Dear Amber:
I am doing the mmpbsa.py to calculate the free energy for trajectory. When I constructed the topfile as follow the amber18 manual and tutorials, and I saw the sentence of "each must have the same charges for the same atoms, the same force field must be used for all three of the required prmtops, and they must have the same PBRadii set " in amber manual for mmpbsa.sy, especially for " the same force field must be used for all three of the required prmtops". However, I want to combine DNA and small organic molecule and construct the corresponding the prmtops. Is it mean that the I can not use the leaprc.DNA.bsc1 and leaprc.gaff2 for DNA and small organic molecule, respectively? Hence, How can I do for this situation?
I'm looking forward to your reply
Best regards
Manyi Yang
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Received on Sun Mar 03 2019 - 18:00:03 PST
