On Sun, Jul 15, 2012 at 10:38 PM, Yun Shi <yunshi09.gmail.com> wrote:
> Hi everyone,
>
> I am reading dihedral parameters with rdparm, and it displays:
>
> ........
> 103: 2.175 3.14 2.0 :1.C6 :1.C5 :1.C4 :1.O4
> (14,16,18,19)
> E 104: 0.300 0.00 3.0 :1.C6 :1.C5 :1.C4 :1.O4
> (14,16,18,19)
> E 105: 2.175 3.14 2.0 :1.C6 :1.C5 :1.C4 :1.N3
> (14,16,18,20)
> 106: 1.850 3.14 2.0 :1.C5 :1.C6 :1.N1 :1.C2
> (16,14,13,22)
> E 107: 1.350 3.14 2.0 :1.C5 :1.C4 :1.N3 :1.C2
> (16,18,20,22)
> 108: 1.350 3.14 2.0 :1.C4 :1.N3 :1.C2 :1.O2
> (18,20,22,23)
> 109: 1.350 3.14 2.0 :1.O4 :1.C4 :1.N3 :1.C2
> (19,18,20,22)
> 110: 0.000 0.00 2.0 :1.C2 :1.N1 :1.C1' :1.C2'
> (22,13,11,26)
> 111: 1.175 0.00 2.0 :1.O2' :1.C2' :1.C3' :1.O3'
> (28,26,24,30)
> E 112: 0.144 0.00 3.0 :1.O2' :1.C2' :1.C3' :1.O3'
> (28,26,24,30)
> B 113: 1.000 3.14 2.0 :1.C2 :1.C6 :1.N1 :1.C1'
> (22,14,13,11)
> B 114: 10.500 3.14 2.0 :1.C5 :1.N3 :1.C4 :1.O4
> (16,20,18,19)
> B 115: 10.500 3.14 2.0 :1.N1 :1.N3 :1.C2 :1.O2
> (13,20,22,23)
> ...
>
> So I wonder what do the letters "E" and "B" at the beginning of some lines
> indicate?
>
The "B" means this is an "improper" dihedral. The "E" means that 1-4
non-bonded interactions are not calculated for this particular dihedral
term, but that it is still a 'proper' dihedral.
Because impropers are treated the same way as normal dihedrals in Amber,
"B" really just means the same as "E" (except the 1-4 NBs are not
calculated because it's an improper). In practice "E" either means that
dihedral is one term in a multi-term dihedral (only one term from a
multi-term dihedral does NOT have "E" beside it, so that the 1-4 nonbonded
interactions are calculated only once), or that the atom is in a 6 (or
lower)-member ring, in which case two dihedrals may have the same two 1,4
atoms, but different 2,3 atoms (in which case, you still want to calculate
those 1,4-atom interactions only once).
If you use ParmEd to print out this information, "I" means improper and "M"
means "multi-term" (which is the same as "B" and "E", in rdparm,
respectively).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jul 15 2012 - 20:30:02 PDT
