[gmx-users] after using ACPYPE , GROMACS OPLS itp file generated an atom type like opls_x with mass 0.000

aditya sarma adityasrm027 at gmail.com
Fri Nov 8 05:42:33 CET 2013


Hi,
i was trying to generate topology for p-phenylene vinylene polymer for OPLS
forcefield using acpype . The itp file i got has the atomtype opls_x with
mass 0.00. Is there any way to rectify this?

After reading through how acpype works i found out this was one of the
possible errors but there was no solution to it.

This is a part of the itp file generated:

 [ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
bond_type
     1 opls_145     1   LIG     C    1    -0.117500     12.01100 ; qtot
-0.118  CA
     2 opls_145     1   LIG    C1    2    -0.055800     12.01100 ; qtot
-0.173  CA
     3 opls_145     1   LIG    C2    3    -0.117500     12.01100 ; qtot
-0.291  CA
     4 opls_145     1   LIG    C3    4    -0.131000     12.01100 ; qtot
-0.422  CA
     5 opls_145     1   LIG    C4    5    -0.125000     12.01100 ; qtot
-0.547  CA
     6 opls_145     1   LIG    C5    6    -0.131000     12.01100 ; qtot
-0.678  CA
     7 opls_x     1   LIG    C6    7    -0.099200      0.00000 ; qtot
-0.777  x
     8 opls_x     1   LIG    C7    8    -0.105200      0.00000 ; qtot
-0.882  x
     9 opls_145     1   LIG    C8    9    -0.048800     12.01100 ; qtot
-0.931  CA
    10 opls_145     1   LIG    C9   10    -0.119500     12.01100 ; qtot
-1.051  CA
    11 opls_145     1   LIG   C10   11    -0.118500     12.01100 ; qtot
-1.169  CA
    12 opls_145     1   LIG   C11   12    -0.051800     12.01100 ; qtot
-1.221  CA
    13 opls_145     1   LIG   C12   13    -0.118500     12.01100 ; qtot
-1.339  CA
    14 opls_145     1   LIG   C13   14    -0.119500     12.01100 ; qtot
-1.459  CA
    15 opls_x     1   LIG   C14   15    -0.101200      0.00000 ; qtot
-1.560  x
    16 opls_x     1   LIG   C15   16    -0.103200      0.00000 ; qtot
-1.663  x
    17 opls_145     1   LIG   C16   17    -0.049800     12.01100 ; qtot
-1.713  CA
    18 opls_145     1   LIG   C17   18    -0.119500     12.01100 ; qtot
-1.833  CA
    19 opls_145     1   LIG   C18   19    -0.119000     12.01100 ; qtot
-1.952  CA
    20 opls_145     1   LIG   C19   20    -0.050800     12.01100 ; qtot
-2.002  CA
    21 opls_145     1   LIG   C20   21    -0.119000     12.01100 ; qtot
-2.121  CA
    22 opls_145     1   LIG   C21   22    -0.119500     12.01100 ; qtot
-2.241  CA
    23 opls_x     1   LIG   C22   23    -0.102200      0.00000 ; qtot
-2.343  x
    24 opls_x     1   LIG   C23   24    -0.102200      0.00000 ; qtot
-2.445  x
    25 opls_145     1   LIG   C24   25    -0.050800     12.01100 ; qtot
-2.496  CA
    26 opls_145     1   LIG   C25   26    -0.119000     12.01100 ; qtot
-2.615  CA
    27 opls_145     1   LIG   C26   27    -0.119000     12.01100 ; qtot
-2.734  CA
    28 opls_145     1   LIG   C27   28    -0.050800     12.01100 ; qtot
-2.785  CA
    29 opls_145     1   LIG   C28   29    -0.119000     12.01100 ; qtot
-2.904  CA
    30 opls_145     1   LIG   C29   30    -0.119000     12.01100 ; qtot
-3.023  CA
    31 opls_x     1   LIG   C30   31    -0.102200      0.00000 ; qtot
-3.125  x
    32 opls_x     1   LIG   C31   32    -0.102200      0.00000 ; qtot
-3.227  x
    33 opls_145     1   LIG   C32   33    -0.050800     12.01100 ; qtot
-3.278  CA
    34 opls_145     1   LIG   C33   34    -0.119000     12.01100 ; qtot
-3.397  CA
    35 opls_145     1   LIG   C34   35    -0.119000     12.01100 ; qtot
-3.516  CA
    36 opls_145     1   LIG   C35   36    -0.050800     12.01100 ; qtot
-3.567  CA
    37 opls_145     1   LIG   C36   37    -0.119000     12.01100 ; qtot
-3.686  CA
    38 opls_145     1   LIG   C37   38    -0.119000     12.01100 ; qtot
-3.805  CA
    39 opls_x     1   LIG   C38   39    -0.102200      0.00000 ; qtot
-3.907  x
    40 opls_x     1   LIG   C39   40    -0.102200      0.00000 ; qtot
-4.009  x
    41 opls_145     1   LIG   C40   41    -0.050800     12.01100 ; qtot
-4.060  CA
    42 opls_145     1   LIG   C41   42    -0.119000     12.01100 ; qtot
-4.179  CA
    43 opls_145     1   LIG   C42   43    -0.119500     12.01100 ; qtot
-4.299  CA
    44 opls_145     1   LIG   C43   44    -0.049800     12.01100 ; qtot
-4.348  CA
    45 opls_145     1   LIG   C44   45    -0.119500     12.01100 ; qtot
-4.468  CA
    46 opls_145     1   LIG   C45   46    -0.119000     12.01100 ; qtot
-4.587  CA
    47 opls_x     1   LIG   C46   47    -0.103200      0.00000 ; qtot
-4.690  x
    48 opls_x     1   LIG   C47   48    -0.101200      0.00000 ; qtot
-4.791  x



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