During the energy minimization of a protein before Molecular Dynamic Simulation in GROMACS software, I am getting this error: "One or more water molecules can not be settled in GROMACS".
Just like 99% of the solutions given in online forums, I have only found people giving answers full of jargon and blabbering about their knowledge about random stuff without offering any solution to the problem.
Can someone break this chain and give me a straightforward solution for this problem?
It is hard to answer it without more information.
A few ideas:
- check the input structure - anything obiously wrong?
- check the mdp file, anything strange there? maybe try to download another em.mdp;
- try to decrease the time-step in em.mdp.
Ishtiaque Ahammad if you post or send me the input pdb, I could give it a try.
Ishtiaque Ahammad
OK - I can not reproduce the error - I do not know which force-field, water model and box size you wanted to use... But I managed to solvate and energy-minimize it. Here are the steps, output and em.mdp.
Please note that you have non-zero net charge, so I would recommend adding (at least) counter-ions in the next step. Good luck!
# making topology - amber99sb-ildn and tip3p
gmx pdb2gmx -f B.1.351_ACE2.pdb -ff amber99sb-ildn -water tip3p -o processed.pdb
# put protein in a box
gmx editconf -f processed.pdb -c -d 1.0 -bt dodecahedron -o box.gro
#energy-minimize the box
gmx grompp -f em -c box.gro -o embox.tpr
gmx mdrun -v -s embox.tpr -c embox.pdb
#solvate
gmx solvate -cp embox.pdb -p topol.top -o solv.pdb
#energy-minimize
gmx grompp -f em.mdp -c solv.pdb -p topol.top -o em.tpr
gmx mdrun -s em.tpr -nt 1 -v -c em_solv.pdb
Dear Miloš T. Ivanović Thanks you so much! I have looked at your files and saw what was different from mine. In the em.mdp file you added "define= -DFLEXIBLE" which I didn't. I added it to my em.mdp file and it worked! I can't thank you enough!
Do you always use this em.mdp file for energy minimization before simulations?
Ishtiaque Ahammad
depends on the purpose.
You can also use ""integrator = steep" and remove "define= -DFLEXIBLE"
Miloš T. Ivanović Is it okay to use both "integrator = steep" and "define= -DFLEXIBLE" in the em.mdp file or do I have to choose one? For example take a look my em.mdp file. Is this okay?
Miloš T. Ivanović Thank you very much for your help. I also had the same problem and your em.mdp file works when both integrator and define are used together
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