Dear All,<br> When I try to run Benzene Simulation I am getting following error after the grompp for energy minimization.<br>ERROR 1 [file benz.top, line 115]:<br> No default Proper Dih. types<br><br><br>ERROR 2 [file benz.top, line 116]:<br>
No default Proper Dih. types<br><br><br>ERROR 3 [file benz.top, line 117]:<br> No default Proper Dih. types<br><br><br>ERROR 4 [file benz.top, line 118]:<br> No default Proper Dih. types<br><br><br>ERROR 5 [file benz.top, line 119]:<br>
No default Proper Dih. types<br><br><br>ERROR 6 [file benz.top, line 120]:<br> No default Proper Dih. types<br><br><br>ERROR 7 [file benz.itp, line 112]:<br> No default Proper Dih. types<br><br><br>ERROR 8 [file benz.itp, line 113]:<br>
No default Proper Dih. types<br><br><br>ERROR 9 [file benz.itp, line 114]:<br> No default Proper Dih. types<br><br><br>ERROR 10 [file benz.itp, line 115]:<br> No default Proper Dih. types<br><br><br>ERROR 11 [file benz.itp, line 116]:<br>
No default Proper Dih. types<br><br><br>ERROR 12 [file benz.itp, line 117]:<br> No default Proper Dih. types<br><br>My Benzene.top file is as follows:<br><br>[ dihedrals ] ; propers<br>; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet<br>
; i j k l func C0 C1 C2 C3 C4 C5<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br> 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<br>
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<br><br>[ dihedrals ] ; impropers<br>; treated as propers in GROMACS to use correct AMBER analytical function<br>
; i j k l func phase kd pn<br> 1 3 2 8 1 ; 180.00 4.60240 2 ; C- C2- C1- H1<br> 1 5 6 12 1 ; 180.00 4.60240 2 ; C- C4- C5- H5<br>
2 4 3 9 1 ; 180.00 4.60240 2 ; C1- C3- C2- H2<br> 3 5 4 10 1 ; 180.00 4.60240 2 ; C2- C4- C3- H3<br> 4 6 5 11 1 ; 180.00 4.60240 2 ; C3- C5- C4- H4<br>
7 1 6 2 1 ; 180.00 4.60240 2 ; H- C- C5- C1<br><br>I am showing only the problem creating part, that is the Dihedral and Improper Dihedrals. Please help me sort this problem out.<br>
<br><b>With Regards,<br>Ravi Kumar Venkatraman,<br>IPC Dept., IISc,<br>Bangalore, INDIA.<br><br><span style="color:rgb(0,102,0)">+91-9686933963.</span></b><br><br>