Usage of pdb2adf
The program works interactively. Given below in bold are the parts that the user has to type. In cases where the user agrees with the suggestion given by the program, the user can press the Enter key indicated with Enter.
P D B 2 A D F - program
version 2005.01
Written by: Marcel Swart, 2005
This program uses AMBER parameter files
see: http://amber.scripps.edu
Do you want a logfile to be written (Y/n) ?
Enter
Please give name of PDB-file
1DYZ.pdb
read fragments
Data Processed:
Nat: 2519
Nmol: 196
NChains: 1
Please wait, making connection tables
Now finding nearby atoms
Assigning chain ID to all residues
Completing residues for which only option is available
Found the following terminal amino acid residues : (C-term) 129 (N-term) 1
Do you want to use these as terminal residues (Y/n) ?
Enter
Refinding nearby atoms (including atoms added in residue completion) Multiple AMBER options for HIS : 0 Decide every time differently 1 HID Histidine Delta Hydrogen 2 HIE Histidine Epsilon Hydrogen 3 HIP Histidine E & D Hydrogens Suggested option: 0
Enter
Using 0: Decide every time differently Multiple AMBER options for GLU : 0 Decide every time differently 1 GLU Glutamic acid (COO-) 2 GLH Neutral Glutamic acid (COOH) Suggested option: 1
Enter
Using 17 GLU Glutamic acid (COO-) Multiple AMBER options for ASP : 0 Decide every time differently 1 ASP Aspartic acid (COO-) 2 ASH Neutral Aspartatic acid (COOH) Suggested option: 1
Enter
Using 18 ASP Aspartic acid (COO-) Multiple AMBER options for LYS : 0 Decide every time differently 1 LYS Charged Lysine (NH3+) 2 LYN Neutral Lysine (NH2) Suggested option: 1
Enter
Using 19 LYS Charged Lysine (NH3+) Multiple AMBER options for CYS : 0 Decide every time differently 1 CYS Cysteine (SH) 2 CYM Deprotonated Cysteine (S-) 3 CYX Cystine (S-S bridge) Suggested option: 0
Enter
Using 0: Decide every time differently
- - - - - - - - - - - - - - - - - - - - - - - - - - -
Making Choices for Chain 0
- - - - - - - - - - - - - - - - - - - - - - - - - - -
Multiple AMBER options for CYS 3 ( 3) :
1 CYS Cysteine (SH)
2 CYM Deprotonated Cysteine (S-)
3 CYX Cystine (S-S bridge)
Connections and Nearest Atoms for SG CYS 3 SG ( P2A # 41 PDB# 20 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.82 38 19 CB CYS 3 CB 1 3.79 2382 980 O HOH 151 O
2 2.02 461 193 SG CYS 26 SG 2 3.80 22 0 HC GLN 2
3 4.04 2391 983 O HOH 154 O
4 4.15 509 206 O GLN 28 O
5 4.18 522 0 HA PHE 29
Suggestion: 3
Enter
Multiple AMBER options for CYS 26 ( 26) :
1 CYS Cysteine (SH)
2 CYM Deprotonated Cysteine (S-)
3 CYX Cystine (S-S bridge)
Connections and Nearest Atoms for SG CYS 26 SG ( P2A # 461 PDB# 193 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.82 458 192 CB CYS 26 CB 1 3.41 522 0 HA PHE 29
2 2.02 41 20 SG CYS 3 SG 2 3.43 411 168 O ASP 23 O
3 3.60 2322 960 O HOH 131 O
4 3.91 403 169 CB ASP 23 CB
5 4.15 387 0 HC VAL 22
Suggestion: 3
Enter
Multiple AMBER options for HIS 32 ( 32) :
1 HID Histidine Delta Hydrogen
2 HIE Histidine Epsilon Hydrogen
3 HIP Histidine E & D Hydrogens
