From owner-chemistry@ccl.net Fri Jun 16 09:59:01 2017 From: "KARTHICK Neelamegam Kannan nkkarthick1021-#-gmail.com" To: CCL Subject: CCL:G: clarification -input methods to study the dispersion interactions Message-Id: <-52849-170616014751-22768-+pru4QUvyy939xBuOOOiAQ-$-server.ccl.net> X-Original-From: "KARTHICK Neelamegam Kannan" Date: Fri, 16 Jun 2017 01:47:50 -0400 Sent to CCL by: "KARTHICK Neelamegam Kannan" [nkkarthick1021~~gmail.com] Hello, I am a research scholar working on Chemical Physics. I use Density Functional Theory to study the weak molecular interactions. I am using Gaussian09W program for simulating the molecular complexes. Can you please provide me information regarding the identification of dispersion interactions in optimized molecular complexes? Moreover please help me by providing the input methods or keywords in Gaussian programme which is required for studying the dispersion interactions. Because one of my papers got rejected recently, in which i had employed B3LYP methods . The reviewer commented me that B3LYP method is not appropriate to study the dispersion interactions. So Kindly help me on how to study the dispersion interactions in molecular complexes using Gaussian programme. Regards, N. K. Karthick Research Scholar Department of Physics Thiagarajar College Madurai Tamilnadu India e mail id nkkarthick1021 at gmail dot com From owner-chemistry@ccl.net Fri Jun 16 10:34:01 2017 From: "Nico Grimblat nicogreen6 ~ gmail.com" To: CCL Subject: CCL: MM RMSD Message-Id: <-52850-170616053945-11501-YkknMEewDyZPW6jpnkk+Ag/./server.ccl.net> X-Original-From: "Nico Grimblat" Date: Fri, 16 Jun 2017 05:39:44 -0400 Sent to CCL by: "Nico Grimblat" [nicogreen6]![gmail.com] Dear all, I'm working with organic molecules performing conformational searches with tinker employing MMFF and MM3 with dielectric constant 80 to avoid hydrogen bonds. This generates a lot of conformations, including some that the only difference is a 60 variation of a H of an hydroxy group. Since I will be performing DFT optimization is extremely likely that the confirmations that have such difference will be the same after optimization. Based on this idea, I was thinking in performing a RMSD comparison in order to compare by a script all molecules and remove the ones that will end up in the same optimised molecule as others. What is the cutoff that will remove this kind of conformations and be able to keep the ones that are different enough to question the geometry of the optimised molecule. Kind regards, Nico From owner-chemistry@ccl.net Fri Jun 16 12:21:01 2017 From: "Peter Jarowski peterjarowski|,|gmail.com" To: CCL Subject: CCL: MM RMSD Message-Id: <-52851-170616114952-26578-4TrzJLB8RWfRgH6qPKwOpQ- -server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary="001a11401772038ce8055215bc5b" Date: Fri, 16 Jun 2017 15:49:34 +0000 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski~!~gmail.com] --001a11401772038ce8055215bc5b Content-Type: text/plain; charset="UTF-8" Dear Nico: Your exact problem is addressed by our automation environment, ChemAlive C currently in beta. Run a few molecules through our interface: Http://www.chemslive.com/C/interfaceC.html We manage the MM conformational analysis using RDKIT and then RMSD filter. After this all confirmations are further optimized with PM6 semi-empirical level with CP2K and further RMSD filtered. These calculations are free. In the coming weeks we will be adding batch submission and DFT follow on calculation using a proprietary on-the-fly selector for the most relevant conformations at the DFT level. This will be free for a while :) Please register and let us know what you think. ChemAlive Team www.chemalive.com On Fri, 16 Jun 2017 at 16:54, Nico Grimblat nicogreen6 ~ gmail.com < owner-chemistry ~ ccl.net> wrote: > > Sent to CCL by: "Nico Grimblat" [nicogreen6]![gmail.com] > Dear all, > > I'm working with organic molecules performing conformational searches with > tinker employing MMFF and > MM3 with dielectric constant 80 to avoid hydrogen bonds. > This generates a lot of conformations, including some that the only > difference is a 60 variation of a H of > an hydroxy group. > Since I will be performing DFT optimization is extremely likely that the > confirmations that have such > difference will be the same after optimization. > Based on this idea, I was thinking in performing a RMSD comparison in > order to compare by a script > all molecules and remove the ones that will end up in the same optimised > molecule as others. > What is the cutoff that will remove this kind of conformations and be able > to keep the ones that are > different enough to question the geometry of the optimised molecule. > > Kind regards, > > Nico> > > --001a11401772038ce8055215bc5b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Nico:=C2=A0

