I am going to use MARTINI force field. According to the MARTINI tutorial (http://md.chem.rug.nl/cgmartini/index.php/proteins), I am trying to convert my atomistic protein model to CG model using "martinize.py" script. My protein contain few numbers of crystal waters and When I am applying the python script, it converts my protein to CG model by removing the crystal waters. But I want to keep the waters as it is in the crystal structure. Please suggest me the proper modifications of the script that are required to map those waters or any hetero atoms to CG model.
Thank you Marko for your suggestion and I understand the CG scaling feature i.e. basically happens in 4:1 ratio. But my protein is a dimer and the dimer interface is stabilized by few water molecules. If I going remove these waters, the proper dimeric structure is going to destabilize. So deletion of these water molecules is not a rational idea. Is there any procedure to scaling this things by changing the scaling parameters?
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