From owner-chemistry@ccl.net Thu Dec 21 23:44:01 2017 From: "Martin C. Schwarzer schwarzer]=[mail.de" To: CCL Subject: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian Message-Id: <-53115-171221023023-9919-MVFOKb8Oy3pReD8PnUyFOA-$-server.ccl.net> X-Original-From: "Martin C. Schwarzer" Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="ECnlTHY3NZPXOEtIz9qSxOwbJ27kaVHMs" Date: Thu, 21 Dec 2017 16:29:58 +0900 MIME-Version: 1.0 Sent to CCL by: "Martin C. Schwarzer" [schwarzer_-_mail.de] This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --ECnlTHY3NZPXOEtIz9qSxOwbJ27kaVHMs Content-Type: multipart/mixed; boundary="ePz8VLtfryI4mvx9pcKyBhxT5RVGrktdk"; protected-headers="v1" > From: "Martin C. Schwarzer" To: CCL Subscribers Message-ID: Subject: Re: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian References: <53110-171220231326-13195-ECRg4LaDg3cm/SIQOwak0A_-_server.ccl.net> In-Reply-To: <53110-171220231326-13195-ECRg4LaDg3cm/SIQOwak0A_-_server.ccl.net> --ePz8VLtfryI4mvx9pcKyBhxT5RVGrktdk Content-Type: text/plain; charset=utf-8 Content-Language: en-GB Content-Transfer-Encoding: quoted-printable 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=3D1.2) and changed to pm6 for testing. I= t should work for other methods, too. Note that this is not available in G09. Best regards, Martin %chk=3Dpm6.scan.chk %nproc=3D2 %mem=3D8000MB #P PM6 OPT(MaxCycle=3D100) SYMMETRY(PG=3DC4v) SCF(MaxCycle=3D500,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)=3DXCntr(1) YZinc(inactive)=3DYCntr(1) ZZinc(inactive)=3DZCntr(1) XLiga(inactive)=3DXCntr(2-5) YLiga(inactive)=3DYCntr(2-5) ZLiga(inactive)=3DZCntr(2-5) OoPla=3Dsqrt[(XZinc-XLiga)^2+(YZinc-YLiga)^2+(ZZinc-ZLiga)^2]*0.529 OoPla(NSteps=3D20, StepSize=3D0.2) Am Thu 21/12/2017 um 1:13 PM schrieb Guzman, Francisco fg58-$-njit.edu: > If you try opt=3D(modredundant,cartesian) >=20 > You should see the following error at the end of the output file: > =C2=A0----------------------------------------- > =C2=A0Cannot AddRedundant with Cartesian or Z-matrix opts. > =C2=A0Error termination via Lnk1e in l1.exe >=20 > From the description of your problem, you should be able to use > modredundant as a method of freezing a bond/angle/dihedral and relax th= e > rest of the structures by adding the following 1 space after your z-mat= rix. >=20 > *Freeze bond between atom 1 & 2: > * > B 1 2 F >=20 > *Freeze angle between atom 1 , 2, & 3: > * > A 1 2 3 F >=20 > *Freeze dihedral between atom 1 , 2,=C2=A0 3, & 4: > * > D 1 2 3 4 F >=20 > This is all with Gaussian 09, Rev. C,=C2=A0 At least for Gaussian, I do= not > know of another way to freeze part of a structure and optimize without > using modredundant. > ** > ** > ** >=20 > On Tue, Dec 19, 2017 at 10:20 AM, Grigoriy Zhurko > reg_zhurko#chemcraftprog.com > > wrote: >=20 >=20 > Sent to CCL by: Grigoriy Zhurko [reg_zhurko:chemcraftprog.com > ] >=20 >=20 > > What are the errors? >=20 > =C2=A0 Most atoms are frozen. >=20 > > It's also unclear what you are trying to do. > > Are you trying to do a relaxed scan (PES), rigid scan,=C2=A0 or j= ust > > optimize? >=20 > Relaxed PES scan. >=20 > > If it's a relaxed scan, then opt=3Dmodredundant is > > required. >=20 > =C2=A0 Usually opt=3Dmodredundant implies fixing (scanning) a dista= nce, > 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. >=20 > >=C2=A0 I believe for any modredundant job Gaussian internally > > optimizes with a z-matrix only. >=20 > This is strange for me. I found that Z-matrices are a very bad > choice for optimizing rings. >=20 > > Something along the lines of forcing > > the job to optimize using cartesian coordinates, opt=3D(modreduda= nt, > > cartersian), will not work. >=20 > Are you sure? >=20 >=20 >=20 >=20 > =C2=A0 Sincerely, > =C2=A0 Grigoriy Zhurko. >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing scr= ipt =3D- > To recover the email address of the author of the message, please c= hange > E-mail to subscribers: CHEMISTRY^-^ccl.net > or use: > =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_messag= e > >=20 > E-mail to administrators: CHEMISTRY-REQUEST^-^ccl.net > or use > =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_messag= e > >=20> =C2=A0 =C2=A0 =C2=A0> >=20>=20> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > >=20= > >=20 > =C2=A0 =C2=A0 =C2=A0 >=20> >=20 >=20 >=20 >=20 >=20 > --=20 > Francisco Guzman > PhD Candidate > Otto H. York Department of Chemical, Biological and Pharmaceutical > Engineering > New Jersey Institute of Technology > Email:=C2=A0fg58^-^njit.edu > ,=C2=A0guzman.research^-^gmail.com > --ePz8VLtfryI4mvx9pcKyBhxT5RVGrktdk-- --ECnlTHY3NZPXOEtIz9qSxOwbJ27kaVHMs Content-Type: application/pgp-signature; name="signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJaO2L8AAoJEIYALUULs51WJygH/1Wc/iA2YLFEp8wFF6bRqwRu 2Z8axxAe2LY2lW2nCTBPChlUUnw9b84Am7JXWEYrY7WHL/LePWB2Xr3173+ZofGs Z6tcSZAwDX4JtQKYCdz7ABUCEkX6IUukYi81Csie3hpMeVXvg/hEiF/a7GGU17NY 62Wwga/c9FwjQJPBzE5A+5C4sxT6J+fSZ8QgZ4hQCeNX5CNtRNeH3oH7KiC15o0x nJ6EPzywcWeCLGKeJsT6boPOCwfXUr+S8sGY+7QIpCnwEGGR5K3oFro6gcFDvEul Y3Opn8YugjXul1fCVSrXpHUXxhG5U//wmVdhTFAf7r/5reo4wBhei1QP1b6h6Ok= =fkIi -----END PGP SIGNATURE----- --ECnlTHY3NZPXOEtIz9qSxOwbJ27kaVHMs--