\-/ -/- PTRAJ: a utility for processing trajectory files /-\ \-/ Version: "AMBER 9.0 integrated" (April 2006) -/- Executable is: "ptraj" /-\ \-/ ASN ASN ASP ILE THR LEU LEU LYS LEU SER THR ALA WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT ... WAT WAT WAT WAT PTRAJ: Processing input from "STDIN" ... PTRAJ: trajin ../../cga_10ns_slv_prod.crd.gz PTRAJ: solvent byres :WAT Mask [:WAT] represents 6636 atoms Searching for solvent by mask :13-2224 PTRAJ: closestwater 100 :1-190 first Mask [:1-190] represents 724 atoms PTRAJ: donor mask :GLN@OE1 Mask [:GLN@OE1] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:GLN@OE1), ignoring... PTRAJ: donor mask :GLN@NE2 Mask [:GLN@NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:GLN@NE2), ignoring... PTRAJ: donor mask :ASN@OD1 Mask [:ASN@OD1] represents 2 atoms PTRAJ: donor mask :ASN@ND2 Mask [:ASN@ND2] represents 2 atoms PTRAJ: donor mask :TYR@OH Mask [:TYR@OH] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:TYR@OH), ignoring... PTRAJ: donor mask :ASP@OD1 Mask [:ASP@OD1] represents 1 atoms PTRAJ: donor mask :ASP@OD2 Mask [:ASP@OD2] represents 1 atoms PTRAJ: donor mask :GLU@OE1 Mask [:GLU@OE1] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:GLU@OE1), ignoring... PTRAJ: donor mask :GLU@OE2 Mask [:GLU@OE2] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:GLU@OE2), ignoring... PTRAJ: donor mask :SER@OG Mask [:SER@OG] represents 1 atoms PTRAJ: donor mask :THR@OG1 Mask [:THR@OG1] represents 2 atoms PTRAJ: donor mask :HIS@ND1 Mask [:HIS@ND1] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:HIS@ND1), ignoring... PTRAJ: donor mask :HIE@ND1 Mask [:HIE@ND1] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:HIE@ND1), ignoring... PTRAJ: donor mask :HID@NE2 Mask [:HID@NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, donor: No atoms selected (:HID@NE2), ignoring... PTRAJ: acceptor mask :ASN@ND2 :ASN@HD21 Mask [:ASN@ND2] represents 2 atoms Mask [:ASN@HD21] represents 2 atoms PTRAJ: acceptor mask :ASN@ND2 :ASN@HD22 Mask [:ASN@ND2] represents 2 atoms Mask [:ASN@HD22] represents 2 atoms PTRAJ: acceptor mask :TYR@OH :TYR@HH Mask [:TYR@OH] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:TYR@HH] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:TYR@OH), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:TYR@HH), ignoring... PTRAJ: acceptor mask :GLN@NE2 :GLN@HE21 Mask [:GLN@NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:GLN@HE21] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:GLN@NE2), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:GLN@HE21), ignoring... PTRAJ: acceptor mask :GLN@NE2 :GLN@HE22 Mask [:GLN@NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:GLN@HE22] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:GLN@NE2), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:GLN@HE22), ignoring... PTRAJ: acceptor mask :TRP@NE1 :TRP@HE1 Mask [:TRP@NE1] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:TRP@HE1] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:TRP@NE1), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:TRP@HE1), ignoring... PTRAJ: acceptor mask :LYS@NZ :LYS@HZ1 Mask [:LYS@NZ] represents 1 atoms Mask [:LYS@HZ1] represents 1 atoms PTRAJ: acceptor mask :LYS@NZ :LYS@HZ2 Mask [:LYS@NZ] represents 1 atoms Mask [:LYS@HZ2] represents 1 atoms PTRAJ: acceptor mask :LYS@NZ :LYS@HZ3 Mask [:LYS@NZ] represents 1 atoms Mask [:LYS@HZ3] represents 1 atoms PTRAJ: acceptor mask :SER@OG :SER@HG Mask [:SER@OG] represents 1 atoms Mask [:SER@HG] represents 1 atoms PTRAJ: acceptor mask :THR@OG1 :THR@HG1 Mask [:THR@OG1] represents 2 atoms Mask [:THR@HG1] represents 2 atoms PTRAJ: acceptor mask :ARG@NH2 :ARG@HH21 Mask [:ARG@NH2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:ARG@HH21] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:ARG@NH2), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:ARG@HH21), ignoring... PTRAJ: acceptor mask :ARG@NH2 :ARG@HH22 Mask [:ARG@NH2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:ARG@HH22] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:ARG@NH2), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:ARG@HH22), ignoring... PTRAJ: acceptor mask :ARG@NH1 :ARG@HH11 Mask [:ARG@NH1] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:ARG@HH11] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:ARG@NH1), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:ARG@HH11), ignoring... PTRAJ: acceptor mask :ARG@NH1 :ARG@HH12 Mask [:ARG@NH1] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:ARG@HH12] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:ARG@NH1), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:ARG@HH12), ignoring... PTRAJ: acceptor mask :ARG@NE :ARG@HE Mask [:ARG@NE] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:ARG@HE] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:ARG@NE), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:ARG@HE), ignoring... PTRAJ: acceptor mask :HIS@NE2 :HIS@HE2 Mask [:HIS@NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:HIS@HE2] represents 1 atoms WARNING in ptraj, acceptor: No heavy atom was selected (:HIS@NE2), ignoring... WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the atom selection in the two masks :HIS@NE2 and :HIS@HE2 which contain 0 and 1 atoms respectively. Ignoring... PTRAJ: acceptor mask :HIE@NE2 :HIE@HE2 Mask [:HIE@NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:HIE@HE2] represents 1 atoms WARNING in ptraj, acceptor: No heavy atom was selected (:HIE@NE2), ignoring... WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the