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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

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

Download water01.gro from figShare: http://figshare.com/articles/water01_gro_Water_coordinate_file_for_cryo_EM_image_simulation/1238172