Connections and Nearest Atoms for ND HIS 32 ND1 ( P2A # 581 PDB# 244 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.39 580 243 CG HIS 32 CG 1 3.41 545 0 HC THR 30
2 1.33 583 246 CE HIS 32 CE1 2 3.43 76 33 O ALA 5 O
3 3.58 90 40 OH THR 6 OG1
4 3.99 91 0 HO THR 6
5 4.17 68 0 H ALA 5
Connections and Nearest Atoms for NE HIS 32 NE2 ( P2A # 585 PDB# 247 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.31 583 246 CE HIS 32 CE1 1 2.86 544 0 HC THR 30
2 1.37 587 245 CD HIS 32 CD2 2 3.00 545 0 HC THR 30
3 3.14 1677 0 HO SER 94
4 3.42 542 229 CT THR 30 CG2
5 3.65 1676 688 OH SER 94 OG
Suggestion: 1
3
Multiple AMBER options for HIS 35 ( 35) :
1 HID Histidine Delta Hydrogen
2 HIE Histidine Epsilon Hydrogen
3 HIP Histidine E & D Hydrogens
Connections and Nearest Atoms for ND HIS 35 ND1 ( P2A # 649 PDB# 271 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.38 648 270 CG HIS 35 CG 1 2.46 682 0 H GLY 37
2 1.32 651 273 CE HIS 35 CE1 2 2.69 1604 0 H1 GLY 89
3 3.31 681 282 N GLY 37 N
4 3.56 1602 653 CT GLY 89 CA
5 3.67 152 0 H1 ASN 10
Connections and Nearest Atoms for NE HIS 35 NE2 ( P2A # 653 PDB# 274 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.33 651 273 CE HIS 35 CE1 1 HB 2.91 822 332 O MET 44 O
2 1.37 655 272 CD HIS 35 CD2 2 3.24 814 0 H1 MET 44
3 3.24 850 348 CD HIS 46 CD2
4 3.34 1593 0 H1 GLY 88
5 3.75 848 350 NE HIS 46 NE2
Suggestion: 2
3
Multiple AMBER options for HIS 46 ( 46) :
1 HID Histidine Delta Hydrogen
2 HIE Histidine Epsilon Hydrogen
3 HIP Histidine E & D Hydrogens
Connections and Nearest Atoms for ND HIS 46 ND1 ( P2A # 844 PDB# 347 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.37 843 346 CG HIS 46 CG 1 2.62 2166 0 H1 MET 121
2 1.33 846 349 CE HIS 46 CE1 2 3.23 2080 863 ND HIS 117 ND1
3 2.04 2318 959 CU CU 130 CU 3 HB 3.33 2163 900 S MET 121 SD
4 3.40 2164 901 CT MET 121 CE
5 3.57 2082 865 CE HIS 117 CE1
Connections and Nearest Atoms for NE HIS 46 NE2 ( P2A # 848 PDB# 350 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.32 846 349 CE HIS 46 CE1 1 HB 2.70 162 67 O ASN 10 O
2 1.37 850 348 CD HIS 46 CD2 2 2.83 814 0 H1 MET 44
3 3.23 2166 0 H1 MET 121
4 3.52 822 332 O MET 44 O
5 3.74 813 334 CT MET 44 CG
Suggestion: 2
Enter
Multiple AMBER options for HIS 83 ( 83) :
1 HID Histidine Delta Hydrogen
2 HIE Histidine Epsilon Hydrogen
3 HIP Histidine E & D Hydrogens
Connections and Nearest Atoms for ND HIS 83 ND1 ( P2A # 1494 PDB# 613 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.39 1493 612 CG HIS 83 CG 1 2.67 1317 0 HC VAL 73
2 1.33 1496 615 CE HIS 83 CE1 2 3.63 1315 542 CT VAL 73 CG2
3 3.74 1310 0 HC VAL 73
4 3.82 1316 0 HC VAL 73
5 3.86 1313 0 HC VAL 73
Connections and Nearest Atoms for NE HIS 83 NE2 ( P2A # 1498 PDB# 616 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.32 1496 615 CE HIS 83 CE1 1 3.09 1313 0 HC VAL 73
2 1.38 1500 614 CD HIS 83 CD2 2 3.44 1317 0 HC VAL 73
3 3.88 2385 981 O HOH 152 O
4 3.93 1311 541 CT VAL 73 CG1
5 4.03 1309 540 CT VAL 73 CB
Suggestion: 2
3
Multiple AMBER options for CYS 112 ( 112) :
1 CYS Cysteine (SH)
