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



With Gaussian 16, use generalised internal coordinates (GIC), see
 http://gaussian.com/geom/ (GIC tab)
 The following should do what you desire. I have symmetrised the molecule
 at first (it breaks around OoPla=1.2) and changed to pm6 for testing. It
 should work for other methods, too.
 Note that this is not available in G09.
 Best regards, Martin
 %chk=pm6.scan.chk
 %nproc=2
 %mem=8000MB
 #P PM6
 OPT(MaxCycle=100)
 SYMMETRY(PG=C4v)
 SCF(MaxCycle=500,xqc)
 GEOM(ModRedundant,GIC)
 title
 0 1
 Zn       0.000000000      0.000000000      0.200000000
 N       -2.045528736      0.000000000      0.000000000
 N        0.000000000      2.045528736      0.000000000
 N        0.000000000     -2.045528736      0.000000000
 N        2.045528736      0.000000000      0.000000000
 C        1.125466850      2.875570225      0.000000000
 C        2.453389936      2.453389936      0.000000000
 C        2.875570225      1.125466850      0.000000000
 H        3.227317131      3.227317131      0.000000000
 C       -1.125466850      2.875570225      0.000000000
 C       -2.453389936      2.453389936      0.000000000
 C       -2.875570225      1.125466850      0.000000000
 H       -3.227317131      3.227317131      0.000000000
 C       -2.875570225     -1.125466850      0.000000000
 C       -2.453389936     -2.453389936      0.000000000
 C       -1.125466850     -2.875570225      0.000000000
 H       -3.227317131     -3.227317131      0.000000000
 C        1.125466850     -2.875570225      0.000000000
 C        2.453389936     -2.453389936      0.000000000
 C        2.875570225     -1.125466850      0.000000000
 H        3.227317131     -3.227317131      0.000000000
 C        0.680645967     -4.281390432      0.000000000
 C       -0.680645967     -4.281390432      0.000000000
 C       -4.281390432     -0.680645967      0.000000000
 C       -4.281390432      0.680645967      0.000000000
 C        4.281390432     -0.680645967      0.000000000
 C        4.281390432      0.680645967      0.000000000
 C        0.680645967      4.281390432      0.000000000
 C       -0.680645967      4.281390432      0.000000000
 H        1.354119189     -5.116535609      0.000000000
 H       -1.354119189     -5.116535609      0.000000000
 H       -5.116535609     -1.354119189      0.000000000
 H       -5.116535609      1.354119189      0.000000000
 H       -1.354119189      5.116535609      0.000000000
 H        1.354119189      5.116535609      0.000000000
 H        5.116535609     -1.354119189      0.000000000
 H        5.116535609      1.354119189      0.000000000
 A(*,1,*) remove
 XZinc(inactive)=XCntr(1)
 YZinc(inactive)=YCntr(1)
 ZZinc(inactive)=ZCntr(1)
 XLiga(inactive)=XCntr(2-5)
 YLiga(inactive)=YCntr(2-5)
 ZLiga(inactive)=ZCntr(2-5)
 OoPla=sqrt[(XZinc-XLiga)^2+(YZinc-YLiga)^2+(ZZinc-ZLiga)^2]*0.529
 OoPla(NSteps=20, StepSize=0.2)
 Am Thu 21/12/2017 um 1:13 PM schrieb Guzman, Francisco fg58-$-njit.edu:
 > If you try opt=(modredundant,cartesian)
 >
 > You should see the following error at the end of the output file:
 >  -----------------------------------------
 >  Cannot AddRedundant with Cartesian or Z-matrix opts.
 >  Error termination via Lnk1e in l1.exe
 >
 > From the description of your problem, you should be able to use
 > modredundant as a method of freezing a bond/angle/dihedral and relax the
 > rest of the structures by adding the following 1 space after your z-matrix.
 >
 > *Freeze bond between atom 1 & 2:
 > *
 > B 1 2 F
 >
 > *Freeze angle between atom 1 , 2, & 3:
 > *
 > A 1 2 3 F
 >
 > *Freeze dihedral between atom 1 , 2,  3, & 4:
 > *
 > D 1 2 3 4 F
 >
 > This is all with Gaussian 09, Rev. C,  At least for Gaussian, I do not
 > know of another way to freeze part of a structure and optimize without
 > using modredundant.
 > **
 > **
 > **
 >
 > On Tue, Dec 19, 2017 at 10:20 AM, Grigoriy Zhurko
 > reg_zhurko#chemcraftprog.com <http://chemcraftprog.com>;
 > <owner-chemistry^-^ccl.net <mailto:owner-chemistry^-^ccl.net>> wrote:
 >
 >
 >     Sent to CCL by: Grigoriy Zhurko [reg_zhurko:chemcraftprog.com
 >     <http://chemcraftprog.com>;]
 >
 >
 >     > What are the errors?
 >
 >       Most atoms are frozen.
 >
 >     > It's also unclear what you are trying to do.
 >     > Are you trying to do a relaxed scan (PES), rigid scan,  or
 just
 >     > optimize?
 >
 >     Relaxed PES scan.
 >
 >     > If it's a relaxed scan, then opt=modredundant is
 >     > required.
 >
 >       Usually opt=modredundant implies fixing (scanning) a distance,
 >     angle or a dihedral, but I need to fix a distance between a real
 >     atom and a dummy atom between two other real atoms. I don't see how
 >     I can specify this constraint with modreduntant only.
 >
 >     >  I believe for any modredundant job Gaussian internally
 >     > optimizes with a z-matrix only.
 >
 >     This is strange for me. I found that Z-matrices are a very bad
 >     choice for optimizing rings.
 >
 >     > Something along the lines of forcing
 >     > the job to optimize using cartesian coordinates, opt=(modredudant,
 >     > cartersian), will not work.
 >
 >     Are you sure?
 >
 >
 >
 >
 >       Sincerely,
 >       Grigoriy Zhurko.
 >
 >
 >
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 >
 >
 > --
 > Francisco Guzman
 > PhD Candidate
 > Otto H. York Department of Chemical, Biological and Pharmaceutical
 > Engineering
 > New Jersey Institute of Technology
 > Email: fg58^-^njit.edu
 > <mailto:fg58^-^njit.edu>, guzman.research^-^gmail.com
 > <mailto:guzman.research^-^gmail.com>
 

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