Dear Amber users,
I want to obtain parameters to simulate arginine fully protonated (i.e. all protonable side chain and backbone atoms). I thought that an option could be to use antechamber with the “-at amber” option but I am not sure how it works. My guess is that after using that option, if later on I use the ff99SB forcefield with Leap (the -at amber option is said to work with that version of the force field), I would end up using ff99SB force field parameters for standard arginine, when possible, and antechamber generated parameters when not. Is that correct? Could you give me any advise on how to obtain reliable parameters?
Best
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Received on Wed Nov 14 2018 - 23:30:02 PST