2 CYM Deprotonated Cysteine (S-)
3 CYX Cystine (S-S bridge)
Connections and Nearest Atoms for SG CYS 112 SG ( P2A # 2001 PDB# 828 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.82 1998 827 CB CYS 112 CB 1 2.53 858 0 H ASN 47
2 2.14 2318 959 CU CU 130 CU 2 2.65 2023 0 H PHE 114
3 3.00 2028 0 HC PHE 114
4 3.29 868 0 H ASN 47
5 3.39 2027 0 HC PHE 114
Suggestion: 2
Enter
Multiple AMBER options for HIS 117 ( 117) :
1 HID Histidine Delta Hydrogen
2 HIE Histidine Epsilon Hydrogen
3 HIP Histidine E & D Hydrogens
Connections and Nearest Atoms for ND HIS 117 ND1 ( P2A # 2080 PDB# 863 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.37 2079 862 CG HIS 117 CG 1 2.82 2028 0 HC PHE 114
2 1.34 2082 865 CE HIS 117 CE1 2 3.23 844 347 ND HIS 46 ND1
3 1.99 2318 959 CU CU 130 CU 3 3.26 2031 0 HA PHE 114
4 3.27 832 340 O GLY 45 O
5 3.43 846 349 CE HIS 46 CE1
Connections and Nearest Atoms for NE HIS 117 NE2 ( P2A # 2084 PDB# 866 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.31 2082 865 CE HIS 117 CE1 1 2.57 209 0 H1 MET 13
2 1.37 2086 864 CD HIS 117 CD2 2 2.65 2031 0 HA PHE 114
3 HB 2.74 2406 988 O HOH 159 O
4 3.34 2030 841 CA PHE 114 CD1
5 3.41 204 0 H1 MET 13
Suggestion: 2
Enter
- - - - - - - - - - - - - - - - - - - - - - - - - - -
Making Choices for Chain 1
- - - - - - - - - - - - - - - - - - - - - - - - - - -
Completing residues with multiple options available, and solvent molecules
Checking positions of newly added atoms
Making choice for which molecules should be QM, which MM
Residues belonging to chain 0
Option Molecule Option Molecule Option Molecule Option Molecule Option Molecule
1: ALA 1 28: GLN 28 55: ASP 55 82: ALA 82 109: ALA 109
2: GLN 2 29: PHE 29 56: LYS 56 83: HIS 83 110: TYR 110
3: CYS 3 30: THR 30 57: GLN 57 84: THR 84 111: PHE 111
4: GLU 4 31: MET 31 58: ALA 58 85: LYS 85 112: CYS 112
5: ALA 5 32: HIS 32 59: VAL 59 86: VAL 86 113: SER 113
6: THR 6 33: LEU 33 60: ALA 60 87: ILE 87 114: PHE 114
7: VAL 7 34: LYS 34 61: THR 61 88: GLY 88 115: PRO 115
8: GLU 8 35: HIS 35 62: ASP 62 89: GLY 89 116: GLY 116
9: SER 9 36: VAL 36 63: GLY 63 90: GLY 90 117: HIS 117
10: ASN 10 37: GLY 37 64: MET 64 91: GLU 91 118: TRP 118
11: ASP 11 38: LYS 38 65: GLY 65 92: SER 92 119: ALA 119
12: ALA 12 39: MET 39 66: ALA 66 93: ASP 93 120: MET 120
13: MET 13 40: ALA 40 67: GLY 67 94: SER 94 121: MET 121
14: GLN 14 41: LYS 41 68: LEU 68 95: VAL 95 122: LYS 122
15: TYR 15 42: VAL 42 69: ALA 69 96: THR 96 123: GLY 123
16: ASN 16 43: ALA 43 70: GLN 70 97: PHE 97 124: THR 124
17: VAL 17 44: MET 44 71: ASP 71 98: ASP 98 125: LEU 125
18: LYS 18 45: GLY 45 72: TYR 72 99: VAL 99 126: LYS 126
19: GLU 19 46: HIS 46 73: VAL 73 100: SER 100 127: LEU 127
20: ILE 20 47: ASN 47 74: LYS 74 101: LYS 101 128: GLY 128
21: VAL 21 48: LEU 48 75: ALA 75 102: ILE 102 129: SER 129
22: VAL 22 49: VAL 49 76: GLY 76 103: ALA 103 130: CU 130
23: ASP 23 50: LEU 50 77: ASP 77 104: ALA 104
24: LYS 24 51: THR 51 78: THR 78 105: GLY 105
25: SER 25 52: LYS 52 79: ARG 79 106: GLU 106
26: CYS 26 53: ASP 53 80: VAL 80 107: ASN 107
