Recently, I am working on some Gaussian jobs. The error “angle Alpha is outside the valid range of 0 to 180” always makes me upset.
Learning by oneself is really low-efficient and time-consuming. : (
I got some help from internet. Dummy atom could solve this problem. Please read the article first to know dummy atom at http://www.cup.uni-muenchen.de/ch/compchem/geom/internal.html. Please pay attention to the example at the end of the paper.
The origin coordinate is
C1 C2 1 r2 H3 1 r3 2 a3 H4 1 r3 2 a3 3 120. H5 1 r3 2 a3 3 -120. N6 2 r6 1 180.0 3 180.0 r2=1.45 r3=1.1 r6=1.2 a3=110.
The coordinate with dummy atom is
C1 C2 1 r2 H3 1 r3 2 a3 H4 1 r3 2 a3 3 120.0 H5 1 r3 2 a3 3 -120.0 X6 2 1.0 1 90.0 3 0.0 N7 2 r7 6 90.0 1 180.0 r2=1.45 r3=1.1 r7=1.2 a3=110.
So the key to set dummy atom in your system is:
- Add it before the atom you want to modify. Here is N7;
- Divide the problem angle to half. Here is N7-C2-C1. X should have a bond with C2 and an angle with C1. Set the bond length to 1.0 and the angle to 90.0;
- Dihedral analysis. The original N7 has dihedral N6-C2-C1-H3. Put X in the plane of C2-C1-H3, so that you do not need to change the dihedral for the new N7. You may tell the old dihedral N6-C2-C1-H3 is the same with N7-C2-X6-C1. So X6-C2-C1-H3 is 0.
- Modify the N7 data. N7 still has a bond with C2. N7 form a new angle with X6, which is 90.0. And find a nearby atom, here is C1. Since the old dihedral N6-C2-C1-H3 is the same with N7-C2-X6-C1, you may set N7-C2-X6-C1 as original N6-C2-C1-H3 with 180.0
Now, you may use it to optimize or scan operations.