From owner-chemistry@ccl.net Mon Jul 4 19:56:01 2016 From: "David Mannock dmannock(0)yahoo.com" To: CCL Subject: CCL: Detecting non-covalent interactions Message-Id: <-52277-160704190607-15255-2LiMi1fhhE2HPs4XHSHdww#,#server.ccl.net> X-Original-From: David Mannock Content-Type: multipart/alternative; boundary="----=_Part_1697584_1340181706.1467673388448" Date: Mon, 4 Jul 2016 23:03:08 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock^yahoo.com] ------=_Part_1697584_1340181706.1467673388448 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable It's a good idea to try each option and let people know what works for you/= gives the best answer. David =20 On Sunday, July 3, 2016 7:33 PM, Henrique C. S. Junior henriquecsj:-:gm= ail.com wrote: =20 Dear colleagues, thank you all for such detailed answers.I'll give a try t= o all suggested options. Thank you again. 2016-07-03 16:01 GMT-03:00 V=C3=ADctor Lua=C3=B1a Cabal victor{}fluor.quimi= ca.uniovi.es : Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor _ f= luor.quimica.uniovi.es] =C2=A0On 2/7/2016 15:41, Henrique C. S. Junior henriquecsj,gmail.com wrote: > Sent to CCL by: "Henrique C. S. Junior" [henriquecsj*gmail.com] > > I=E2=80=99m trying to use nciplot to detect a intermolecular interaction > between two monomers of the type [Cu(II)Cl2(L)2] (L is an inorganic > ligand). The supposed interaction is like this: Henrique, 1) Using an ECP wavefunction requires completing the core electron density appropriately, as the QTAIM analysis must be done on the ED for all electrons. The advise from Sebastian is right in this. 2) Better than nciplot, a preliminary code, you can use a far more advanced version: critic2, distributed freely from the github of the current maintainer: 3) Do not depend on the wfn output from g09. The wfx is better suited for your purpose, and critic2 is able to work with both. From the wfx the program can complete the core density appropriately for the ECP used in your calculation. Good luck and enjoy, =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 V=C3= =ADctor Lua=C3=B1a -- =C2=A0 =C2=A0 =C2=A0.=C2=A0 .=C2=A0 =C2=A0 "In science a person can be conv= inced by a good argument. =C2=A0 =C2=A0 / `' \=C2=A0 =C2=A0That is almost impossible in politics or r= eligion" =C2=A0 =C2=A0/(o)(o)\=C2=A0 (Adapted from Carl Sagan) =C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo bueno, pero tambi=C3=A9= n es peor =C2=A0/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ que lo malo, porque la mediocridad n= o es un grado, es una =C2=A0|=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge Wasenberg, 2015 =C2=A0|=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than good, but it is also w= orse than =C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity is not a grade, it is an at= titude) =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail:=C2=A0 =C2=A0 ! ! phone: +34-985-103491=C2=A0 fax: +34-985-103125 ! +--------------------------------------------+ =C2=A0GroupPage: =C2=A0Articles:=C2=A0 =C2=A0git-hub:=C2=A0 =C2=A0 -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY{}ccl.net or use: =C2=A0 =C2=A0 =C2=A0E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0--=20 Henrique C. S. Junior Qu=C3=ADmico Industrial - UFRRJMestrando em Qu=C3=ADmica Inorg=C3=A2nica - = UFRRJ Centro de Processamento de Dados - PMP ------=_Part_1697584_1340181706.1467673388448 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
It's a goo= d idea to try each option and let people know what works for you/gives the = best answer. David



On Sunday, July 3, 2016 7:33 PM, = Henrique C. S. Junior henriquecsj:-:gmail.com <owner-chemistry]~[ccl.net&g= t; wrote:


Dear colleagues, thank you a= ll for such detailed answers.
I'll give a try to all sugges= ted options.

Thank you again.

2016-07-03 16:01 GMT-03:00 V=C3=ADctor Lua=C3=B1a Cabal victor{= }fluor.quimica.uniovi.es <owner-chemistry{}ccl.net>:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor _ <= a rel=3D"nofollow" target=3D"_blank" href=3D"http://fluor.quimica.uniovi.es= /">fluor.quimica.uniovi.es]
 On 2/7/2016 15:41, Henrique C. S. Junior henriquecsj,gmail.com wrote:
> Sent to CCL by: "Henrique C. S. Junior" [henriquecsj*gmail.com]
>
> I=E2=80=99m trying to use nciplot to detect a intermolecular interacti= on
> between two monomers of the type [Cu(II)Cl2(L)2] (L is an inorganic > ligand). The supposed interaction is like this:

Henrique,

1) Using an ECP wavefunction requires completing the core electron
density appropriately, as the QTAIM analysis must be done on the ED for
all electrons. The advise from Sebastian is right in this.

2) Better than nciplot, a preliminary code, you can use a far more
advanced version: critic2, distributed freely from the github of the
current maintainer: <https://github.com/aoterodelaroza>

3) Do not depend on the wfn output from g09. The wfx is better suited
for your purpose, and critic2 is able to work with both. From the wfx
the program can complete the core density appropriately for the ECP
used in your calculation.

Good luck and enjoy,
                    V=C3= =ADctor Lua=C3=B1a

--
     .  .    "In science a person can be conv= inced by a good argument.
    / `' \   That is almost impossible in politics or r= eligion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero tambi=C3=A9= n es peor
 /   '`'`   \ que lo malo, porque la mediocridad n= o es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also w= orse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an at= titude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:  <victor#fluor.quimica.uniovi.es>  !
! phone: +34-985-103491  fax: +34-985-103125 !
+--------------------------------------------+
 GroupPage: <http://azufre.quimica.uniovi.es/>
 Articles:  <http://sc= holar.google.com/citations?user=3DIbl1BWAAAAAJ&hl=3Des>
 git-hub:   <https://github.com/aoterodelaroza>



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--
Henrique C. S. Junior
Qu=C3=ADmico Industrial - UFRRJ
Mestrando em Qu=C3=ADmica Inorg=C3=A2nica - UFRRJ
Centro de Processam= ento de Dados - PMP


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