# How To Scan “improper dihedrals” in Gaussian 09?

I am trying to parameterize Amber force field for a novel molecule, but I couldn't obtain improper dihedrals. Because if I scan impropers like dihedrals; later or sooner the molecule is overlapping and Gaussian exits with errors.
Let's say it is the $$\ce{BH3}$$ molecule. I tried many things for example with/without symmetry=none keyword, with O 4 2 3 1 S 10 18.000000 or D 4 2 3 1 S 10 18.0 (out of plane), but I couldn't get the results for a 360° improper scan.

I got this error at step 6:

 Old curvilinear step not converged, using linear step
Error imposing constraints
Error termination via Lnk1e in C:\G09W\l103.exe


What should I do?

Here is my gjf file:

%nprocshared=4
# opt=modredundant am1 geom=connectivity

Title Card Required

0 1
B                  0.00000000    0.00000000    0.00000000
H                  0.00000000    1.10873800    0.00000000
H                  0.96019500   -0.55436900    0.00000000
H                 -0.96019500   -0.55436900    0.00000000

1 2 1.0 3 1.0 4 1.0
2
3
4

D 4 2 3 1 S 10 18.000000

• Please define what you understand as an improper dihedral angle, or out of plane angle (or what is the definition for them in the program you are calculating them for). I could not find a common definition for these, and it appears to me that they are 'special' for force fields. I have a very hard time understanding what you are actually trying to accomplish. – Martin - マーチン Jan 15 '19 at 14:04

I want to add Dac's answer about $$\ce{NH3}$$ impropers here I think it will help you:

The very simple answer to your question, is that improper dihedrals are needed when they are necessary. (Not very helpful, huh :) ) Let me elaborate some. In my experience, there are times when improper dihedrals are not needed because proper dihedrals are sufficient for modeling the energetics and the conformations of the atoms in question. (Note that in Amber proper and improper dihedral angles are defined by the same functional form.) Other times the person who has done the parameterization deems it necessary to use impropers. So ultimately, to use or not use impropers often comes down to the individual tastes of the person who created the parameters. I personally feel that impropers are need in selected case to correctly model out-of-plane bending, and there are very few, if any, force fields that do not use them.

Some else who knows better can correct me if I am wrong, but I believe that parmchk reports provides any improper dihedrals if it recognizes that they are present in the molecule's topology. A value of 10.5 kcal/mol is reasonable for an improper dihedral. If you are uncertain, the best way to determine if you need the impropers, or not, is to run some test simulations with and without them - then choose the setup that gives the best results. (However, if the goal is to force the improper dihedrals to be 100% planar, then adding an additional force constant to do so is "probably" okay. What you will miss by doing this is the proper modeling of out-of-plane bending, but I am not sure how well Parm99 models this anyway.)

Yes, this is David's opinion from the amber forum.

Additionally, if you can not scan improper dihedrals using ab inito method, you can use genetic algorythm with sander.

To do this first use in your *.frcmod file:

I-J-K-L  1          180.0         0.0


and draw chart with CPPTRAJ, then change energy and repeat it until you get a reasonable result. Actually you can find for this some software, too. Or you can use ATB server for gromacs. If your molecule doesn't have metal ion, upload pdb format to ATB server and then it will give you force all force constants with improper dihedrals. If you use it in amber, just change the energy from joule to kcal ($$\pu{1 kcal} = \pu{4.18 J}$$) and multiply it by 0.5 and then use it in your *.frcmod file.

After I asked this question, I found answer. I am putting the solution here so maybe somebody else use this. The solution is this: if gaussian exit from the job (for example) at step 6; change starting geometry and take it 6 step back. How? For example in my question every step size is 18 degree and step 6 is 90 degree. Open your *.gjf or *.com file select the same dihedral and decrease angle 90 by degree (don't forget 90 degree is just for this example, you wil change it according to your step and the size of step) *sometimes you may have to fix one group . And then start job again.

you can see my "wrong gjf file" in the question. And here is the my "right gjf file": I only changed the starting dihedral angles.

%nprocshared=4
# opt=modredundant am1 geom=connectivity

Title Card Required

0 1
B                 -0.54526231    0.17208210    0.44752404
H                  0.54967689    0.02475247    0.03303383
H                 -1.22032311    1.04666245    0.03303383
H                 -0.96514071   -0.55516861   -1.21043678

1 2 1.0 3 1.0 4 1.0
2
3
4

D 1 2 3 4 S 9 18.000000


NOTE: it seems I defined different dihedrals at first glance.
in question I defined: D 4 2 3 1 S 10 18.000000 and here I defined: D 1 2 3 4 S 9 18.000000 but out of the symmetry and all H bonds are equal two dihedrals are the same indeed. Here is the article about this: https://pdfs.semanticscholar.org/ab92/5f43824e59dd9e3be3474ebbac57a64998c3.pdf (DOI 10.1002/jcc.21425 - "Symmetrization of the AMBER and CHARMM Force Fields", 2009, EDYTA M. et all) in this article in figure 5 shows only 3 different improper can exist for I–J–K–L but in my question I=L=J and thus actually 1234 dihedral and 2314 dihedral are the same and gave the same results for the same technics.