v4-1h04-0

command from alatis:
	antechamber -i updated_alatis_output_compound_3D_h_sdf.pdb -fi pdb -o  updated_alatis_output_compound_3D_h_sdf.mol2 -fo mol2 -c bcc -s 2
antechamber:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
Warning: Small distance for BOND	1	C01	C03	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	2	C01	H011	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	3	C01	H012	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	4	C01	H013	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	5	C02	C07	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	6	C02	H021	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	7	C02	H022	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	8	C03	C07	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	9	C03	H031	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	10	C03	H032	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	11	C04	C05	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	12	C04	C08	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	13	C04	H04	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	14	C05	C09	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	15	C05	H05	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	16	C06	C10	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	17	C06	O19	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	18	C06	H061	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	19	C06	H062	0	     0.00  [0.75 - 1.28]
Warning: Small distance for BOND	20	C07	C13	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	21	C08	C11	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	22	C08	C13	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	23	C09	C12	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	24	C09	O19	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	25	C10	O16	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	26	C10	O17	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	27	C11	C12	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	28	C11	Cl14	0	     0.00  [1.15 - 1.92]
Warning: Small distance for BOND	29	C12	Cl15	0	     0.00  [1.15 - 1.92]
Warning: Small distance for BOND	30	C13	O18	0	     0.00  [1.10 - 1.84]
Warning: Small distance for BOND	31	O17	H17	0	     0.00  [0.75 - 1.28]
      for those not bonded   
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 2, Name: C02).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 4, Name: C04).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 5, Name: C05).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 6, Name: C06).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 7, Name: C07).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 8, Name: C08).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 9, Name: C09).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 1, Name: C01) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 3, Name: C03).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 4, Name: C04).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 5, Name: C05).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 6, Name: C06).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 8, Name: C08).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 9, Name: C09).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 2, Name: C02) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 4, Name: C04).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 5, Name: C05).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 6, Name: C06).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 8, Name: C08).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 9, Name: C09).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 3, Name: C03) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 6, Name: C06).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 7, Name: C07).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 9, Name: C09).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 4, Name: C04) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 6, Name: C06).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 7, Name: C07).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 8, Name: C08).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 5, Name: C05) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 7, Name: C07).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 8, Name: C08).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 9, Name: C09).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 6, Name: C06) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 8, Name: C08).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 9, Name: C09).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 7, Name: C07) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 9, Name: C09).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 8, Name: C08) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 10, Name: C10).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 9, Name: C09) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 11, Name: C11).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 12, Name: C12).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 10, Name: C10) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 11, Name: C11) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 13, Name: C13).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 12, Name: C12) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 14, Name: Cl14).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 13, Name: C13) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 15, Name: Cl15).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 14, Name: Cl14) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 16, Name: O16).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 15, Name: Cl15) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 17, Name: O17).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 16, Name: O16) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 18, Name: O18).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 17, Name: O17) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 19, Name: O19).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 18, Name: O18) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 20, Name: H011).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 19, Name: O19) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 21, Name: H012).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 20, Name: H011) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 22, Name: H013).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 21, Name: H012) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 23, Name: H021).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 22, Name: H013) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 24, Name: H022).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 23, Name: H021) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: H022) and (ID: 25, Name: H031).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: H022) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: H022) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: H022) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: H022) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: H022) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 24, Name: H022) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 25, Name: H031) and (ID: 26, Name: H032).
Warning: Close ( 0.00) nonbonded atoms (ID: 25, Name: H031) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 25, Name: H031) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 25, Name: H031) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 25, Name: H031) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 25, Name: H031) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 26, Name: H032) and (ID: 27, Name: H04).
Warning: Close ( 0.00) nonbonded atoms (ID: 26, Name: H032) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 26, Name: H032) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 26, Name: H032) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 26, Name: H032) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 27, Name: H04) and (ID: 28, Name: H05).
Warning: Close ( 0.00) nonbonded atoms (ID: 27, Name: H04) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 27, Name: H04) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 27, Name: H04) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 28, Name: H05) and (ID: 29, Name: H061).
Warning: Close ( 0.00) nonbonded atoms (ID: 28, Name: H05) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 28, Name: H05) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 29, Name: H061) and (ID: 30, Name: H062).
Warning: Close ( 0.00) nonbonded atoms (ID: 29, Name: H061) and (ID: 31, Name: H17).
Warning: Close ( 0.00) nonbonded atoms (ID: 30, Name: H062) and (ID: 31, Name: H17).
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /usr/software/amber16/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 156; net charge: 0

Running: /usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DIVIDE_BY_ZERO IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Unable to find sqm charges in file (sqm.out).
Verify the filename and the file contents.

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_3D_h_sdf.mol2) with mode (r).
No such file or directory

<***************>
tleap:
0
-I: Adding /usr/software/amber16/dat/leap/prep to search path.
-I: Adding /usr/software/amber16/dat/leap/lib to search path.
-I: Adding /usr/software/amber16/dat/leap/parm to search path.
-I: Adding /usr/software/amber16/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/software/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/software/amber16/dat/leap/lib/amino12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminoct12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminont12.lib
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Could not open file updated_alatis_output_compound_3D_h_sdf.mol2: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
Could not open file updated_alatis_output_compound_3D_h_sdf.frcmod: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
saveOff: Argument #1 is type String must be of type: [unit parameter_set list]
usage:  saveOff <object> <filename>
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
	Quit

<***************>
charmm:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot open the input file (updated_alatis_output_compound_3D_h_sdf.mol2).
No such file or directory

<***************>
