[gmx-users] Error running simulations with the protein frozen

Nuo Wang wolich22 at gmail.com
Sat Mar 26 06:28:14 CET 2016

Hi Justin,

This "freeze-protocol" is published here in Methods:
My goal is to use the MD-calculated free energy to validate the
electrostatic solvation free energies produced by software like APBS. In
APBS, the protein takes one conformation (typically a PDB structure) and
the solvent is modeled by mean-field theory. The only rigorous way to
compare MD to the "single-conformation" APBS result is by freezing the
protein and sampling only the solvent.

The system does look artificial but from an algorithmic point of view,
my protocol should be very doable. The protein is frozen, so its high
internal energy doesn't matter. And water is reasonably placed around the
protein by Gromacs, water themselves should pass the minimization safely.

To give you more information, I have done the exactly same thing in NAMD --
freezing the crystal structure protein -- and it works just fine. But now I
have to switch to Gromacs to use the free energy calculation procedure I
need. (Long time NAMD user, first time Gromacs user)

Last, I have already tried to use restraints, simulation runs fine, but it
is not what I want to do.

I think this is a input file setup issue, not an issue with the physics of
the seemingly artificial system.

Thanks ahead for any further help on this!


On Fri, Mar 25, 2016 at 8:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 3/25/16 9:42 PM, Nuo Wang wrote:
>> Hi Gromacs admins,
>> I am trying to run MD simulations of protein solvated in water. I want to
>> completely freeze the protein at its crystal conformation and only sample
>> the solvent degrees of freedom (for comparison with Poisson-Boltzmann
>> calculations that only use the crystal structure). I tried to follow the
>> typical minimization-equilibration-production procedure described here:
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
>> But I get this error at the energy minimization step:
>> "Fatal error:
>> step 11: Water molecule starting at atom 60322 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate."
>> If I take away the freeze protein commands in my minimize.mdp, then no
>> error occurs:
>> freezegrps    = Protein
>> freezedim     = Y Y Y
>> I checked my atom 60322, it is next to the protein, but it is neither
>> clashing with anyone nor moving rapidly in my trajectory. Reducing
>> timestep
>> by 1000 times won't help either, error just occurs at a later step.
>> I wonder how can I resolve this problem?
> Freezing is a severe perturbation on the system, and taking a protein out
> of its crystal environment, dunking it in water, and expecting that
> conformation to be happy (or even sensible) is a bad assumption.  If you
> want to preserve the overall conformation, try something gentler like
> normal position restraints.
> -Justin
> The script that I used is shown here, the input files in the script are
>> linked below:
>> ### Generate topology
>> echo 9  | gmx pdb2gmx -f complex.pdb -o complex.gro -p complex.top -merge
>> all -ignh -water tip3p
>> ### Generate box information
>>            gmx editconf -f complex.gro -o complex_newbox.gro -bt cubic -c
>> -box 11 11 11
>> ### Add water
>>            gmx solvate -cp complex_newbox.gro -cs spc216.gro -o
>> complex_solvated.gro -p complex.top
>> ### Prepare ion parameters
>>            gmx grompp -f ions.mdp -c complex_solvated.gro -p complex.top
>> -o
>> ions.tpr
>> ### Add ions
>> echo 13 | gmx genion -s ions.tpr -o complex_solvated_ions.gro -p
>> complex.top -pname NA -nname CL -neutral -conc 0
>> ### Generate index file
>> echo q  | gmx make_ndx -f complex_solvated_ions.gro -o index.ndx
>> ### Preparation for energy minimization for the non-protein atoms
>>            gmx grompp -f minimize.mdp -c complex_solvated_ions.gro -n
>> index.ndx -p complex.top -o em.tpr
>> ### Energy minimization for the non-protein atoms
>>            gmx mdrun -v -deffnm em -nt 1
>> complex.pdb:
>> https://drive.google.com/file/d/0B8oskrjCa2EMQURKd0J5bXdNRk0/view?usp=sharing
>> ions.mdp:
>> https://drive.google.com/file/d/0B8oskrjCa2EMS3M4cTdkRXRTRE0/view?usp=sharing
>> minimize.mdp:
>> https://drive.google.com/file/d/0B8oskrjCa2EMU0hZT0lxXzZuM1U/view?usp=sharing
>> Thanks a lot!
>> Nuo
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================
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