Your exact problem is addressed by our automation environme= nt, ChemAlive C currently in beta.=C2=A0

<= div dir=3D"auto">=C2=A0Run a few molecules through our interface:
<= div dir=3D"auto">
We manage the MM conformationa= l analysis using RDKIT and then RMSD filter. After this all confirmations a= re further optimized with PM6 semi-empirical level with CP2K and further RM= SD filtered.=C2=A0

These= calculations are free.

= In the coming weeks we will be adding batch submission and DFT follow on ca= lculation using a proprietary on-the-fly selector for the most relevant con= formations at the DFT level.

This will be free for a while :)

Please register and let us know what you think.

ChemAlive Team

On Fri, 16 Jun 2017 at 16:54, Nico Grimblat nicog= reen6 ~ gmail.com <owner-chemistry ~ ccl.net> wrote:

Sent to CCL by: "Nico=C2=A0 Grimblat" [nicogreen6]![gmail.com]
Dear all,

I'm working with organic molecules performing conformational searches w= ith tinker employing MMFF and
MM3 with dielectric constant 80 to avoid hydrogen bonds.
This generates a lot of conformations, including some that the only differe= nce is a 60 variation of a H of
an hydroxy group.
Since I will be performing DFT optimization is extremely likely that the co= nfirmations that have such
difference will be the same after optimization.
Based on this idea, I was thinking in performing a RMSD comparison in order= to compare by a script
all molecules and remove the ones that will end up in the same optimised mo= lecule as others.
What is the cutoff that will remove this kind of conformations and be able = to keep the ones that are
different enough to question the geometry of the optimised molecule.

