Dear users and developers
I got four parameters for a single dihedral from AMBER topology files by
'parmed' command as shown below
Atom 1 Atom 2 Atom 3
Atom 4 Height Periodic. Phase EEL Scale VDW Scale
11 C ( C) 13 N ( N) 15 CA ( CX)
17 CB ( CT) 2.0000 1.0000 0.0000 1.2000 2.0000
M 11 C ( C) 13 N ( N) 15 CA ( CX)
17 CB ( CT) 1.8000 2.0000 0.0000 1.2000 2.0000
M 11 C ( C) 13 N ( N) 15 CA ( CX)
17 CB ( CT) 0.8000 3.0000 0.0000 1.2000 2.0000
M 11 C ( C) 13 N ( N) 15 CA ( CX)
17 CB ( CT) 0.0000 4.0000 0.0000 1.2000 2.0000
These four parameters correspond to four periodicities of the same dihedral
. Since periodicity is different, height of the potential barrier is
different. The question is can a dihedral have different periodicity? Out
of four periodicities, which is considered in a calculation? What 'M" in
the first column stands for?
Sincerely
Abdul Basit
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
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Received on Sun May 16 2021 - 10:00:02 PDT
