1 |
< |
// This is the forcefield file generated from amber99.prm |
2 |
< |
// |
3 |
< |
// The sections are divided into AtomTypes |
4 |
< |
// |
1 |
> |
begin Options |
2 |
> |
Name = "Amber" |
3 |
> |
end Options |
4 |
|
|
6 |
– |
|
5 |
|
begin BaseAtomTypes |
6 |
|
//number name mass (amu) |
7 |
|
CT 12.01 |
49 |
|
K+ 39.100 |
50 |
|
Rb+ 85.470 |
51 |
|
Cs+ 132.910 |
52 |
< |
Mg+ 24.305 |
53 |
< |
Ca+ 40.080 |
54 |
< |
Zn+ 65.400 |
52 |
> |
Mg+2 24.305 |
53 |
> |
Ca+2 40.080 |
54 |
> |
Zn+2 65.400 |
55 |
|
Cl- 35.450 |
56 |
|
end BaseAtomTypes |
57 |
|
|
401 |
|
ACE-HA HC |
402 |
|
ACE-C C |
403 |
|
ACE-O O |
404 |
< |
C-Term N |
405 |
< |
C-Term H |
406 |
< |
N-MeAmide N |
407 |
< |
N-MeAmide H |
408 |
< |
N-MeAmide CT |
409 |
< |
N-MeAmide H1 |
404 |
> |
C-Term-N N |
405 |
> |
C-Term-H H |
406 |
> |
N-MeAmide-N N |
407 |
> |
N-MeAmide-H H |
408 |
> |
N-MeAmide-C CT |
409 |
> |
N-MeAmide-H1 H1 |
410 |
|
NGLY-N N3 |
411 |
|
NGLY-CA CT |
412 |
|
NGLY-C C |
935 |
|
DT-C7 CT |
936 |
|
DT-H7 HC |
937 |
|
DT-H6 H4 |
938 |
< |
R-Phosphodiester P |
939 |
< |
R-Phosphodiester O2 |
938 |
> |
R-Phosphodiester-P P |
939 |
> |
R-Phosphodiester-O O2 |
940 |
|
R5H-O5' OH |
941 |
|
R5H-H5T HO |
942 |
|
R5P-O5' OS |
947 |
|
R3P-O3' OS |
948 |
|
R3P-P P |
949 |
|
R3P-OP O2 |
950 |
< |
D-Phosphodiester P |
951 |
< |
D-Phosphodiester O2 |
950 |
> |
D-Phosphodiester-P P |
951 |
> |
D-Phosphodiester-O O2 |
952 |
|
D5H-O5' OH |
953 |
|
D5H-H5T HO |
954 |
|
D5P-O5' OS |
959 |
|
D3P-O3' OS |
960 |
|
D3P-P P |
961 |
|
D3P-OP O2 |
962 |
< |
TIP3P OW |
963 |
< |
TIP3P HW |
966 |
< |
Li+ Li+ |
967 |
< |
Na+ Na+ |
968 |
< |
K+ K+ |
969 |
< |
Rb+ Rb+ |
970 |
< |
Cs+ Cs+ |
971 |
< |
Mg+2 Mg+ |
972 |
< |
Ca+2 Ca+ |
973 |
< |
Zn+2 Zn+ |
974 |
< |
Cl- Cl- |
962 |
> |
TIP3P-O OW |
963 |
> |
TIP3P-H HW |
964 |
|
end AtomTypes |
965 |
|
|
966 |
|
|
1309 |
|
ACE-HA 0.1123 |
1310 |
|
ACE-C 0.5972 |
1311 |
|
ACE-O -0.5679 |
1312 |
< |
C-Term -0.8400 |
1313 |
< |
C-Term 0.4200 |
1314 |
< |
N-MeAmide -0.4157 |
1315 |
< |
N-MeAmide 0.2719 |
1316 |
< |
N-MeAmide -0.1490 |
1317 |
< |
N-MeAmide 0.0976 |
1312 |
> |
C-Term-N -0.8400 |
1313 |
> |
C-Term-H 0.4200 |
1314 |
> |
N-MeAmide-N -0.4157 |
1315 |
> |
N-MeAmide-H 0.2719 |
1316 |
> |
N-MeAmide-C -0.1490 |
1317 |
> |
N-MeAmide-H1 0.0976 |
1318 |
|
NGLY-N 0.2943 |
1319 |
|
NGLY-CA -0.0100 |
1320 |
|
NGLY-C 0.6163 |
1843 |
|
DT-C7 -0.2269 |
1844 |
|
DT-H7 0.0770 |
1845 |
|
DT-H6 0.2607 |
1846 |
< |
R-Phosphodiester 1.1662 |
1847 |
< |
R-Phosphodiester -0.7760 |
1846 |
> |
R-Phosphodiester-P 1.1662 |
1847 |
> |
R-Phosphodiester-O -0.7760 |
1848 |
|
R5H-O5' -0.6223 |
1849 |
|
R5H-H5T 0.4295 |
1850 |
|
R5P-O5' -0.6328 |
1855 |
|
R3P-O3' -0.6565 |
1856 |
|
R3P-P 0.9000 |
1857 |
|
R3P-OP -0.8200 |
1858 |
< |
D-Phosphodiester 1.1659 |
1859 |
< |
D-Phosphodiester -0.7761 |
1858 |
> |
D-Phosphodiester-P 1.1659 |