Kind regards,

Nico



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--001a11401772038ce8055215bc5b-- From owner-chemistry@ccl.net Fri Jun 16 12:56:00 2017 From: "Michel Petitjean petitjean.chiral-*-gmail.com" To: CCL Subject: CCL: MM RMSD Message-Id: <-52852-170616122322-6884-fbewr/jwGETcj4/FGzizEQ^^^server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset="UTF-8" Date: Fri, 16 Jun 2017 18:23:16 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral*gmail.com] Pls. have a look at the DIVCF software: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html It clusters the conformers and exhibits the "mean" conformer within each cluster. The number of clusters is computed from the input data. No cut-off is needed. Best regards, Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral- -gmail.com (preferred), michel.petitjean- -univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2017-06-16 11:39 GMT+02:00 Nico Grimblat nicogreen6 ~ gmail.com : > Sent to CCL by: "Nico Grimblat" [nicogreen6]![gmail.com] > Dear all, > > I'm working with organic molecules performing conformational searches with tinker employing MMFF and MM3 with dielectric constant 80 to avoid hydrogen bonds. > This generates a lot of conformations, including some that the only difference is a 60 variation of a H of an hydroxy group. > Since I will be performing DFT optimization is extremely likely that the confirmations that have such difference will be the same after optimization. > Based on this idea, I was thinking in performing a RMSD comparison in order to compare by a script all molecules and remove the ones that will end up in the same optimised molecule as others. > What is the cutoff that will remove this kind of conformations and be able to keep the ones that are different enough to question the geometry of the optimised molecule. > > Kind regards, > > Nico From owner-chemistry@ccl.net Fri Jun 16 15:55:00 2017 From: "Rodriguez, Jorge H jhrodrig::purdue.edu" To: CCL Subject: CCL:G: clarification -input methods to study the dispersion interactions Message-Id: <-52853-170616130200-23614-9aI+TdHefOa3avoPRmHMNQ:-:server.ccl.net> X-Original-From: "Rodriguez, Jorge H" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 16 Jun 2017 17:01:44 +0000 MIME-Version: 1.0 Sent to CCL by: "Rodriguez, Jorge H" [jhrodrig\a/purdue.edu] Dear N. K. Your reviewer is correct pointing out the inability of B3LYP to accurately capture the subtle effects of "dispersion". You can take a look at our paper/methodology which explicitly introduces empirical corrections for B3LYP, namely what we called the B3LYP-DD methodology. Here DD indicates that such empirical correction ""is achieved by optimizing parameters that moderate the empirical correction by explicit comparison of density functional (B3LYP) energies with distance-dependent (DD) reference values obtained at the CCSD(T)/CBS limit."" Reference: "Correction to DFT interaction energies by an empirical dispersion term valid for a range of intermolecular distances" [Deligkaris & Rodriguez, Phys. Chem. Chem. Phys., 2012,14, 3414-3424] Best wishes, ______________________________________________ Jorge H. Rodriguez Associate Professor Computational Biomolecular & Mesoscopic Physics Group Department of Physics Purdue University West Lafayette, IN 47907 URL: http://www.physics.purdue.edu/biomolecular_physics/ ________________________________________ > From: owner-chemistry+jhrodrig==purdue.edu%ccl.net on behalf of KARTHICK Neelamegam Kannan nkkarthick1021-#-gmail.com Sent: Friday, June 16, 2017 1:47 AM To: Rodriguez, Jorge H Subject: CCL:G: clarification -input methods to study the dispersion interactions Sent to CCL by: "KARTHICK Neelamegam Kannan" [nkkarthick1021~~gmail.com] Hello, I am a research scholar working on Chemical Physics. I use Density Functional Theory to study the weak molecular interactions. I am using Gaussian09W program for simulating the molecular complexes. Can you please provide me information regarding the identification of dispersion interactions in optimized molecular complexes? Moreover please help me by providing the input methods or keywords in Gaussian programme which is required for studying the dispersion interactions. Because one of my papers got rejected recently, in which i had employed B3LYP methods . The reviewer commented me that B3LYP method is not appropriate to study the dispersion interactions. So Kindly help me on how to study the dispersion interactions in molecular complexes using Gaussian programme. Regards, N. K. Karthick Research Scholar Department of Physics Thiagarajar College Madurai Tamilnadu India e mail id nkkarthick1021 at gmail dot com From owner-chemistry@ccl.net Fri Jun 16 16:30:01 2017 From: "David Shobe avidshobe*yahoo.com" To: CCL Subject: CCL:G: clarification -input methods to study the dispersion interactions Message-Id: <-52854-170616134400-15474-BZ3ZruyQLjACxJ1vDIoyRw+/-server.ccl.net> X-Original-From: David Shobe Content-Type: multipart/alternative; boundary="----=_Part_14419029_194096939.1497634793414" Date: Fri, 16 Jun 2017 17:39:53 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: David Shobe [avidshobe]*[yahoo.com] ------=_Part_14419029_194096939.1497634793414 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable N.K.-- I suppose a literature search for "(density functional or dft) and dispersi= on" gives too many answers to be useful, but maybe just randomly pick a few= recent papers and see what density functionals they used?=C2=A0 Don't use = Google, but something that knows what and and or mean.=C2=A0 Hopefully your= university has a suitable literature database. --David Shobe =20 On Friday, June 16, 2017 11:20 AM, KARTHICK Neelamegam Kannan nkkarthic= k1021-#-gmail.com wrote: =20 =20 Sent to CCL by: "KARTHICK Neelamegam Kannan" [nkkarthick1021~~gmail.com] Hello, =C2=A0 I am a research scholar working on Chemical Physics. I use Density= =20 Functional Theory to study the weak molecular interactions. I am using=20 Gaussian09W program for simulating the molecular complexes. Can you please= =20 provide me information regarding the identification of dispersion=20 interactions in optimized molecular complexes? Moreover please help me by= =20 providing the input methods or keywords in Gaussian programme which is=20 required for studying the dispersion interactions. Because one of my papers= =20 got rejected recently, in which i had employed B3LYP methods . The reviewer= =20 commented me that B3LYP method is not appropriate to study the dispersion= =20 interactions. So Kindly help me on how to study the dispersion interactions= =20 in molecular complexes using Gaussian programme.=20 Regards, N. K. Karthick Research Scholar Department of Physics Thiagarajar College Madurai Tamilnadu India e mail id=C2=A0 nkkarthick1021 at gmail dot com -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0=20 ------=_Part_14419029_194096939.1497634793414 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
N.K.--
<= div id=3D"yui_3_16_0_ym19_1_1497632241350_26318">
I suppose a literature search for "(densi= ty functional or dft) and dispersion" gives too many answers to be useful, = but maybe just randomly pick a few recent papers and see what density funct= ionals they used?  Don't use Google, but something that knows what and= and or mean.  Hopefully your university has a suitable literature dat= abase.

