I have protein that consist of bay ligand. I follow the antechamber
tutorial for protein ligand. I extract the ligand and reduced it after that
I produced mol2 file of ligand then by using AM1-BCC charge model.
Then i produced frcmod file my ligand frcmod file have no missing parameter
for bond angle and dihedral. It have 7 missing parameters for improper. I
also attached the frcmod file kindly check and guide if it is right.
Then i use this script for producing prmtop and inpcrd for ligand (non
standred residue)
then i prepared the prmtop and inpcrd file for protein complex. BUT this
file work for NBT=0, not work for periodic boundary conditions. How I can
make it workable to run periodic boundary simulation because i want to
compare this simulation with other simulation by employing similar flag
commands.
Kindly guide
Thanks
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Received on Wed Sep 20 2017 - 10:00:04 PDT