atom selection in the two masks :HIE@NE2 and :HIE@HE2 which contain 0 and 1 atoms respectively. Ignoring... PTRAJ: acceptor mask :HID@ND1 :HID@HD1 Mask [:HID@ND1] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:HID@HD1] represents 0 atoms !!!NO ATOMS DETECTED!!! WARNING in ptraj, acceptor: No heavy atom was selected (:HID@ND1), ignoring... WARNING in ptraj, acceptor: No hydrogen atom was selected (:HID@HD1), ignoring... PTRAJ: acceptor mask :HIP@ND1,NE2 :HIP@HE2,HD1 Mask [:HIP@ND1,NE2] represents 0 atoms !!!NO ATOMS DETECTED!!! Mask [:HIP@HE2,HD1] represents 1 atoms WARNING in ptraj, acceptor: No heavy atom was selected (:HIP@ND1,NE2), ignoring... WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the atom selection in the two masks :HIP@ND1,NE2 and :HIP@HE2,HD1 which contain 0 and 1 atoms respectively. Ignoring... PTRAJ: donor mask @O Mask [@O] represents 112 atoms PTRAJ: acceptor mask :2-12@N :2-12@H Mask [:2-12@N] represents 11 atoms Mask [:2-12@H] represents 11 atoms PTRAJ: donor mask @OXT Mask [@OXT] represents 1 atoms PTRAJ: acceptor mask :1@N :1@H1 Mask [:1@N] represents 1 atoms Mask [:1@H1] represents 1 atoms PTRAJ: acceptor mask :1@N :1@H2 Mask [:1@N] represents 1 atoms Mask [:1@H2] represents 1 atoms PTRAJ: acceptor mask :1@N :1@H3 Mask [:1@N] represents 1 atoms Mask [:1@H3] represents 1 atoms PTRAJ: donor WAT O PTRAJ: acceptor WAT O H1 PTRAJ: acceptor WAT O H2 PTRAJ: hbond solventneighbor 4 print .05 series hbt [No output trajectory specified (trajout)] PTRAJ: Successfully read the input file. Coordinate processing will occur on 10000 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (../../cga_10ns_slv_prod.crd.gz) is an AMBER trajectory (with box info) with 10000 sets NO OUTPUT COORDINATE FILE WAS SPECIFIED ACTIONS 1> CLOSESTWATERS: saving the 100 closest solvent molecules around atoms :1-190 The current solvent mask is :13-2224 7> HBOND saved to series hbt, data will be sorted, intra-residue interactions will NOT be included, Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees Hydrogen bond information will be dumped for occupancies > 0.05 Estimated memory usage for this hbond call: 3.05 GB donors: 122 acceptors: 224 frames: 10000 Processing AMBER trajectory file ../../cga_10ns_slv_prod.crd.gz Set 1 ................................................. Set 50 ................................................. Set 100 ................................................. Set 150 ................................................. Set 200 ................................................. Set 250 ................................................. Set 300 ................................................. Set 350 ................................................. Set 400 ................................................. Set 450 ................................................. Set 500 ................................................. Set 550 ................................................. Set 600 ................................................. Set 650 ................................................. Set 700 ................................................. Set 750 ................................................. Set 800 ................................................. Set 850 ................................................. Set 900 ................................................. Set 950 ................................................. Set 1000 ................................................. Set 1050 ................................................. Set 1100 ................................................. Set 1150 ................................................. Set 1200 ................................................. Set 1250 ................................................. Set 1300 ................................................. Set 1350 ................................................. Set 1400 ................................................. Set 1450 ................................................. Set 1500 ................................................. Set 1550 ................................................. Set 1600 ................................................. Set 1650 ................................................. Set 1700 ................................................. Set 1750 ................................................. Set 1800 ................................................. Set 1850 ................................................. Set 1900 ................................................. Set 1950 ................................................. Set 2000 ................................................. Set 2050 ................................................. Set 2100 ................................................. Set 2150 ................................................. Set 2200 ................................................. Set 2250 ................................................. Set 2300 ................................................. Set 2350 ................................................. Set 2400 ................................................. Set 2450 ................................................. Set 2500 ................................................. Set 2550 ................................................. Set 2600 ................................................. Set 2650 ................................................. Set 2700 ................................................. Set 2750 ................................................. Set 2800 ................................................. Set 2850 ................................................. Set 2900 ................................................. Set 2950 ................................................. Set 3000 ................................................. Set 3050 ................................................. Set 3100 ................................................. Set 3150 ................................................. Set 3200 ................................................. Set 3250 ................................................. Set 3300 ................................................. Set 3350 ................................................. Set 3400 ................................................. Set 3450 ................................................. Set 3500 ................................................. Set 3550 ................................................. Set 3600 ................................................. Set 3650 ................................................. Set 3700 ................................................. Set 3750 ................................................. Set 3800 ................................................. Set 3850 ................................................. Set 3900 ................................................. Set 3950 ................................................. Set 4000 ................................................. Set 4050 ................................................. Set 4100 ................................................. Set 4150 ................................................. Set 4200 ................................................. Set 4250 ................................................. Set 4300 ................................................. Set 4350 ................................................. Set 4400 ................................................. Set 4450 ................................................. Set 4500 ................................................. Set 4550 ................................................. Set 4600 ................................................. Set 4650 ................................................. Set 4700 ................................................. Set 4750 ................................................. Set 4800 ................................................. Set 4850 ................................................. Set 4900 ................................................. Set 4950 ................................................. Set 5000 ................................................. Set 5050 ................................................. Set 5100 ................................................. Set 5150 ................................................. Set 5200 ................................................. Set 5250 ................................................. Set 5300 ................................................. Set 5350 ................................................. Set 5400 ................................................. Set 5450 ................................................. Set 5500 ................................................. Set 5550 ................................................. Set 5600 ................................................. Set 5650 ................................................. Set 5700 ................................................. Set 5750 ................................................. Set 5800 ................................................. Set 5850 ................................................. Set 5900 ................................................. Set 5950 ................................................. Set 6000 ................................................. Set 6050 ................................................. Set 6100 ................................................. Set 6150 ................................................. Set 6200 ................................................. Set 6250 ................................................. Set 6300 ................................................. Set 6350 ................................................. Set 6400 ................................................. Set 6450 ................................................. Set 6500 ................................................. Set 6550 ................................................. Set 6600 ................................................. Set 6650 ................................................. Set 6700 ................................................. Set 6750 ................................................. Set 6800 ................................................. Set 6850 ................................................. Set 6900 ................................................. Set 6950 ................................................. Set 7000 ................................................. Set 7050 ................................................. Set 7100 ................................................. Set 7150 ................................................. Set 7200 ................................................. Set 7250 ................................................. Set 7300 ................................................. Set 7350 ................................................. Set 7400 ................................................. Set 7450 ................................................. Set 7500 ................................................. Set 7550 ................................................. Set 7600 ................................................. Set 7650 ................................................. Set 7700 ................................................. Set 7750 ................................................. Set 7800 ................................................. Set 7850 ................................................. Set 7900 ................................................. Set 7950 ................................................. Set 8000 ................................................. Set 8050 ................................................. Set 8100 ................................................. Set 8150 ................................................. Set 8200 ................................................. Set 8250 ................................................. Set 8300 ................................................. Set 8350 ................................................. Set 8400 ................................................. Set 8450 ................................................. Set 8500 ................................................. Set 8550 ................................................. Set 8600 ................................................. Set 8650 ................................................. Set 8700 ................................................. Set 8750 ................................................. Set 8800 ................................................. Set 8850 ................................................. Set 8900 ................................................. Set 8950 ................................................. Set 9000 ................................................. Set 9050 ................................................. Set 9100 ................................................. Set 9150 ................................................. Set 9200 ................................................. Set 9250 ................................................. Set 9300 ................................................. Set 9350 ................................................. Set 9400 ................................................. Set 9450 ................................................. Set 9500 ................................................. Set 9550 ................................................. Set 9600 ................................................. Set 9650 ................................................. Set 9700 ................................................. Set 9750 ................................................. Set 9800 ................................................. Set 9850 ................................................. Set 9900 ................................................. Set 9950 ................................................. Set 10000 PTRAJ: Successfully read in 10000 sets and processed 10000 sets. Dumping accumulated results (if any) HBOND SUMMARY: Data was saved to series hbt, data was sorted, intra-residue interactions are NOT included, Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees Hydrogen bond information dumped for occupancies > 0.05 Dumping schematic of time series after each h-bond, key follows: | . - o x * @ | 0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy DONOR ACCEPTORH ACCEPTOR atom# :res@atom atom# :res@atom atom# :res@atom %occupied distance angle lifetime maxocc | 39 :3@OD1 | 73 :5@HG1 72 :5@OG1 | 29.76 2.720 ( 0.13) 21.14 (12.02) 5.9 ( 7.8) 64 | --*--xoxo-oo-| | 40 :3@OD2 | 73 :5@HG1 72 :5@OG1 | 28.38 2.720 ( 0.13) 21.40 (12.25) 5.5 ( 8.8) 89 | *oo.x--------o| | 39 :3@OD1 | 63 :5@H 62 :5@N | 17.31 2.864 ( 0.09) 29.60 (12.17) 2.0 ( 1.5) 13 | ..o.---------| | 40 :3@OD2 | 63 :5@H 62 :5@N | 15.96 2.864 ( 0.09) 30.81 (12.20) 2.1 ( 1.6) 13 | o-- -..-..-.--| | 42 :3@O | 77 :6@H 76 :6@N | 15.39 2.884 ( 0.08) 29.84 (10.49) 1.6 ( 1.1) 15 | -----..-....-.| | 16 :1@O | 156 :10@H 155 :10@N | 13.09 2.864 ( 0.08) 24.06 (12.83) 2.6 ( 2.0) 12 | -xo. -o | | 25 :2@OD1 | 32 :3@H 31 :3@N | 11.50 2.852 ( 0.09) 41.05 (10.21) 1.6 ( 1.1) 11 |. . .--.....-... | | 40 :3@OD2 | 96 :7@H 95 :7@N | 9.07 2.864 ( 0.09) 26.58 (14.49) 1.7 ( 1.1) 10 | ..- .. .. ...-| | 75 :5@O | 96 :7@H 95 :7@N | 8.63 2.865 ( 0.09) 39.61 (11.37) 1.6 ( 1.2) 13 | . -.-..-....| | 165 :10@O | 177 :11@HG1 176 :11@OG1 | 8.19 2.743 ( 0.13) 22.33 (12.49) 3.1 ( 3.3) 29 |.. -. . . . .--.| | 11 :1@OD1 | 18 :2@H 17 :2@N | 8.13 2.855 ( 0.09) 43.84 (10.73) 1.4 ( 1.0) 12 |... ... . ....... | | 40 :3@OD2 | 115 :8@H 114 :8@N | 7.58 2.860 ( 0.09) 25.32 (11.96) 2.2 ( 1.8) 14 | .-..- - .| | 190 :12@OXT | 163 :10@HG 162 :10@OG | 7.46 2.656 ( 0.13) 19.03 (10.58) 5.6 ( 6.2) 33 | . . ..- -. | | 154 :9@O | 163 :10@HG 162 :10@OG | 6.29 2.725 ( 0.13) 27.59 (12.73) 2.9 ( 3.8) 29 |. . -...... . . .| | 39 :3@OD1 | 96 :7@H 95 :7@N | 5.83 2.877 ( 0.09) 27.08 (14.55) 1.6 ( 1.1) 8 | . - ...... . | | 11 :1@OD1 | 156 :10@H 155 :10@N | 5.68 2.850 ( 0.09) 26.76 (13.50) 2.7 ( 2.6) 21 | -. .o.| | 189 :12@O | 163 :10@HG 162 :10@OG | 5.31 2.662 ( 0.13) 19.94 (11.21) 5.2 ( 4.5) 24 | ... . .. -. | | 165 :10@O | 4 :1@H3 1 :1@N | 5.18 2.815 ( 0.10) 27.86 (13.98) 2.7 ( 2.9) 17 | .--. .. | | 40 :3@OD2 | 77 :6@H 76 :6@N | 5.18 2.846 ( 0.10) 41.87 (13.15) 1.5 ( 1.1) 11 | ... ......| | 39 :3@OD1 | 44 :4@H 43 :4@N | 5.18 2.817 ( 0.11) 43.08 (11.67) 1.4 ( 1.1) 12 | . . .. . . .| ---------------- --------------------------------- -------------------------------------