########################################################################## # Read datafiles created with the other CPPTRAJ script # ########################################################################## readdata base3.dat name base3 readdata base5.dat name base5 readdata base7.dat name base7 readdata base9.dat name base9 readdata base11.dat name base11 readdata base13.dat name base13 readdata base15.dat name base15 readdata base21.dat name base21 readdata base23.dat name base23 readdata base25.dat name base25 readdata base27.dat name base27 readdata base29.dat name base29 readdata base31.dat name base31 readdata base33.dat name base33 # ########################################################################## # # HG hydrogen bonding: Both AN7—TN3 and AN6—TO4 distances ≤3.5 Å for A•T # ########################################################################## # filter l3 min 3.5 max 10 ll3 min 3.5 max 10 out data/l3ll3.dat # filter l5 min 3.5 max 10 ll5 min 3.5 max 10 out data/l5ll5.dat # filter l7 min 3.5 max 10 ll7 min 3.5 max 10 out data/l7ll7.dat # filter l9 min 3.5 max 10 ll9 min 3.5 max 10 out data/l9ll9.dat # filter l11 min 3.5 max 10 ll11 min 3.5 max 10 out data/l11ll11.dat # filter l13 min 3.5 max 10 ll13 min 3.5 max 10 out data/l13ll13.dat # filter l15 min 3.5 max 10 ll15 min 3.5 max 10 out data/l15ll15.dat # filter l21 min 3.5 max 10 ll21 min 3.5 max 10 out data/l21ll21.dat # filter l23 min 3.5 max 10 ll23 min 3.5 max 10 out data/l23ll23.dat # filter l25 min 3.5 max 10 ll25 min 3.5 max 10 out data/l25ll25.dat # filter l27 min 3.5 max 10 ll27 min 3.5 max 10 out data/l27ll27.dat # filter l29 min 3.5 max 10 ll29 min 3.5 max 10 out data/l29ll29.dat # filter l31 min 3.5 max 10 ll31 min 3.5 max 10 out data/l31ll31.dat # filter l33 min 3.5 max 10 ll33 min 3.5 max 10 out data/l33ll33.dat ########################################################################## # The distance between the C1′ atoms of the purine and pyrimidine pair is restricted to ≤9.5 Å ########################################################################## datafilter base3:4 min 7 max 9.8 out base3-C1_C1-filtered.dat datafilter base5:4 min 7 max 9.8 out base5-C1_C1-filtered.dat datafilter base7:4 min 7 max 9.8 out base7-C1_C1-filtered.dat datafilter base9:4 min 7 max 9.8 out base9-C1_C1-filtered.dat datafilter base11:4 min 7 max 9.8 out base11-C1_C1-filtered.dat datafilter base13:4 min 7 max 9.8 out base13-C1_C1-filtered.dat datafilter base15:4 min 7 max 9.8 out base15-C1_C1-filtered.dat datafilter base21:4 min 7 max 9.8 out base21-C1_C1-filtered.dat datafilter base23:4 min 7 max 9.8 out base23-C1_C1-filtered.dat datafilter base25:4 min 7 max 9.8 out base25-C1_C1-filtered.dat datafilter base27:4 min 7 max 9.8 out base27-C1_C1-filtered.dat datafilter base29:4 min 7 max 9.8 out base29-C1_C1-filtered.dat datafilter base31:4 min 7 max 9.8 out base31-C1_C1-filtered.dat datafilter base33:4 min 7 max 9.8 out base33-C1_C1-filtered.dat ########################################################################## # syn purine: The syn glycosidic torsion angle (χ angle) of the purine base is in the range 0° ≤ χ ≤ 90°. ########################################################################## datafilter base3:5 min 0 max 90 out base3-chi-filtered.dat datafilter base5:5 min 0 max 90 out base5-chi-filtered.dat datafilter base7:5 min 0 max 90 out base7-chi-filtered.dat datafilter base9:5 min 0 max 90 out base9-chi-filtered.dat datafilter base11:5 min 0 max 90 out base11-chi-filtered.dat datafilter base13:5 min 0 max 90 out base13-chi-filtered.dat datafilter base15:5 min 0 max 90 out base15-chi-filtered.dat datafilter base21:5 min 0 max 90 out base21-chi-filtered.dat datafilter base23:5 min 0 max 90 out base23-chi-filtered.dat datafilter base25:5 min 0 max 90 out base25-chi-filtered.dat datafilter base27:5 min 0 max 90 out base27-chi-filtered.dat datafilter base29:5 min 0 max 90 out base29-chi-filtered.dat datafilter base31:5 min 0 max 90 out base31-chi-filtered.dat datafilter base33:5 min 0 max 90 out base33-chi-filtered.dat ########################################################################## # Combine both chi and C1 filters ########################################################################## datafilter base3:5 min 0 max 90 base3:4 min 7 max 9.8 out base3-C1+chi-filtered.dat datafilter base5:5 min 0 max 90 base5:4 min 7 max 9.8 out base5-C1+chi-filtered.dat datafilter base7:5 min 0 max 90 base7:4 min 7 max 9.8 out base7-C1+chi-filtered.dat datafilter base9:5 min 0 max 90 base9:4 min 7 max 9.8 out base9-C1+chi-filtered.dat datafilter base11:5 min 0 max 90 base11:4 min 7 max 9.8 out base11-C1+chi-filtered.dat datafilter base13:5 min 0 max 90 base13:4 min 7 max 9.8 out base13-C1+chi-filtered.dat datafilter base15:5 min 0 max 90 base15:4 min 7 max 9.8 out base15-C1+chi-filtered.dat datafilter base21:5 min 0 max 90 base21:4 min 7 max 9.8 out base21-C1+chi-filtered.dat datafilter base23:5 min 0 max 90 base23:4 min 7 max 9.8 out base23-C1+chi-filtered.dat datafilter base25:5 min 0 max 90 base25:4 min 7 max 9.8 out base25-C1+chi-filtered.dat datafilter base27:5 min 0 max 90 base27:4 min 7 max 9.8 out base27-C1+chi-filtered.dat datafilter base29:5 min 0 max 90 base29:4 min 7 max 9.8 out base29-C1+chi-filtered.dat datafilter base31:5 min 0 max 90 base31:4 min 7 max 9.8 out base31-C1+chi-filtered.dat datafilter base33:5 min 0 max 90 base33:4 min 7 max 9.8 out base33-C1+chi-filtered.dat run