1859 |
> |
D-Phosphodiester-O -0.7761 |
1860 |
|
D5H-O5' -0.6318 |
1861 |
|
D5H-H5T 0.4422 |
1862 |
|
D5P-O5' -0.6296 |
1867 |
|
D3P-O3' -0.6553 |
1868 |
|
D3P-P 0.9000 |
1869 |
|
D3P-OP -0.8200 |
1870 |
< |
TIP3P -0.834 |
1871 |
< |
TIP3P 0.417 |
1870 |
> |
TIP3P-O -0.834 |
1871 |
> |
TIP3P-H 0.417 |
1872 |
|
Li+ 1.000 |
1873 |
|
Na+ 1.000 |
1874 |
|
K+ 1.000 |
1929 |
|
K+ 0.000328 4.736018 |
1930 |
|
Rb+ 0.000170 5.266993 |
1931 |
|
Cs+ 0.000081 6.049202 |
1932 |
< |
Mg+ 0.894700 1.412253 |
1933 |
< |
Ca+ 0.459789 3.052397 |
1934 |
< |
Zn+ 0.012500 1.959977 |
1932 |
> |
Mg+2 0.894700 1.412253 |
1933 |
> |
Ca+2 0.459789 3.052397 |
1934 |
> |
Zn+2 0.012500 1.959977 |
1935 |
|
Cl- 0.100000 4.401040 |
1936 |
|
end LennardJonesAtomTypes |
1937 |
|
|
2020 |
|
S S Harmonic 2.038000 166.000000 |
2021 |
|
SH HS Harmonic 1.336000 274.000000 |
2022 |
|
HW HW Harmonic 1.513600 553.000000 |
2023 |
< |
end BondType |
2023 |
> |
end BondTypes |
2024 |
|
|
2025 |
|
|
2026 |
|
begin BendTypes |
2555 |
|
end TorsionTypes |
2556 |
|
|
2557 |
|
|
2558 |
< |
begin Improper TorsionTypes |
2559 |
< |
CT N C O 10.500000 2 180.000000 |
2560 |
< |
CM NA C O 10.500000 2 180.000000 |
2561 |
< |
CB NA C O 10.500000 2 180.000000 |
2562 |
< |
N* NA C O 10.500000 2 180.000000 |
2563 |
< |
CT O2 C O2 10.500000 2 180.000000 |
2564 |
< |
CA CA CA CT 1.100000 2 180.000000 |
2565 |
< |
CA CA CA OH 1.100000 2 180.000000 |
2566 |
< |
CA CA CA HA 1.100000 2 180.000000 |
2567 |
< |
CN CA CA HA 1.100000 2 180.000000 |
2568 |
< |
NC CM CA N2 1.100000 2 180.000000 |
2569 |
< |
CA CB CA HA 1.100000 2 180.000000 |
2570 |
< |
CB NC CA N2 1.100000 2 180.000000 |
2571 |
< |
NA NC CA N2 1.100000 2 180.000000 |
2572 |
< |
N2 N2 CA N2 10.500000 2 180.000000 |
2573 |
< |
CM CA CM HA 1.100000 2 180.000000 |
2574 |
< |
C CM CM CT 1.100000 2 180.000000 |
2575 |
< |
C CM CM HA 1.100000 2 180.000000 |
2576 |
< |
N* CM CM H4 1.100000 2 180.000000 |
2577 |
< |
NA CV CC CT 1.100000 2 180.000000 |
2578 |
< |
NA CW CC CT 1.100000 2 180.000000 |
2579 |
< |
NB CW CC CT 1.100000 2 180.000000 |
2580 |
< |
CC NB CV H4 1.100000 2 180.000000 |
2581 |
< |
CC NA CW H4 1.100000 2 180.000000 |
2582 |
< |
C* NA CW H4 1.100000 2 180.000000 |
2583 |
< |
NA NA CR H5 1.100000 2 180.000000 |
2584 |
< |
NB NA CR H5 1.100000 2 180.000000 |
2585 |
< |
NA NB CR H5 1.100000 2 180.000000 |
2586 |
< |
CW CB C* CT 1.100000 2 180.000000 |
2587 |
< |
NB N* CK H5 1.100000 2 180.000000 |
2588 |
< |
NC NC CQ H5 1.100000 2 180.000000 |
2589 |
< |
C CT N CT 1.000000 2 180.000000 |
2590 |
< |
C CT N H 1.000000 2 180.000000 |
2591 |
< |
C H N H 1.000000 2 180.000000 |
2592 |
< |
C C NA H 1.000000 2 180.000000 |
2593 |
< |
C CA NA H 1.000000 2 180.000000 |
2594 |
< |
CR CW NA H 1.000000 2 180.000000 |
2595 |
< |
CC CR NA H 1.000000 2 180.000000 |
2596 |
< |
CW CN NA H 1.000000 2 180.000000 |
2597 |
< |
