[gmx-users] atom type errer

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Dec 22 16:04:26 CET 2010


Dear All

I am using protein-drug binding.
when I am using grompp this error occuring:

Atomtype CR6 not found
and
Atomtype CR5 not found.
by what can I replace these atom types?
this is my drug.itp file:
[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CR61     1  LIG     C11     1    0.021  13.0190
     2       CR61     1  LIG     C15     1    0.020  13.0190
     3        CB        1  LIG     C17     1    0.040  12.0110
     4         O         1  LIG      F1      1   -0.162  18.9984
     5       CR61     1  LIG     C16     1    0.021  13.0190
     6       CR61     1  LIG     C12     1    0.020  13.0190
     7        CB        1  LIG      C6      1    0.040  12.0110
     8       CH1       1  LIG      C1       2    0.000  12.0110
     9       CH2      1  LIG      C2       2    0.000  14.0270
    10       CH2     1  LIG      C5       3    0.120  14.0270
    11       CH2     1  LIG      C8       3    0.120  14.0270
    12        NL     1  LIG      N1     3    0.675  14.0067
    13       CH3     1  LIG     C18     3    0.085  15.0350
    14       CH3     1  LIG     C19     4    0.071  15.0350
    15         H     1  LIG     HAA     4    0.052   1.0080
    16        OS     1  LIG      O1     4   -0.147  15.9994
    17       CR51     1  LIG      C7     4   -0.010  13.0190
    18        CB     1  LIG      C4     4    0.034  12.0110
    19       CR61     1  LIG     C10     5    0.034  13.0190
    20        CB     1  LIG      C3     5    0.067  12.0110
    21       CR61     1  LIG      C9     5    0.034  13.0190
    22       CR61     1  LIG     C13     5    0.034  13.0190
    23        CB     1  LIG     C14     5    0.067  12.0110
    24        CB     1  LIG     C20     5    0.307  12.0110
    25         N     1  LIG      N2     5   -0.543  14.0067

thanks in advance
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