Project 4oie_MD 2 Output

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Summary settings

Project information

Project name	4oie_MD 2
Workflow	GROMACS Set Up

Checking

Parameter	Value
Assembly	Asymmetric unit
Selected Model	All
Selected Chains	All
Amide Assignment	Original Amide: GLN A347.NE2
Ligands	Ligands to Remove: A184 , A241 , A333 , A401

Settings for GROMACS Set Up

Parameter	Value
Force field	AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
Solvent water type	TIP3P
Box size in MD simulations (nm)	0.8
Box type in MD simulations	octahedron
Ionic concentration	0.05
Parameters for MD Configuration Files
Time step (fs)	0.002
Temperature (K)	300
Total time (ps)	20000
Output freq. (steps)	500

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Initial structure

Output structure

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