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# This script is to examine the average H-bonding of CAR residues.
parm /mindstore/home33ext/kscopino/COD1_GCN_SUBS/5JUP/GCC/TLEAP/5JUP_COD1_GCC_wat.prmtop
trajin /mindstore/home33ext/kscopino/COD1_GCN_SUBS/5JUP/GCC/NEUTRAL/NEUTRAL_28/mdcrd_nd_28 2500 last

### A-site anticodon nt1 to A-site codon nt1 ###
hbond nhb_AVE_169_all_175_all :169|:175 avgout nhb_AVE_169_all_175_all.dat
### A-site anticodon nt2 to A-site codon nt1 ###
hbond nhb_AVE_168_all_175_all :168|:175 avgout nhb_AVE_168_all_175_all.dat

### A-site anticodon nt1 to A-site codon nt2 ###
hbond nhb_AVE_169_all_176_all :169|:176 avgout nhb_AVE_169_all_176_all.dat
### A-site anticodon nt2 to A-site codon nt2 ###
hbond nhb_AVE_168_all_176_all :168|:176 avgout nhb_AVE_168_all_176_all.dat
### A-site anticodon wobble to A-site codon nt2 ###
hbond nhb_AVE_167_all_176_all :167|:176 avgout nhb_AVE_167_all_176_all.dat

### A-site anticodon nt2 to A-site codon wobble ###
hbond nhb_AVE_168_all_177_all :168|:177 avgout nhb_AVE_168_all_177_all.dat
### A-site anticodon wobble to A-site codon wobble ###
hbond nhb_AVE_167_all_177_all :167|:177 avgout nhb_AVE_167_all_177_all.dat
### C1054 to A-site codon wobble ###
hbond nhb_AVE_105_all_177_all :105|:177 avgout nhb_AVE_105_all_177_all.dat

### A-site anticodon wobble to +1 codon nt1 ###
hbond nhb_AVE_167_all_178_all :167|:178 avgout nhb_AVE_167_all_178_all.dat
### C1054 to +1 codon nt1 ###
hbond nhb_AVE_105_all_178_all :105|:178 avgout nhb_AVE_105_all_178_all.dat
### A1196 to +1 codon nt1 ###
hbond nhb_AVE_114_all_178_all :114|:178 avgout nhb_AVE_114_all_178_all.dat

### C1054 to +1 codon nt2 ###
hbond nhb_AVE_105_all_179_all :105|:179 avgout nhb_AVE_105_all_179_all.dat
### A1196 to +1 codon nt2 ###
hbond nhb_AVE_114_all_179_all :114|:179 avgout nhb_AVE_114_all_179_all.dat
### R146 to +1 codon nt2 ###
hbond nhb_AVE_368_all_179_all :368|:179 avgout nhb_AVE_368_all_179_all.dat

### A1196 to +1 codon nt3 ###
hbond nhb_AVE_114_all_180_all :114|:180 avgout nhb_AVE_114_all_180_all.dat
### R146 to +1 codon nt3 ###
hbond nhb_AVE_368_all_180_all :368|:180 avgout nhb_AVE_368_all_180_all.dat
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Page last modified on July 20, 2020, at 03:19 PM