CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian

Is it really a valid geometry?  From a quick glance at your coordinates, it appears that all your Z-matrix coordinates are defined, first, relative to the dummy atom and then all the absolute coordinates come next. Is it obvious how the two pieces would fit together?  You should make sure your coordinates make sense with what Gaussian expects.

http://gaussian.com/zmat/


On Tue, Dec 19, 2017 at 6:20 AM, Guzman, Francisco fg58%njit.edu <owner-chemistry-*-ccl.net> wrote:
What are the errors? It's also unclear what you are trying to do. Are you trying to do a relaxed scan (PES), rigid scan,  or just optimize? If it's a relaxed scan, then opt=modredundant is required.  I believe for any modredundant job Gaussian internally optimizes with a z-matrix only. Something along the lines of forcing the job to optimize using cartesian coordinates, opt=(modredudant, cartersian), will not work. For a rigid scan (molecule is frozen except bond/angle/dihedral of interest) use the "scan" keyword followed by specifying in the z-matrix which angle/bond/dihedral of interest is to be scanned. Scan also requires the use of a z-matrix.

I've had many many issues with linear angles myself.  If it's just an optimization, inserting a dummy atom works just fine. However, for a PES it seems to me that the dummy atom is only considered in the first step of your scan and is subsequently discarded. Hence, if a linear angle appears at any place during the scan, my calculations tend to terminate with something along the lines of error L9999, "Error linear angle in bend". 

Maybe try another program if this is an issue. NWCHEM could work.

On Mon, Dec 18, 2017 at 9:34 AM, Grigoriy Zhurko reg_zhurko||chemcraftprog.com <owner-chemistry|a|ccl.net> wrote:

Sent to CCL by: Grigoriy Zhurko [reg_zhurko]~[chemcraftprog.com]
Hello,

I need to perform a PES scan in Gaussian, so that the distance between an atom and the center between two other atoms will be scanned.
When I need to simply scan an iteratomic distance, I use OPT(MODREDUNDANT). But in current case I have to use a z-matrix and add a dummy atom (the center between two real atoms).
It is possible to use only Z-matrix for this job, but the result becomes rather bad: the optimization starts with evident bugs (probably because this geometry has rings).
I tried to combine the Z-matrix with the Cartesians. I created the following input file:

%NPROCSHARED=3
 #P uwB97XD/6-31G(D,P) OPT(Z-Matrix,LOOSE)
 NOSYMM

 Silicon

 0 1
 X
 N 1 R12
 X 1 1.400000 2 90.000000
 N 1 R12 3 90.000000 2 180.000000
 N 1 R15 2 A215 3 -90.000000
 N 1 R16 3 A316 5 D5316
 Zn 1 R17 2 A217 5 -D5217
 6 0.000000000 2.863016000 1.101006000
 6 0.000000000 2.425840000 2.425840000
 6 0.000000000 1.101006000 2.863016000
 1 0.000000000 3.193595000 3.193595000
 6 0.000000000 2.863016000 -1.101006000
 6 0.000000000 2.425840000 -2.425840000
 6 0.000000000 1.101006000 -2.863016000
 1 0.000000000 3.193595000 -3.193595000
 6 0.000000000 -1.101006000 -2.863016000
 6 0.000000000 -2.425840000 -2.425840000
 6 0.000000000 -2.863016000 -1.101006000
 1 0.000000000 -3.193595000 -3.193595000
 6 0.000000000 -2.863016000 1.101006000
 6 0.000000000 -2.425840000 2.425840000
 6 0.000000000 -1.101006000 2.863016000
 1 0.000000000 -3.193595000 3.193595000
 6 0.000000000 -4.245855000 0.681548000
 6 0.000000000 -4.245855000 -0.681548000
 6 0.000000000 -0.681548000 -4.245855000
 6 0.000000000 0.681548000 -4.245855000
 6 0.000000000 -0.681548000 4.245855000
 6 0.000000000 0.681548000 4.245855000
 6 0.000000000 4.245855000 0.681548000
 6 0.000000000 4.245855000 -0.681548000
 1 0.000000000 -5.096481000 1.350466000
 1 0.000000000 -5.096481000 -1.350466000
 1 0.000000000 -1.350466000 -5.096481000
 1 0.000000000 1.350466000 -5.096481000
 1 0.000000000 5.096481000 -1.350466000
 1 0.000000000 5.096481000 1.350466000
 1 0.000000000 -1.350466000 5.096481000
 1 0.000000000 1.350466000 5.096481000
 Variables:
 R12 = 2.04198300
 R15 = 2.04198300
 A215 = 90.00000000
 R16 = 2.04198300
 A316 = 90.00000000
 D5316 = 180.00000000
 A217 = 90.00000000
 D5217 = 90.00000000
 constants
 R17 = 0.40000000 s 20 0.2

This job constructs a valid geometry, the optimization starts, but it starts incorrectly: during the optimization, only the Z-matrix parameters are varied, while the coordinates of most atoms are fixed. Can I do something to make Gaussian optimize these atomic coordinates as well?



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--
Francisco Guzman
PhD Candidate
Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering
New Jersey Institute of Technology