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Simulating cryo-EM images from PDB coordinates

The following is a protocol to simulate cryo-EM images from PDB coordinate files. This procedure will place a PDB model into a 373.4 x 373.4 x 373.4 Angstrom box.

Things you need

• Gromacs
• 64 bit Linux
• PDB file

Convert PDB to .xyz format

1. Convert PDB file into Gromacs format and center in 373.4 x 373.4 x 373.4 Angstrom box:

editconf -f 2DN2.pdb -o 2DN2.gro -box 37.35083 37.35083 37.35083

2. Download water01.gro from figShare