[gmx-users] Regarding Benzene Simulation

Ravi Kumar Venkatraman ravikumarvenkatraman at gmail.com
Sat Dec 24 15:03:35 CET 2011


Dear All,
             When I try to run Benzene Simulation I am getting following
error after the grompp for energy minimization.
ERROR 1 [file benz.top, line 115]:
  No default Proper Dih. types


ERROR 2 [file benz.top, line 116]:
  No default Proper Dih. types


ERROR 3 [file benz.top, line 117]:
  No default Proper Dih. types


ERROR 4 [file benz.top, line 118]:
  No default Proper Dih. types


ERROR 5 [file benz.top, line 119]:
  No default Proper Dih. types


ERROR 6 [file benz.top, line 120]:
  No default Proper Dih. types


ERROR 7 [file benz.itp, line 112]:
  No default Proper Dih. types


ERROR 8 [file benz.itp, line 113]:
  No default Proper Dih. types


ERROR 9 [file benz.itp, line 114]:
  No default Proper Dih. types


ERROR 10 [file benz.itp, line 115]:
  No default Proper Dih. types


ERROR 11 [file benz.itp, line 116]:
  No default Proper Dih. types


ERROR 12 [file benz.itp, line 117]:
  No default Proper Dih. types

My Benzene.top file is as follows:

[ dihedrals ] ; propers
; treated as RBs in GROMACS to use combine multiple AMBER torsions per
quartet
;    i      j      k      l   func    C0         C1         C2
C3         C4         C5
     1      2      3      4      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      C-    C1-    C2-    C3      CA-  CA-
CA-  CA
     1      2      3      9      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      C-    C1-    C2-    H2      CA-  CA-
CA-  HA
     1      6      5      4      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      C-    C5-    C4-    C3      CA-  CA-
CA-  CA
     1      6      5     11      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      C-    C5-    C4-    H4      CA-  CA-
CA-  HA
     2      1      6      5      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C1-     C-    C5-    C4      CA-  CA-
CA-  CA
     2      1      6     12      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C1-     C-    C5-    H5      CA-  CA-
CA-  HA
     2      3      4      5      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C1-    C2-    C3-    C4      CA-  CA-
CA-  CA
     2      3      4     10      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C1-    C2-    C3-    H3      CA-  CA-
CA-  HA
     3      4      5      6      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C2-    C3-    C4-    C5      CA-  CA-
CA-  CA
     3      4      5     11      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C2-    C3-    C4-    H4      CA-  CA-
CA-  HA
     4      3      2      8      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C3-    C2-    C1-    H1      CA-  CA-
CA-  HA
     4      5      6     12      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C3-    C4-    C5-    H5      CA-  CA-
CA-  HA
     5      4      3      9      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C4-    C3-    C2-    H2      CA-  CA-
CA-  HA
     6      1      2      3      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C5-     C-    C1-    C2      CA-  CA-
CA-  CA
     6      1      2      8      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C5-     C-    C1-    H1      CA-  CA-
CA-  HA
     6      5      4     10      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     C5-    C4-    C3-    H3      CA-  CA-
CA-  HA
     7      1      2      3      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      H-     C-    C1-    C2      HA-  CA-
CA-  CA
     7      1      2      8      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      H-     C-    C1-    H1      HA-  CA-
CA-  HA
     7      1      6      5      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      H-     C-    C5-    C4      HA-  CA-
CA-  CA
     7      1      6     12      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;      H-     C-    C5-    H5      HA-  CA-
CA-  HA
     8      2      3      9      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     H1-    C1-    C2-    H2      HA-  CA-
CA-  HA
     9      3      4     10      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     H2-    C2-    C3-    H3      HA-  CA-
CA-  HA
    10      4      5     11      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     H3-    C3-    C4-    H4      HA-  CA-
CA-  HA
    11      5      6     12      3 ;   30.33400    0.00000  -30.33400
0.00000    0.00000    0.00000 ;     H4-    C4-    C5-    H5      HA-  CA-
CA-  HA

[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;    i      j      k      l   func   phase     kd      pn
     1      3      2      8      1 ;   180.00   4.60240   2 ;      C-
C2-    C1-    H1
     1      5      6     12      1 ;   180.00   4.60240   2 ;      C-
C4-    C5-    H5
     2      4      3      9      1 ;   180.00   4.60240   2 ;     C1-
C3-    C2-    H2
     3      5      4     10      1 ;   180.00   4.60240   2 ;     C2-
C4-    C3-    H3
     4      6      5     11      1 ;   180.00   4.60240   2 ;     C3-
C5-    C4-    H4
     7      1      6      2      1 ;   180.00   4.60240   2 ;      H-
C-    C5-    C1

I am showing only the problem creating part, that is the Dihedral and
Improper Dihedrals. Please help me sort this problem out.

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
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