[gmx-users] PDB will not minimize?

[Justin A. Lemkul]

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?

> 
>  
> 
> 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.

> 
>  
> 
> 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.

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

>  
> 
>  
> 
> 
> 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: mustardt at onid.orst.edu
> 

-- 
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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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