--David Shobe



On Fri= day, June 16, 2017 11:20 AM, KARTHICK Neelamegam Kannan nkkarthick1021-#-gm= ail.com <owner-chemistry]*[ccl.net> wrote:


<= div class=3D"y_msg_container">

S= ent to CCL by: "KARTHICK Neelamegam Kannan" [nkkarthick1021~~gmail.com]
=
Hello,
  I am a rese= arch scholar working on Chemical Physics. I use Density
Functional Theory to study the weak molecular interactions. I am u= sing
Gaussian09W program for simulating the mole= cular complexes. Can you please
provide me infor= mation regarding the identification of dispersion
interactions in optimized molecular complexes? Moreover please help me by=
providing the input methods or keywords in Gaus= sian programme which is
required for studying th= e dispersion interactions. Because one of my papers
got rejected recently, in which i had employed B3LYP methods . The revi= ewer
commented me that B3LYP method is not appro= priate to study the dispersion
interactions. So = Kindly help me on how to study the dispersion interactions
in molecular complexes using Gaussian programme.

Regards,
N= . K. Karthick
Research Scholar
Department of Physics
Thiagarajar Colleg= e
Madurai
Tamilnadu
=
India
e mail id  nkka= rthick1021 at gmail dot com



-=3D This is au= tomatically added to each message by the mailing script =3D-
To recover the email address of the author of the message, plea= se change
the strange characters on the top line = to the ]*[ sign. You can also
look up the X-Origina= l-From: line in the mail header.

E-mail to subscribers: CHEMISTRY]*[ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_c= cl_message

