VÝPOČETNÍ METODY
E = Kr(r - r0)2 _-_
#WWW#
Kr
e = ke(0 - e0ý
£ = ^(l + COSn(0-0o))
H
r
e = a - b
(j) I stupně
Parametry silového pole AMBER (parm94.dat)
PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs
C
CA H
HC NB P S
12.01 12.01 1.008 1.008 14.01 30.97 32.06
OW-HW C -CA C -CB C —N*
553.0 469.0 447.0 424.0
HW-OW-HW 100.
HW-HW-OW 0.
CB-C -NA 70.0
CB-C -O 80.0
K -C -CA-X 4
K -C -CB-X 4
CT-CT-OS-CT 1
N -CT-C —N 1
definice
atomových typů
0.9572 1.409 1.419 1.383
14.50 12.00 0.383 0.40
sp2 C carbony1 group
sp2 C pure aromatic (benzene)
H bonded to nitrogen atoms
H aliph. bond, to C without electrwd.group
sp2 N in 5 memb.ring w/LP  (HIS,ADE,GUA)
phosphate
sulphur in disulfide linkage
TIP3P water
JCC,7,(1986),230;
JCC,7,(1986),230;
(1986),230;
JCC,7,
TYR GUA
CYT,URA
104.52 127.74 111.30 128.80
TIP3P water (found in cry NA
pstallographic water with 3 bonds)
J úhly
180.0 180.0 0.0 180.0
2. 2. ■3. ■4.
intrpol.bsd.on C6H6 intrpol.bsd.on C6H6
Í0.6000 0.0000 _ í:Ills
H O
0
o o o o
0157 0000 2100 2500 00277
!Ferguson base pair geom. TIP3P water model OPLS
W.  Cornell CH3SH and CH3SCH3 FEP's Na+ Aqvist JPC 1990,94,8021. (adapted)
Energie