[gmx-users] Atomic Clashes during Energy minimization

neha bharti nehabharty123 at gmail.com
Wed Aug 27 13:54:27 CEST 2014

I am trying to perform MD for protein ligand complex in popc lipid with
charmm36 force field and also follow Justin A. Lemkul tutorial.

I have created protein ligand complex as mention in Justin A. Lemkul
Protein-Ligand Complex tutorial till Build the Topology Step.

Then I perform The following Steps where I get error:

Before Running InflateGRO I have separated the ligand and protein file
because InflateGRO not deal with

1) InflateGRO script run:

perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat

2) Next is energy minimize

grompp -f em.mdp -c system_inflated.gro -p topol.top -o em.tpr

 mdrun -v -deffnm em

another script command:

 perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat

 Another energy minimization step:

grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

mdrun -v -deffnm em

Repeat this step.
area per lipid reached 0.68 nm^2. Then I stop.

3) then again include the Ligand to final system_shrink.gro file

4) Adding Solvent:

editconf -f system_shrink.gro -o POPC_box.gro -box 8 8 15
genbox -cp  POPC_box.gro -cs spc216.gro -o  POPC_sol.gro

5) Adding Ions

Change topology.top file as numbers of SOL and ligand is added

Now, neutralize the system by adding the proper number of counter-ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 3
-nname CL

Select 16 to add 3 positive ion to sol.

6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em

While preforming energy minimization step (mdrun -v -deffnm em)  Atomic
Clashes occur.
And it give following output:

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  6.1499341e+20
Maximum force     =            inf on atom 3300
Norm of force     =  5.4206209e+1

I guess This is because of the ligand is removed before running InflateGRO,
added once the system is properly compressed.

Then I also tried this by without Adding Ligand molecule but it* still
giving the error*

What to do to solve this issue??

When to add the ligand to the system??

Please Help..

With Regards

Neha bharty

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