Hi, I'm trying to use command "findclash" to check the excluded volume effect by detecting overlaps between atoms. The command I use is "findclash #0 test #0" or "findclash #0 overlapCutoff value test #0", but I found that two close atoms (14C,16C, dis=0.8) are not identified as "overlaped" while another two atoms (11C, 16C, dis=1.8) whose distance is larger are overlaped... Is there anything wrong about understanding the overlap? Example molecular (init.mol2): @<TRIPOS>MOLECULE init.mol2 20 19 20 0 0 NUCLEIC_ACID NO_CHARGES @<TRIPOS>ATOM 1 C 14.7888 10.0072 -5.6663 C.3 1 DA 0.0000 2 C 15.4013 8.5150 -3.5012 C.3 2 DA 0.0000 3 C 13.7388 8.7698 -5.6133 C.3 3 DA 0.0000 4 C 14.6414 7.5770 -3.3654 C.3 4 DA 0.0000 5 C 12.9675 5.9273 -2.0359 C.3 5 DA 0.0000 6 C 13.6457 4.0155 -0.2544 C.3 6 DA 0.0000 7 C 12.8822 2.8588 2.0634 C.3 7 DA 0.0000 8 C 11.7541 3.3958 4.4562 C.3 8 DA 0.0000 9 C 11.2290 4.5854 6.8231 C.3 9 DA 0.0000 10 C 13.8907 4.6510 7.2730 C.3 10 DA 0.0000 11 C 15.5581 5.2490 9.3114 C.3 11 DA 0.0000 12 C 17.8150 4.7800 10.7177 C.3 12 DA 0.0000 13 C 18.0666 2.1205 10.3271 C.3 13 DA 0.0000 14 C 16.9288 4.4119 9.4640 C.3 14 DA 0.0000 15 C 14.9471 3.0788 10.7232 C.3 15 DA 0.0000 16 C 16.7345 3.9070 8.8773 C.3 16 DA 0.0000 17 C 15.5384 2.3512 10.7314 C.3 17 DA 0.0000 18 C 16.0476 1.4159 8.2501 C.3 18 DA 0.0000 19 C 17.5152 1.5369 5.9877 C.3 19 DA 0.0000 20 C 17.5650 3.1811 3.8468 C.3 20 DA 0.0000 @<TRIPOS>BOND 1 1 2 1 2 2 3 1 3 3 4 1 4 4 5 1 5 5 6 1 6 6 7 1 7 7 8 1 8 8 9 1 9 9 10 1 10 10 11 1 11 11 12 1 12 12 13 1 13 13 14 1 14 14 15 1 15 15 16 1 16 16 17 1 17 17 18 1 18 18 19 1 19 19 20 1 @<TRIPOS>SUBSTRUCTURE 1 DA 1 RESIDUE 4 A DA 1 ROOT 2 DA 2 RESIDUE 4 A DA 2 3 DA 3 RESIDUE 4 A DA 2 4 DA 4 RESIDUE 4 A DA 2 5 DA 5 RESIDUE 4 A DA 2 6 DA 6 RESIDUE 4 A DA 2 7 DA 7 RESIDUE 4 A DA 2 8 DA 8 RESIDUE 4 A DA 2 9 DA 9 RESIDUE 4 A DA 2 10 DA 10 RESIDUE 4 A DA 2 11 DA 11 RESIDUE 4 A DA 2 12 DA 12 RESIDUE 4 A DA 2 13 DA 13 RESIDUE 4 A DA 2 14 DA 14 RESIDUE 4 A DA 2 15 DA 15 RESIDUE 4 A DA 2 16 DA 16 RESIDUE 4 A DA 2 17 DA 17 RESIDUE 4 A DA 2 18 DA 18 RESIDUE 4 A DA 2 19 DA 19 RESIDUE 4 A DA 2 20 DA 20 RESIDUE 4 A DA 1 Best Wishes! Jiying Jia