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

Repic Matej matej.repic at epfl.ch
Mon Aug 31 12:39:12 CEST 2015


This is only the include topology, but the functional topology for grompp
needs a few more lines. Make another file such as below and this should
run fine through grompp, provided you have a big enough box defined in
5-fu.gro. Note that this will run the 5-FU dynamics in the gas phase,
since there are no water molecules in the topology, nor the necessary
parameters are included to use water. There must be water in the 5-fu.gro
coordinate file as well, of course.

----------------main.top---------------------
[ defaults ]
1               2               yes             0.5     0.8333

#include 5-fu.itp

[ system ]
; Name
5-fluorouracil

[ molecules ]
UNK 1
----------------main.top---------------------




Best,
Matej

------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
BCH 4108
CH - 1015 Lausanne

------------------------------------------------------






On 8/31/15, 12:10, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Mehrnoosh Hazrati"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
mehrnoosh.hazrati at modares.ac.ir> wrote:

>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
>-- 
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