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tinker.key
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tinker.key
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Parameters /home/user/RNA_CG.prm
DEBYE-HUCKEL
ARCHIVE
printout 100
SAVE-CYCLE
WRITEOUT 100
openmp-threads 1
dielectric 25
debye-length 10
vdwtype LJ-LP
#atom 3 3 CG "Base Sugar Connet A&G" 3 53.022 3
#atom 4 4 N6 "Base CG for A&C" 4 42.030 2
#atom 5 5 N2 "Base CG For G" 5 54.030 2
#atom 6 6 O6 "Base CG For G&U" 6 43.014 2
#atom 7 7 O2 "Base CG For C&U" 7 42.006 2
#atom 8 8 CU "Base Sugar Connet C&U" 3 26.016 3
#atom 9 9 CA "Base A" 3 39.015 2
## Hydrogen bonds
#G-C
CGHBOND 3 6 5 8 4 7 2.0 2.9 6.0
##CGHBOND 3 6 5 4 7 8 2.0 2.9 6.0
##CGHBOND 6 5 3 8 4 7 2.0 2.9 6.0
CGHBOND 6 5 3 4 7 8 2.0 2.9 6.0
#G-G
#CGHBOND 3 6 5 6 5 3 2.0 2.9 6.0
#CGHBOND 3 6 5 3 6 5 2.0 2.9 6.0
#CGHBOND 6 5 3 6 5 3 2.0 2.9 6.0
#G-U
#CGHBOND 3 6 5 6 7 8 2.0 2.9 6.0
#GHBOND 3 6 5 8 6 7 2.0 2.9 6.0
#GHBOND 6 5 3 6 7 8 2.0 2.9 6.0
#CGHBOND 6 5 3 8 6 7 2.0 2.9 6.0
#G-A
#CGHBOND 3 6 5 3 4 9 2.0 2.9 6.0
#CGHBOND 3 6 5 4 9 3 2.0 2.9 6.0
#CGHBOND 6 5 3 3 4 9 2.0 2.9 6.0
#CGHBOND 6 5 3 4 9 3 2.0 2.9 6.0
#A-U
#CGHBOND 3 4 9 6 7 8 2.0 2.9 6.0
CGHBOND 3 4 9 8 6 7 2.0 2.9 6.0
#CGHBOND 4 9 3 6 7 8 2.0 2.9 6.0 ## Didn't account for in original hbonds
#CGHBOND 4 9 3 8 6 7 2.0 2.9 6.0
#A-A
#CGHBOND 3 4 9 3 4 9 2.0 2.9 6.0
#CGHBOND 3 4 9 4 9 3 2.0 2.9 6.0
#CGHBOND 4 9 3 4 9 3 2.0 2.9 6.0
#A-C
#CGHBOND 3 4 9 8 4 7 2.0 2.9 6.0
#CGHBOND 3 4 9 4 7 8 2.0 2.9 6.0
#CGHBOND 4 9 3 8 4 7 2.0 2.9 6.0
#CGHBOND 4 9 3 4 7 8 2.0 2.9 6.0
#C-U
#CGHBOND 8 4 7 6 7 8 2.0 2.9 6.0
#CGHBOND 8 4 7 8 6 7 2.0 2.9 6.0
#CGHBOND 4 7 8 6 7 8 2.0 2.9 6.0
#CGHBOND 4 7 8 8 6 7 2.0 2.9 6.0
#C-C
#CGHBOND 8 4 7 8 4 7 2.0 2.9 6.0
#CGHBOND 8 4 7 4 7 8 2.0 2.9 6.0
#CGHBOND 4 7 8 4 7 8 2.0 2.9 6.0
#U-U
#CGHBOND 8 6 7 8 6 7 2.0 2.9 6.0
#CGHBOND 8 6 7 6 7 8 2.0 2.9 6.0
#CGHBOND 6 7 8 6 7 8 2.0 2.9 6.0