diff test-data/ligand.prmtop @ 0:79c856227ff1 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"
author chemteam
date Tue, 30 Nov 2021 10:00:44 +0000
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ligand.prmtop	Tue Nov 30 10:00:44 2021 +0000
@@ -0,0 +1,454 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 10/09/09  16:30:00                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+                                                                                
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
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+     329       1      38      53      91      18      30      19      14       0
+       0       0       0       0       0       0       0       0      61       0
+       0
+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
+O11 H7  C11 C12 C13 H9  H8  C10 H6  C9  H5  C8  C7  S6  C5  C4  H4  C3  O3  H3  
+C2  H2  C1  H1  C14 C15 C16 O16 C17 C22 C21 H12 H13 C18 H10 C19 H11 C20 O23 C24 
+H14 H15 C25 H16 H17 N26 C27 H18 H19 C28 H20 H21 C29 H22 H23 C30 H24 H25 C31 H26 
+H27 
+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
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+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
+  1.60000000E+01  1.00800000E+00  1.20100000E+01  1.20100000E+01  1.20100000E+01
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+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
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+       4       3       3       5       3       3       4       3       1       2
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+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
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+       2       6       9       8      10       9       4       7       4       1
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+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
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+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+RAL 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
+       1
+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG BOND_EQUIL_VALUE                                                          
+%FORMAT(5E16.8)                                                                 
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+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
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+%FLAG ANGLE_EQUIL_VALUE                                                         
+%FORMAT(5E16.8)                                                                 
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+%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
+%FORMAT(5E16.8)                                                                 
+  1.55555556E-01  1.50000000E-01  1.60000000E-01  4.80000000E-01  3.00000000E-01
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+  4.00000000E+00  4.00000000E-01  1.10000000E+00  1.05000000E+01
+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
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+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
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+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
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+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
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+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
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+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
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+%FLAG ANGLES_INC_HYDROGEN                                                       
+%FORMAT(10I8)                                                                   
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+%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
+%FORMAT(10I8)                                                                   
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+%FLAG DIHEDRALS_INC_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
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+      15      12       9      18      11      15      12      33      27      11
+      15      12      33      36      11      12      33      27      30      11
+       9       6      21      24      11       6       9      12      15      11
+       6      21      27      30      11       3       0       6       9      12
+       3       0       6      21      12       0       6       9      18      11
+       0       6      21      24      11      99     111    -105    -108      18
+      84     105     -99    -102      18      87     111     -90     -93      18
+      84      90     -87     -96      18      60      72     -66     -69      18
+      51      66     -60     -63      18      42      51     -45     -48      18
+      21      33     -27     -30      18       6      27     -21     -24      18
+       9      33     -12     -15      18       6      12      -9     -18      18
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
+%FORMAT(10I8)                                                                   
+     147     138     135     174       4     147     138    -135     174       5
+     147     156    -165     174       6     147     156    -165     174       7
+     147     156    -165     174       8     138     135     174     165       4
+     138     135    -174     165       5     138     147    -156     165       6
+     138     147    -156     165       7     138     147    -156     165       8
+     135     138     147     156       1     135     174    -165     156       1
+     126     135     138     147       4     126     135    -138     147       5
+     126     135     174     165       4     126     135    -174     165       5
+     117     126     135     138       4     117     126    -135     138       5
+     117     126     135     174       4     117     126    -135     174       5
+     114     117     126     135       1     111     114     117     126      10
+     105     111     114     117      12      99     105     111     114      11
+      90      87      84      99      11      90     111    -105      99      11
+      90     111     114     117      12      87      84      99     105      11
+      87      90    -111     105      11      87      90     111     114      11
+      84      87      90     111      11      84      99    -105     111      11
+      81      78      84      87      11      81      78      84      99      11
+      78      84      87      90      11      78      84      99     105      11
+      75      78      84      87      11      75      78      84      99      11
+      72      75      78      81      13      72      75      78      84      13
+      66      72      75      78      14      60      66      72      75      11
+      54      51      60      66      11      51      45      42      72      11
+      51      60     -66      72      11      45      42      72      66      11
+      45      42      72      75      11      45      51     -60      66      11
+      42      39     -36      75      15      42      45      51      54      11
+      42      45      51      60      11      42      72     -66      60      11
+      42      72      75      78      14      39      36     -75      72      16