27: LYS 27 54: ALA 54 81: ILE 81 108: TYR 108
Give option number of molecules to be put in QM region (or 'c' to continue):
Note: by specifying a negative number a molecule is removed from the QM region
45 46 112 117 121 130
Putting GLY 45 in QM region Putting HIS 46 in QM region Putting CYS 112 in QM region Putting HIS 117 in QM region Putting MET 121 in QM region Putting CU 130 in QM region Give option number of molecules to be put in QM region (or 'c' to continue): Note: by specifying a negative number a molecule is removed from the QM region
c
Make a choice for the QM/MM treatment of GLY 45
0: Put completely in QM region
1: Cut off at C-alpha (put NH in QM region, CO in MM region)
2: Cut off at C-alpha (put NH in MM region, CO in QM region)
3: Cut off at C-alpha (put NH and CO in MM region)
4: Cut off at C-alpha (put NH and CO in QM region, sidechain in MM region)
5: Put only part of sidechain in QM region
Suggestion: 2
Give choice:
Enter
Make a choice for the QM/MM treatment of HIS 46
0: Put completely in QM region
1: Cut off at C-alpha (put NH in QM region, CO in MM region)
2: Cut off at C-alpha (put NH in MM region, CO in QM region)
3: Cut off at C-alpha (put NH and CO in MM region)
4: Cut off at C-alpha (put NH and CO in QM region, sidechain in MM region)
5: Put only part of sidechain in QM region
Suggestion: 1
Give choice:
Enter
Make a choice for the QM/MM treatment of CYS 112 0: Put completely in QM region 1: Cut off at C-alpha (put NH in QM region, CO in MM region) 2: Cut off at C-alpha (put NH in MM region, CO in QM region) 3: Cut off at C-alpha (put NH and CO in MM region) 4: Cut off at C-alpha (put NH and CO in QM region, sidechain in MM region) 5: Put only part of sidechain in QM region Suggestion: 3 Give choice:
Enter
Make a choice for the QM/MM treatment of HIS 117 0: Put completely in QM region 1: Cut off at C-alpha (put NH in QM region, CO in MM region) 2: Cut off at C-alpha (put NH in MM region, CO in QM region) 3: Cut off at C-alpha (put NH and CO in MM region) 4: Cut off at C-alpha (put NH and CO in QM region, sidechain in MM region) 5: Put only part of sidechain in QM region Suggestion: 3 Give choice:
Enter
Make a choice for the QM/MM treatment of MET 121 0: Put completely in QM region 1: Cut off at C-alpha (put NH in QM region, CO in MM region) 2: Cut off at C-alpha (put NH in MM region, CO in QM region) 3: Cut off at C-alpha (put NH and CO in MM region) 4: Cut off at C-alpha (put NH and CO in QM region, sidechain in MM region) 5: Put only part of sidechain in QM region Suggestion: 3 Give choice:
Enter
Make a choice for the QM/MM treatment of CU 130 0: Put completely in QM region 1: Put only part of molecule in QM region Suggestion: 0 Give choice:
Enter
Total formal charge on molecule CU 130 2.0000
Solvent molecules (SOL/HOH) belonging to this chain:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66
Give the number of the molecule to be put in QM region (or 'c' to continue):
c
Residues belonging to chain 1 Do you want to add solvent to your system (Y/n) ?
