Platform>Globular AIMD >Globular AIMD platform

Globular AIMD

From The Mind Come Drugs of the Future


Preparing complex and topology

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    Target protein from X-ray, NMR, or Cryo-EM

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    Formatting Initial PDB to GROMACS types (gro, itp, top, et al.)

    • $> gmx pdb2gmx -f avb3grgdsp.pdb -o complex.gro -ignh -ter -ss -water spc -merge all–missing
    • $> gmx editconf -f het.pdb -o het.gro

Solvating a Globular Protein

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    Adding Solvent Water

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    Adding Neutralizing Counter-ions

    • gmx editconf -f system1.gro -o system1_newbox.gro -c -d 1.2 -bt cubic
    • gmx solvate -cp system1_newbox.gro -cs spc216.gro -o system1_solv.gro -p
    • gmx genion -s ions.tpr -o system1_solv1_ions.gro -p –pname NA -nname CL -conc 0.15 -neutral

Energy Minimization

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    EM for avoiding atomic crash

    • $> gmx grompp -f commonfiles/minim.mdp -c system1_solv1_ions.gro –r system1_solv1_ions.gro -p -o em.tpr
    • $> gmx mdrun -v -deffnm em
    • $> gmx energy -f em.edr -o potential.xvg

System Equilibration

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    Equilibration with Stepwise reduced force constants (5 to 0 kcal/mol)

    • gmx grompp -f commonfiles/nvt.mdp -c em.gro -r em.gro –p -n index_ini.ndx -o nvt.tpr

MD & Post-Analysis

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    Receptor-Ligand binding affinity (MM/GBSA & BAR)