+      39      36      75      78      16      39      42      45      51      11
+      39      42      72      66      11      39      42     -72      75      11
+      36      39      42      45      17      36      39     -42      72      17
+      36      75      72      66      14      36      75     -72      42      14
+      36      75      78      81      13      36      75      78      84      13
+      33      36      39      42      15      33      36      75      72      16
+      33      36      75      78      16      27      33      36      39      14
+      27      33      36      75      14      21      27      33      36      11
+      12       9       6      21      11      12      33     -27      21      11
+      12      33      36      39      14      12      33      36      75      14
+       9       6      21      27      11       9      12     -33      27      11
+       9      12      33      36      11       6       9      12      33      11
+       6      21     -27      33      11       0       6       9      12      11
+       0       6      21      27      11      90     105    -111    -114      18
+      78      87     -84     -99      18      84      75     -78     -81      19
+      78      72     -75     -36      18      42      66     -72     -75      18
+      45      60     -51     -54      18      45      72     -42     -39      18
+      33      75     -36     -39      18      12      27     -33     -36      18
+       0       6     -21      -9      18
+%FLAG EXCLUDED_ATOMS_LIST                                                       
+%FORMAT(10I8)                                                                   
+       2       3       4       5       7       8       9      10       3       4
+       8       4       5       6       7       8       9      10      11      12
+       5       6       7       8       9      10      12      13       6       7
+       8      10      11      12      13      14      26       7      10      12
+      13       8      12       9      10      11      12      13      10      11
+      12      11      12      13      14      26      12      13      13      14
+      15      25      26      27      14      15      16      23      25      26
+      27      28      29      15      16      17      18      23      25      26
+      27      16      17      18      19      21      23      24      25      26
+      27      17      18      19      20      21      22      23      25      26
+      18      19      21      25      19      20      21      22      23      24
+      25      20      21      22      23      21      22      23      24      25
+      26      23      24      25      24      25      26      27      25      26
+      26      27      28      29      27      28      29      30      34      28
+      29      30      31      33      34      35      36      29      30      34
+      30      31      32      33      34      35      36      37      38      31
+      32      33      34      35      36      38      39      32      33      34
+      36      37      38      39      40      33      36      38      39      34
+      38      35      36      37      38      39      36      37      38      37
+      38      39      40      38      39      39      40      41      42      43
+      40      41      42      43      44      45      46      41      42      43
+      44      45      46      47      59      42      43      44      45      46
+      43      44      45      46      44      45      46      47      48      49
+      50      56      59      60      61      45      46      47      59      46
+      47      59      47      48      49      50      51      52      53      56
+      57      58      59      60      61      48      49      50      51      52
+      53      54      55      56      59      60      61      49      50      51
+      52      53      59      50      51      52      53      59      51      52
+      53      54      55      56      57      58      59      52      53      54
+      55      56      53      54      55      56      54      55      56      57
+      58      59      60      61      55      56      57      58      59      56
+      57      58      59      57      58      59      60      61      58      59
+      60      61      59      60      61      60      61      61       0
+%FLAG HBOND_ACOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBOND_BCOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBCUT                                                                     
+%FORMAT(5E16.8)                                                                 
+
+%FLAG AMBER_ATOM_TYPE                                                           
+%FORMAT(20a4)                                                                   
+oh  ho  ca  ca  ca  ha  ha  ca  ha  ca  ha  ca  cc  ss  ca  ca  ha  ca  oh  ho  
+ca  ha  ca  ha  ca  cd  c   o   ca  ca  ca  ha  ha  ca  ha  ca  ha  ca  os  c3  
+h1  h1  c3  h1  h1  n3  c3  h1  h1  c3  hc  hc  c3  hc  hc  c3  hc  hc  c3  h1  
+h1  
+%FLAG TREE_CHAIN_CLASSIFICATION                                                 
+%FORMAT(20a4)                                                                   
+M   E   M   M   M   E   E   B   E   S   E   M   M   S   B   S   E   S   S   E   
+B   E   B   E   S   M   M   E   M   B   S   E   E   M   E   M   E   M   M   M   
+E   E   M   E   E   M   3   E   E   3   E   E   3   E   E   B   E   E   M   E   
+E   
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0
+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+H(N)-modified Bondi radii (mbondi2)                                             
+%FLAG RADII                                                                     
+%FORMAT(5E16.8)                                                                 
+  1.50000000E+00  1.20000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00
+  1.20000000E+00  1.20000000E+00  1.70000000E+00  1.20000000E+00  1.70000000E+00
+  1.20000000E+00  1.70000000E+00  1.70000000E+00  1.80000000E+00  1.70000000E+00
+  1.70000000E+00  1.20000000E+00  1.70000000E+00  1.50000000E+00  1.20000000E+00
+  1.70000000E+00  1.20000000E+00  1.70000000E+00  1.20000000E+00  1.70000000E+00
+  1.70000000E+00  1.70000000E+00  1.50000000E+00  1.70000000E+00  1.70000000E+00
+  1.70000000E+00  1.20000000E+00  1.20000000E+00  1.70000000E+00  1.20000000E+00
+  1.70000000E+00  1.20000000E+00  1.70000000E+00  1.50000000E+00  1.70000000E+00
+  1.20000000E+00  1.20000000E+00  1.70000000E+00  1.20000000E+00  1.20000000E+00
+  1.55000000E+00  1.70000000E+00  1.20000000E+00  1.20000000E+00  1.70000000E+00
+  1.20000000E+00  1.20000000E+00  1.70000000E+00  1.20000000E+00  1.20000000E+00
+  1.70000000E+00  1.20000000E+00  1.20000000E+00  1.70000000E+00  1.20000000E+00
+  1.20000000E+00
+%FLAG SCREEN                                                                    
+%FORMAT(5E16.8)                                                                 
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  7.20000000E-01  7.20000000E-01  9.60000000E-01  7.20000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01
+  7.20000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01  7.20000000E-01
+  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  7.90000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01
+  8.50000000E-01