From owner-chemistry@ccl.net Thu May 2 13:46:00 2019 From: "Carlos Nieto carlostnietog:_:gmail.com" To: CCL Subject: CCL: Gold output & receptor-ligand complex files Message-Id: <-53721-190502035710-5254-OFAb50uxbyzldyYAvZsZ6g++server.ccl.net> X-Original-From: "Carlos Nieto" Date: Thu, 2 May 2019 03:57:08 -0400 Sent to CCL by: "Carlos Nieto" [carlostnietog*|*gmail.com] Hi, I'm wondering if it is possible to obtain all the docking solutions of a GOLD output as individual complex (receptor-ligand pose) files. I think GOLD can only generate the individual n mol2 files (for each solution of a total of n docking runs). Gold only allows to save a complex one a time, but not the whole set of solutions. If not possible, do you know any program, online tool or script to combine 1 single receptor structure with n mol2 files and generate n complex files? Thank you, Carlos From owner-chemistry@ccl.net Thu May 2 14:21:00 2019 From: "Robert Molt rwmolt07=gmail.com" To: CCL Subject: CCL: Molpro SAPT Notation Message-Id: <-53722-190502120257-5036-7PsYfBPBEsHUvUKgHqKZRw~!~server.ccl.net> X-Original-From: Robert Molt Content-Language: en-US Content-Type: multipart/alternative; boundary="------------5010E6C3B6E93C2642543339" Date: Thu, 2 May 2019 12:02:49 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [rwmolt07/a\gmail.com] This is a multi-part message in MIME format. --------------5010E6C3B6E93C2642543339 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit I am confused by the notation used in the Molpro manual for SAPT expansions. There are /seemingly/ contradictions, caveated with the fact that I am a neophyte with Molpro. 1.) On https://www.molpro.net/info/release/doc/manual/node750.html , the SAPT expansion is defined with performing E10 (pol), E10(exch), E20(ind), etc. On https://www.molpro.net/info/release/doc/manual/node762.html , the SAPT expansion is defined with respect to E1(pol), E1(exch), etc. This would imply NOT just the zero term. I am used to the notation that E1(pol)= sum over n=0, m=0, of Epol (i,nm)= E(1,01)+E(1,10)+E(1,11) To what nomenclature I am accustomed, these are seemingly mutually exclusive. 2.) Furthermore, at the bottom of https://www.molpro.net/info/release/doc/manual/node750.html , there is a statement which I find peculiar. It reads: "This means that if Hartree-Fock wave functions are used for monomer, the following quantity is obtained (zero in superscript denotes that no intramonomer correlation is accounted for) [1]." The reference of [1] presumably refers to the one given in the previous slide, referring to Chem. Rev. 94, 1887, published 1994 by Jeziorski, Szalewicz, and Moszynski. I do not see that this paper defines the second superscript index as meaning no intramonomer correlation effects. Rather, the paper  does not use the double superscript notation at all. To me, relative to my potentially flawed understanding of SAPT, the meaning of the second superscript follows from what I wrote previously. Can someone clarify this notation difference? --------------5010E6C3B6E93C2642543339 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit I am confused by the notation used in the Molpro manual for SAPT expansions. There are seemingly contradictions, caveated with the fact that I am a neophyte with Molpro.

1.) 

On https://www.molpro.net/info/release/doc/manual/node750.html , the SAPT expansion is defined with performing E10 (pol), E10(exch), E20(ind), etc.

On https://www.molpro.net/info/release/doc/manual/node762.html , the SAPT expansion is defined with respect to E1(pol), E1(exch), etc. This would imply NOT just the zero term.

I am used to the notation that
E1(pol)= sum over n=0, m=0, of Epol (i,nm)= E(1,01)+E(1,10)+E(1,11)

To what nomenclature I am accustomed, these are seemingly mutually exclusive.

2.) 

Furthermore, at the bottom of https://www.molpro.net/info/release/doc/manual/node750.html , there is a statement which I find peculiar. It reads:

"This means that if Hartree-Fock wave functions are used for monomer, the following quantity is obtained (zero in superscript denotes that no intramonomer correlation is accounted for) [1]."

The reference of [1] presumably refers to the one given in the previous slide, referring to Chem. Rev. 94, 1887, published 1994 by Jeziorski, Szalewicz, and Moszynski. I do not see that this paper defines the second superscript index as meaning no intramonomer correlation effects. Rather, the paper  does not use the double superscript notation at all.

To me, relative to my potentially flawed understanding of SAPT, the meaning of the second superscript follows from what I wrote previously.

