[gmx-users] Fatal error: No molecule were defined in the system

[Mehrnoosh Hazrati]

Dear all,

hi,

I'm simulating the drug "5-Flouorouracil", since its topology file is not
available, I've written it by hand.
But I got the error "No molecule were defined in the system" when run
grompp.
where could be the problem?

Thank you in advance.

Regards,
Mehrnoosh

The .itp file is attached below:


[ moleculetype ]
; Name nrexcl
UNK      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1      opls_719  1  UNK     F     0    -0.325   18.9984
     2      opls_328  1  UNK     O     1    -0.567   15.9994
     3      opls_326  1  UNK     O     2    -0.613   15.9994
     4      opls_321  1  UNK     N     3    -0.641   14.0067
     5      opls_319  1  UNK     N     4    -0.603   14.0067
     6      opls_322  1  UNK     C     5    +0.602   12.0110
     7      opls_320  1  UNK     C     6    +0.805   12.0110
     8      opls_718  1  UNK     C     7    +0.275   12.0110
     9      opls_324  1  UNK     C     8    -0.005   12.0110
    10      opls_327  1  UNK     H     9    +0.424    1.0079
    11      opls_327  1  UNK     H    10    +0.421    1.0079
    12      opls_330  1  UNK     H    11    +0.227    1.0079
; total charge of the molecule: 0.000
[ bonds ]
;  ai    aj  funct     c0            c1
    1     8    1     1.33863      323004.8
    2     6    1     1.21616      476976.0
    3     7    1     1.21609      476976.0
    4     6    1     1.40749      349782.4
    4     7    1     1.39161      349782.4
    4    10    1     1.01427      363171.2
    5     7    1     1.39060      349782.4
    5     9    1     1.38105      357313.6
    5    11    1     1.01039      363171.2
    6     8    1     1.46503      392459.2
    8     9    1     1.34636      392459.2
    9    12    1     1.08322      307105.6

[ angles ]
;  ai    aj    ak   funct    c0     c1     c2      c3
   1      8     6       1       117.02620      585.760
   1      8     9       1       121.35396      585.760
   2      6     4       1       122.04483      669.440
   2      6     8       1       125.88929      669.440
   3      7     4       1       124.02387      669.440
   3      7     5       1       123.24541      669.440
   4      6     8       1       112.06588      585.760
   4      7     5       1       112.73072      585.760
   5      9     8       1       120.66155      585.760
   5      9    12       1       117.10729      418.400
   6      4     7       1       128.91643      585.760
   6      4    10       1       115.76471      418.400
   6      8     9       1       121.61985      527.184
   7      4    10       1       115.31885      418.400
   7      5    11       1       115.20972      418.400
   8      9    12       1       122.23116      418.400
   9      5    11       1       120.78471      418.400

[ dihedrals ]
; improper dihedral
;  ai     aj    ak     al    func    t0    k
   4      6     7     10      2      0.0   167.36
   5      9     7     11      2      0.0   167.36
   6      4     8      2      2      0.0   167.36
   7      4     5      3      2      0.0   167.36
   8      9     6      1      2      0.0   167.36
   9      5     8     12      2      0.0   167.36
[ dihedrals ]
;  ai     aj    ak     al    func    t0    k        mult
   1      8     6      4     1     180.0    41.80    2
   2      6     4      7     1     180.0    41.80    2
   3      7     4      6     1     180.0    41.80    2
   4      7     5     11     1     180.0    41.80    2
   7      5     9     12     1     180.0    41.80    2
   8      9     5     11     1     180.0    41.80    2