I am using force field ff02 and water model POL3. I am having difficulty in minimizing the system. In the Minimization output file after 100 steps of minimization
EPOLAR = ************
EEL = *************
I'll appreciate any minor suggestions.
Can you share the input structure in PDB format?
In my PDB, I having protein, ligand and the water box. I used the leap script as
Source leaprc.ff02
Source leaprc.gaff2
Loadamberparams frcmod.pol3
Mol=loadpdb complex.pdb
Set default IPOL 1
Solvatebox mol POL3BOX 12.0
addions mol Na+ 0
SaveAmberParmPol mol complex.prmtop complex.inpcrd
Quit
If you visualize "complex.pdb" in a molecular graphics program, everything is okay?
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