[gmx-users] Atomic Clashes during Energy minimization

[Justin Lemkul]

On 8/27/14, 7:54 AM, neha bharti wrote:
> 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
> using:
>
> 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,
> then
> 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??

Go back to step 3 and verify that things look fine.  Then do the next step, 
visuzlize, etc.  Don't just plow ahead - looking and making sure will take the 
guesswork out of things.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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