Can someone clarify this notation difference?
--------------5010E6C3B6E93C2642543339-- From owner-chemistry@ccl.net Thu May 2 16:57:01 2019 From: "Vitor Hugo Paschoal paschoal.vhp]_[usp.br" To: CCL Subject: CCL: Molpro SAPT Notation Message-Id: <-53723-190502163934-23803-+k+py3m06s2CcVTQ61kaJA#,#server.ccl.net> X-Original-From: Vitor Hugo Paschoal Content-Type: multipart/alternative; boundary="0000000000005749550587eda143" Date: Thu, 2 May 2019 17:39:15 -0300 MIME-Version: 1.0 Sent to CCL by: Vitor Hugo Paschoal [paschoal.vhp#%#usp.br] --0000000000005749550587eda143 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Robert, Your first link refers to SAPT, or as represented in psi4's "manual", SAPT(HF). The second link refers to SAPT(DFT). Although both methods are similar, they have their own "peculiarities" including their notation. This is outlined in A. J. Stone's book (theory of intermolecular forces) in chapter 6, but you might find a more in depth explanation consulting the original works by Szalewicz on SAPT and by Misquitta on SAPT(DFT). Best regards, Vitor H. Paschoal, https://orcid.org/0000-0002-0935-3772 https://scholar.google.com.br/citations?user=3DVh1RI_MAAAAJ&hl PhD Candidate at the Molecular Spectroscopy Laboratory-LEM, Chemistry Institute, University of S=C3=A3o Paulo Av. Prof. Lineu Prestes, 748 - Butant=C3=A3 - S=C3=A3o Paulo SP, Brazil +55 11 3091-3853 On Thu, May 2, 2019 at 5:13 PM Robert Molt rwmolt07=3Dgmail.com < owner-chemistry]=[ccl.net> wrote: > I am confused by the notation used in the Molpro manual for SAPT > expansions. There are *seemingly* contradictions, caveated with the fact > that I am a neophyte with Molpro. > > 1.) > > On https://www.molpro.net/info/release/doc/manual/node750.html , the SAPT > expansion is defined with performing E10 (pol), E10(exch), E20(ind), etc. > > On https://www.molpro.net/info/release/doc/manual/node762.html , the SAPT > expansion is defined with respect to E1(pol), E1(exch), etc. This would > imply NOT just the zero term. > > I am used to the notation that > E1(pol)=3D sum over n=3D0, m=3D0, of Epol (i,nm)=3D E(1,01)+E(1,10)+E(1,1= 1) > > To what nomenclature I am accustomed, these are seemingly mutually > exclusive. > > 2.) > > Furthermore, at the bottom of > https://www.molpro.net/info/release/doc/manual/node750.html , there is a > statement which I find peculiar. It reads: > > "This means that if Hartree-Fock wave functions are used for monomer, the > following quantity is obtained (zero in superscript denotes that no > intramonomer correlation is accounted for) [1]." > > The reference of [1] presumably refers to the one given in the previous > slide, referring to Chem. Rev. 94, 1887, published 1994 by Jeziorski, > Szalewicz, and Moszynski. I do not see that this paper defines the second > superscript index as meaning no intramonomer correlation effects. Rather, > the paper does not use the double superscript notation at all. > > To me, relative to my potentially flawed understanding of SAPT, the > meaning of the second superscript follows from what I wrote previously. > > Can someone clarify this notation difference? > --0000000000005749550587eda143 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Robert,

Your first link refers to SAPT, or as represented in psi4's &quo= t;manual", SAPT(HF). The second link refers to SAPT(DFT). Although bot= h methods are similar, they have their own "peculiarities" includ= ing their notation. This is outlined in A. J. Stone's book (theory of i= ntermolecular forces) in chapter 6, but you might find a more in depth expl= anation consulting the original works by Szalewicz on SAPT and by Misquitta= on SAPT(DFT).

Best regards,

Vitor =C2=A0H. Paschoal,
https://o= rcid.org/0000-0002-0935-3772
PhD= Candidate at the Molecular Spectroscopy Laboratory-LEM,
<= font size=3D"1" face=3D"times new roman, new york, times, serif">Chemistry = Institute,=C2=A0
University of S=C3=A3o P= aulo
Av. Prof. Lineu Prestes, 748 - Butant=C3=A3 - S=C3=A3o Paulo S= P, Brazil
+55 11 3091-3853

On Thu, May 2, 2019 at 5:13 PM Robert Molt rwmolt07=3Dgmail.com <owner-chemistry]=[ccl.net>= wrote:
=20 =20 =20
I am confused by the notation used in the Molpro manual for SAPT expansions. There are seemingly contradictions, caveated with the fact that I am a neophyte with Molpro.

1.)=C2=A0

On=C2=A0https://www.molpro.net/info/release/doc/man= ual/node750.html=C2=A0, the SAPT expansion is defined with performing E10 (pol), E10(exch), E20(ind), etc.

On=C2=A0https://www.molpro.net/info/release/doc/man= ual/node762.html=C2=A0, the SAPT expansion is defined with respect to E1(pol), E1(exch), etc. This would imply NOT just the zero term.

I am used to the notation that
E1(pol)=3D sum over n=3D0, m=3D0, of Epol (i,nm)=3D E(1,01)+E(1,10)+E(1,11)

To what nomenclature I am accustomed, these are seemingly mutually exclusive.

2.)=C2=A0

Furthermore, at the bottom of=C2=A0https://www.molp= ro.net/info/release/doc/manual/node750.html=C2=A0, there is a statement which I find peculiar. It reads:

"This means that if Hartree-Fock wave functions are used for monomer, the following quantity is obtained (zero in superscript denotes that no intramonomer correlation is accounted for) [1]."

The reference of [1] presumably refers to the one given in the previous slide, referring to Chem. Rev. 94, 1887, published 1994 by Jeziorski, Szalewicz, and Moszynski. I do not see that this paper defines the second superscript index as meaning no intramonomer correlation effects. Rather, the paper=C2=A0 does not use the double superscrip= t notation at all.

To me, relative to my potentially flawed understanding of SAPT, the meaning of the second superscript follows from what I wrote previously.

Can someone clarify this notation difference?
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