Enter
Solvent (box) available: 1: HOH HOH Water molecule 2: MOH MOH Methanol molecule 3: CHL CHL Chloroform molecule
1
Reading contents of solvent box p2abox.HOH Box Shape options: 1 Spherical box 2 Cubic box Make a choice:
1
Writing inputfile for chain 0 Using total charge 1.0 and total spin 1.0 Maximum atomic distance (Angs) from center 25.62 Give boxsize (def.: 28.62 Angs)
30.0
Using BOXSIZE value of 30.0000 Adding atoms for box 1 Added (Box): 0 (Total): 0 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 2 Added (Box): 9 (Total): 9 Excl. (1): 639 Excl. (2): 0 Adding atoms for box 3 Added (Box): 3 (Total): 12 Excl. (1): 645 Excl. (2): 0 Adding atoms for box 4 Added (Box): 0 (Total): 12 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 5 Added (Box): 6 (Total): 18 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 6 Added (Box): 228 (Total): 246 Excl. (1): 420 Excl. (2): 0 Adding atoms for box 7 Added (Box): 219 (Total): 465 Excl. (1): 429 Excl. (2): 0 Adding atoms for box 8 Added (Box): 9 (Total): 474 Excl. (1): 639 Excl. (2): 0 Adding atoms for box 9 Added (Box): 0 (Total): 474 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 10 Added (Box): 225 (Total): 699 Excl. (1): 423 Excl. (2): 0 Adding atoms for box 11 Added (Box): 216 (Total): 915 Excl. (1): 432 Excl. (2): 0 Adding atoms for box 12 Added (Box): 6 (Total): 921 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 13 Added (Box): 0 (Total): 921 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 14 Added (Box): 6 (Total): 927 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 15 Added (Box): 12 (Total): 939 Excl. (1): 636 Excl. (2): 0 Adding atoms for box 16 Added (Box): 0 (Total): 939 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 17 Added (Box): 12 (Total): 951 Excl. (1): 636 Excl. (2): 0 Adding atoms for box 18 Added (Box): 210 (Total): 1161 Excl. (1): 438 Excl. (2): 0 Adding atoms for box 19 Added (Box): 219 (Total): 1380 Excl. (1): 429 Excl. (2): 0 Adding atoms for box 20 Added (Box): 3 (Total): 1383 Excl. (1): 645 Excl. (2): 0 Adding atoms for box 21 Added (Box): 216 (Total): 1599 Excl. (1): 417 Excl. (2): 15 Adding atoms for box 22 Added (Box): 381 (Total): 1980 Excl. (1): 3 Excl. (2): 264 Adding atoms for box 23 Added (Box): 261 (Total): 2241 Excl. (1): 3 Excl. (2): 384 Adding atoms for box 24 Added (Box): 183 (Total): 2424 Excl. (1): 423 Excl. (2): 42 Adding atoms for box 25 Added (Box): 189 (Total): 2613 Excl. (1): 426 Excl. (2): 33 Adding atoms for box 26 Added (Box): 186 (Total): 2799 Excl. (1): 3 Excl. (2): 459 Adding atoms for box 27 Added (Box): 351 (Total): 3150 Excl. (1): 3 Excl. (2): 294 Adding atoms for box 28 Added (Box): 222 (Total): 3372 Excl. (1): 420 Excl. (2): 6 Adding atoms for box 29 Added (Box): 9 (Total): 3381 Excl. (1): 639 Excl. (2): 0 Adding atoms for box 30 Added (Box): 162 (Total): 3543 Excl. (1): 429 Excl. (2): 57 Adding atoms for box 31 Added (Box): 219 (Total): 3762 Excl. (1): 426 Excl. (2): 3 Adding atoms for box 32 Added (Box): 6 (Total): 3768 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 33 Added (Box): 6 (Total): 3774 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 34 Added (Box): 219 (Total): 3993 Excl. (1): 426 Excl. (2): 3 Adding atoms for box 35 Added (Box): 216 (Total): 4209 Excl. (1): 432 Excl. (2): 0 Adding atoms for box 36 Added (Box): 6 (Total): 4215 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 37 Added (Box): 219 (Total): 4434 Excl. (1): 426 Excl. (2): 3 Adding atoms for box 38 Added (Box): 279 (Total): 4713 Excl. (1): 6 Excl. (2): 363 Adding atoms for box 39 Added (Box): 231 (Total): 4944 Excl. (1): 0 Excl. (2): 417 Adding atoms for box 40 Added (Box): 195 (Total): 5139 Excl. (1): 432 Excl. (2): 21 Adding atoms for box 41 Added (Box): 231 (Total): 5370 Excl. (1): 414 Excl. (2): 3 Adding atoms for box 42 Added (Box): 324 (Total): 5694 Excl. (1): 0 Excl. (2): 324 Adding atoms for box 43 Added (Box): 408 (Total): 6102 Excl. (1): 6 Excl. (2): 234 Adding atoms for box 44 Added (Box): 204 (Total): 6306 Excl. (1): 435 Excl. (2): 9 Adding atoms for box 45 Added (Box): 6 (Total): 6312 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 46 Added (Box): 177 (Total): 6489 Excl. (1): 435 Excl. (2): 36 Adding atoms for box 47 Added (Box): 219 (Total): 6708 Excl. (1): 429 Excl. (2): 0 Adding atoms for box 48 Added (Box): 6 (Total): 6714 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 49 Added (Box): 0 (Total): 6714 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 50 Added (Box): 3 (Total): 6717 Excl. (1): 645 Excl. (2): 0 Adding atoms for box 51 Added (Box): 6 (Total): 6723 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 52 Added (Box): 0 (Total): 6723 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 53 Added (Box): 9 (Total): 6732 Excl. (1): 639 Excl. (2): 0 Adding atoms for box 54 Added (Box): 222 (Total): 6954 Excl. (1): 426 Excl. (2): 0 Adding atoms for box 55 Added (Box): 213 (Total): 7167 Excl. (1): 426 Excl. (2): 9 Adding atoms for box 56 Added (Box): 6 (Total): 7173 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 57 Added (Box): 3 (Total): 7176 Excl. (1): 645 Excl. (2): 0 Adding atoms for box 58 Added (Box): 219 (Total): 7395 Excl. (1): 423 Excl. (2): 6 Adding atoms for box 59 Added (Box): 219 (Total): 7614 Excl. (1): 429 Excl. (2): 0 Adding atoms for box 60 Added (Box): 6 (Total): 7620 Excl. (1): 642 Excl. (2): 0 Adding atoms for box 61 Added (Box): 0 (Total): 7620 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 62 Added (Box): 12 (Total): 7632 Excl. (1): 636 Excl. (2): 0 Adding atoms for box 63 Added (Box): 3 (Total): 7635 Excl. (1): 645 Excl. (2): 0 Adding atoms for box 64 Added (Box): 0 (Total): 7635 Excl. (1): 648 Excl. (2): 0 Writing inputfile for chain 1 There are no atoms in this chain, ignoring it Inputfile(s) written, everything processed, work has been done. Thank you for using the PDB2ADF program. ================================ Normal ending of PDB2ADF program ================================