CM C N* CT 1.000000 2 180.000000 |
2598 |
< |
CK CB N* CT 1.000000 2 180.000000 |
2599 |
< |
CT CA N2 H 1.000000 2 180.000000 |
2600 |
< |
CA H N2 H 1.000000 2 180.000000 |
2601 |
< |
end Improper TorsionTypes |
2558 |
> |
begin InversionTypes |
2559 |
> |
CT N C O ImproperCosine 10.500000 2 180.000000 |
2560 |
> |
CM NA C O ImproperCosine 10.500000 2 180.000000 |
2561 |
> |
CB NA C O ImproperCosine 10.500000 2 180.000000 |
2562 |
> |
N* NA C O ImproperCosine 10.500000 2 180.000000 |
2563 |
> |
CT O2 C O2 ImproperCosine 10.500000 2 180.000000 |
2564 |
> |
CA CA CA CT ImproperCosine 1.100000 2 180.000000 |
2565 |
> |
CA CA CA OH ImproperCosine 1.100000 2 180.000000 |
2566 |
> |
CA CA CA HA ImproperCosine 1.100000 2 180.000000 |
2567 |
> |
CN CA CA HA ImproperCosine 1.100000 2 180.000000 |
2568 |
> |
NC CM CA N2 ImproperCosine 1.100000 2 180.000000 |
2569 |
> |
CA CB CA HA ImproperCosine 1.100000 2 180.000000 |
2570 |
> |
CB NC CA N2 ImproperCosine 1.100000 2 180.000000 |
2571 |
> |
NA NC CA N2 ImproperCosine 1.100000 2 180.000000 |
2572 |
> |
N2 N2 CA N2 ImproperCosine 10.500000 2 180.000000 |
2573 |
> |
CM CA CM HA ImproperCosine 1.100000 2 180.000000 |
2574 |
> |
C CM CM CT ImproperCosine 1.100000 2 180.000000 |
2575 |
> |
C CM CM HA ImproperCosine 1.100000 2 180.000000 |
2576 |
> |
N* CM CM H4 ImproperCosine 1.100000 2 180.000000 |
2577 |
> |
NA CV CC CT ImproperCosine 1.100000 2 180.000000 |
2578 |
> |
NA CW CC CT ImproperCosine 1.100000 2 180.000000 |
2579 |
> |
NB CW CC CT ImproperCosine 1.100000 2 180.000000 |
2580 |
> |
CC NB CV H4 ImproperCosine 1.100000 2 180.000000 |
2581 |
> |
CC NA CW H4 ImproperCosine 1.100000 2 180.000000 |
2582 |
> |
C* NA CW H4 ImproperCosine 1.100000 2 180.000000 |
2583 |
> |
NA NA CR H5 ImproperCosine 1.100000 2 180.000000 |
2584 |
> |
NB NA CR H5 ImproperCosine 1.100000 2 180.000000 |
2585 |
> |
NA NB CR H5 ImproperCosine 1.100000 2 180.000000 |
2586 |
> |
CW CB C* CT ImproperCosine 1.100000 2 180.000000 |
2587 |
> |
NB N* CK H5 ImproperCosine 1.100000 2 180.000000 |
2588 |
> |
NC NC CQ H5 ImproperCosine 1.100000 2 180.000000 |
2589 |
> |
C CT N CT ImproperCosine 1.000000 2 180.000000 |
2590 |
> |
C CT N H ImproperCosine 1.000000 2 180.000000 |
2591 |
> |
C H N H ImproperCosine 1.000000 2 180.000000 |
2592 |
> |
C C NA H ImproperCosine 1.000000 2 180.000000 |
2593 |
> |
C CA NA H ImproperCosine 1.000000 2 180.000000 |
2594 |
> |
CR CW NA H ImproperCosine 1.000000 2 180.000000 |
2595 |
> |
CC CR NA H ImproperCosine 1.000000 2 180.000000 |
2596 |
> |
CW CN NA H ImproperCosine 1.000000 2 180.000000 |
2597 |
> |
CM C N* CT ImproperCosine 1.000000 2 180.000000 |
2598 |
> |
CK CB N* CT ImproperCosine 1.000000 2 180.000000 |
2599 |
> |
CT CA N2 H ImproperCosine 1.000000 2 180.000000 |
2600 |
> |
CA H N2 H ImproperCosine 1.000000 2 180.000000 |
2601 |
> |
end InversionTypes |
2602 |
|
|