------=_Part_14419029_194096939.1497634793414-- From owner-chemistry@ccl.net Fri Jun 16 19:41:00 2017 From: "saied soliman saied1soliman]^[yahoo.com" To: CCL Subject: CCL:G: clarification -input methods to study the dispersion interactions Message-Id: <-52855-170616184046-10182-4zD1IvDnHVA7hXWtGT4Xhw+/-server.ccl.net> X-Original-From: saied soliman Content-Type: multipart/alternative; boundary="----=_Part_14677356_1097172952.1497652836329" Date: Fri, 16 Jun 2017 22:40:36 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: saied soliman [saied1soliman*_*yahoo.com] ------=_Part_14677356_1097172952.1497652836329 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Gaussian 09 help contain many default functionals with dispersion correctio= ns such as wb97xd, B97D, ---. May be using one of these methods with a prop= er basis set seems enough for your system.Good luckSaied=20 On Saturday, June 17, 2017 12:19 AM, David Shobe avidshobe*yahoo.com wrote: =20 N.K.-- I suppose a literature search for "(density functional or dft) and dispersi= on" gives too many answers to be useful, but maybe just randomly pick a few= recent papers and see what density functionals they used?=C2=A0 Don't use = Google, but something that knows what and and or mean.=C2=A0 Hopefully your= university has a suitable literature database. --David Shobe =20 On Friday, June 16, 2017 11:20 AM, KARTHICK Neelamegam Kannan nkkarthic= k1021-#-gmail.com wrote: =20 =20 Sent to CCL by: "KARTHICK Neelamegam Kannan" [nkkarthick1021~~gmail.com] Hello, =C2=A0 I am a research scholar working on Chemical Physics. I use Density= =20 Functional Theory to study the weak molecular interactions. I am using=20 Gaussian09W program for simulating the molecular complexes. Can you please= =20 provide me information regarding the identification of dispersion=20 interactions in optimized molecular complexes? Moreover please help me by= =20 providing the input methods or keywords in Gaussian programme which is=20 required for studying the dispersion interactions. Because one of my papers= =20 got rejected recently, in which i had employed B3LYP methods . The reviewer= =20 commented me that B3LYP method is not appropriate to study the dispersion= =20 interactions. So Kindly help me on how to study the dispersion interactions= =20 in molecular complexes using Gaussian programme.=20 Regards, N. K. Karthick Research Scholar Department of Physics Thiagarajar College Madurai Tamilnadu India e mail id=C2=A0 nkkarthick1021 at gmail dot com -=3D This is automatically added to each message by the mailing script =3D-the strange characters on the top line to the ]|[ sign. You can alsoE-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=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0=20 =20 ------=_Part_14677356_1097172952.1497652836329 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Gaussian 09 help contain many default functionals with dispersion co= rrections such as wb97xd, B97D, ---. May be using one of these methods with= a proper basis set seems enough for your system.
Good luck
Saied


On Saturday, June 17, 2017 12:19 AM, = David Shobe avidshobe*yahoo.com <owner-chemistry/./ccl.net> wrote:
<= /font>


N.K.--

I suppose a litera= ture search for "(density functional or dft) and dispersion" gives too many= answers to be useful, but maybe just randomly pick a few recent papers and= see what density functionals they used?  Don't use Google, but someth= ing that knows what and and or mean.  Hopefully your university has a = suitable literature database.

--David Shobe
<= div>


On Friday, June 16, 2017 11:20 AM, KA= RTHICK Neelamegam Kannan nkkarthick1021-#-gmail.com <owner-chemistry]|[c= cl.net> wrote:



Sent to CCL by: "= KARTHICK Neelamegam Kannan" [nkkarthick1021~~gmail.com]
Hello,
  I am a research scholar w= orking on Chemical Physics. I use Density
Functi= onal Theory to study the weak molecular interactions. I am using
=
Gaussian09W program for simulating the molecular complexes= . Can you please
provide me information regardin= g the identification of dispersion
interactions = in optimized molecular complexes? Moreover please help me by
providing the input methods or keywords in Gaussian programme = which is
required for studying the dispersion in= teractions. Because one of my papers
got rejecte= d recently, in which i had employed B3LYP methods . The reviewer
=
commented me that B3LYP method is not appropriate to study= the dispersion
interactions. So Kindly help me = on how to study the dispersion interactions
in m= olecular complexes using Gaussian programme.
Regards,
N. K. Karthick
Research Scholar
Departm= ent of Physics
Thiagarajar College
Madurai
Tamilnadu
India
e mail id  nkkarthick1021 at = gmail dot com



-=3D This is automatically ad= ded to each message by the mailing script =3D-
To= recover the email address of the author of the message, please change
<= /div>
the strange characters on the top line to the ]|[ sig= n. You can also
look up the X-Original-From: line= in the mail header.

E= -mail to subscribers: CHEMISTRY]|[ccl= .net or use:

E-mail to administrators: CHEMISTRY-REQUEST]|[ccl.net= or use
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Before posting, check wait time = at: http= ://www.ccl.net



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