[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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