Dear
Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation?
I have done a calculation on a protein-drug system, for my MD calculation, 20 salts and 20000 water molecules were added. However, when finish the calculation. I want to calculate the mm-pbsa/gbsa energy. I understand I need to exclude all the water molecule in extract snapshot and prepare free of water prmtop files for energy.mmpbsa. How about the counterions that I added? Should I also exclude all them in the snapshot and energy procedures?
Best regards,
Cat
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Received on Fri Jul 09 2010 - 04:30:03 PDT
