBER03 and TIP3P<br />
> ><br />
> > <br />
><br />
> You should have failed right here.  1HNX has missing atoms in a THR residue, so<br />
> pdb2gmx would otherwise exit with a fatal error (I know because I tried).  I<br />
> assume this means you have re-built the appropriate sidechain atoms?  If so, how<br />
> did you do it?  Did you obtain a sensible .pdb file as output from whatever<br />
> process you used?<br />
</div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I would import into swiss pdb to fix the sidechanes and nomenclature. Then I would manually edit out the first phosphorus and its oxygens on both chain a and x. Then I would rename any atoms (ie OP1 - O1P or C* - C').</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<div style="margin: 5px 0px;">
> > ><br />
> > <br />
> ><br />
> > editconf -bt cubic -f "$base".gro -o "$base".gro -c -d 1.5<br />
> ><br />
> > <br />
> ><br />
> > genbox -cp "$base".gro -cs spc216.gro -o "$base"_b4ion.gro -p "$base".top<br />
> ><br />
> > grompp -f em.mdp -c "$base"_b4ion.gro -p "$base".top -o "$base"_b4ion.tpr<br />
> ><br />
> > genion -s "$base"_b4ion.tpr -o "$base"_b4em.gro -neutral -conc 0.001<br />
> > -pname NA -nname CL -g "$base"_ion.log -p "$base".top<br />
> ><br />
> > <br />
> ><br />
> > Here I have some issues too, but it is intermittent. I have a charge of<br />
> > -563 but genion wants to add 580+ NA and one if any CL giving me a<br />
> > possitive charge in the system. My thought is that -neutral would give<br />
> > me a neutral system?<br />
> ><br />
> > <br />
><br />
> Unfortunately, genion doesn't deal well with large numbers for some reason.  If<br />
> you know how many ions you need to neutralize, do it manually with -np or -nn.<br />
><br />
> Also of interest: how did you get this net charge?  When I processed 1HNX (after<br />
> re-building missing atoms, I have a charge in excess of -1000.<br />
</div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Sorry for this exact run I was using a truncated pdb to limit atom numbers. It is over 1000 for the whole ribosome subunit. I have been doing it manually when genion is wrong.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<div style="margin: 5px 0px;">
> > ><br />
> > <br />
> ><br />
> > grompp -f em.mdp -c "$base"_b4em.gro -p "$base".top -o "$base"_em.tpr<br />
> ><br />
> > <br />
> ><br />
> > mdrun -v -s "$base"_em.tpr -c "$base"_after_em.gro -g emlog.log<br />
> ><br />
> > I have set this up to be very thorough and it can run for 1000+ steps.<br />
> > My problem is it never gives me a good Fmax. I am always above 1e-4.<br />
> ><br />
><br />
> An Fmax of 0.0001 is extremely stringent and unlikely to be produced for most<br />
> systems in the absence of exhaustive EM using double precision.  Such<br />
> minimization is usually unnecessary for most systems, unless you're doing normal<br />
> modes.  The fact that you are "above" 0.0001 is thus unsurprising.  How far<br />
> above are you?  Hard numbers, please, and do remind everyone of what your EM<br />
> settings are.<br />
</div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Sorry my energies would never get below 1e4 or 10000.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">EM output</p>
<pre>
Potential Energy = -2.4193396e+07
Maximum force = 2.2069838e+04 on atom 18961
Norm of force = 3.3190449e+01
</pre>
<p style="margin: 0px;">EM Settings:</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">define                   = -DPOSRES_WATER</p>
<p style="margin: 0px;">integrator               = steep</p>
<p style="margin: 0px;">nsteps                   = 10000<br />
nstcomm                  = 1<br />
emtol                    = 200<br />
emstep                   = 0.0001<br />
nstcgsteep               = 10<br />
ns-type                  = Grid<br />
rlist                    = 0.9<br />
coulombtype              = PME<br />
rcoulomb-switch          = 0<br />
rcoulomb-switch          = 0<br />
pme_order                = 6<br />
optimize_fft             = yes</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">PR output (2 fs steps)</p>
<p style="margin: 0px;"> </p>
<pre>
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
</pre>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<div style="margin: 5px 0px;">
> > In assessing the inability to minimize, you should look at the atom on which the<br />
> maximum force resides.  It is likely one of the first to be destabilized during<br />
> any subsequent MD.  What atoms are around it that might be pushing on it?  Is<br />
> there any nonsensical geometry that may be present?<br />
><br />
> What also might be substantially more beneficial would be to minimize in vacuo<br />
> before going through all the effort of adding solvent and ions and thus just<br />
> slowing your whole process down by adding tons more atoms to an already enormous<br />
> system.  If that doesn't work, minimize each chain separately (painstaking, I<br />
> know) in vacuo to see where the problem(s) may lie.<br />
><br />
> -Justin<br />
</div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">The in vacuo I will do. Painstaking is nothing if this will work.</p>
<p style="margin: 0px;"> </p>
<div style="margin: 5px 0px;">
> > > <br />
> ><br />
> > <br />
> ><br />
> ><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 "$base"_pr.trr -e pr.edr -c<br />
> > "$base"_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt<br />
> ><br />
> > This is where I always fail. First I get pressure errors and LINCS<br />
> > errors. I don't know how to minimize my system any farther, and therefor<br />
> > continue my jobs.<br />
> ><br />
> > <br />
> ><br />
> > <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_pr.gro -g<br />
> > md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt<br />
> ><br />
> > I NEVER get to here....<br />
> ><br />
> > <br />
> ><br />
> > <br />
> ><br />
> > I have stripped the MG and ZN. I have removed a significant portion of<br />
> > the protein/rna to limit its size. I have ran it at 1 fs, 2 fs, 4 fs. I<br />
> > have ran it with -heavyh. And I have tried every AMBER force field<br />
> > available in GROMACS 4.5.<br />
> ><br />
> > <br />
> ><br />
> > Any help would be much appreciated.<br />
> ><br />
> > <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 />
> gmx-users mailing list    gmx-users@gromacs.org<br />
> http://lists.gromacs.org/mailman/listinfo/gmx-users<br />
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br />
> Please don't post (un)subscribe requests to the list. Use the<br />
> www interface or send it to gmx-users-request@gromacs.org.<br />
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br />
><br />
</div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I am also running to jobs with PR (-DPOSRES mdrun) settings of 1 fs and tau_p and parrinelo-Rahman p coupling.</p>
<p style="margin: 0px;"> </p>
</div>
<p style="margin: 0px;"><span></span></p>
<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>
</body>
</html>