Preparing complex and topology
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1
Target protein from X-ray, NMR, or Cryo-EM
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2
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