From owner-chemistry@ccl.net Thu Jun 5 09:23:00 2014 From: "Pierre Archirel pierre.archirel .. u-psud.fr" To: CCL Subject: CCL: TDDFT for organic cations Message-Id: <-50169-140605090924-11931-XA2paLI/m9kvG7tlGdeNdg-*-server.ccl.net> X-Original-From: "Pierre Archirel" Date: Thu, 5 Jun 2014 09:09:23 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel===u-psud.fr] Dear colleagues, I have calculated the UV-visible absorption spectrum of an organic (conjugated) molecule and its cation, both in solution in water. I have used TDDFT and B3LYP. The spectrum of the neutral fits rather well with the measured spectrum. The spectrum of the cation has not been measured, but I suspect that my calculated spectrum is poor, because of a large spin contamination in the excited states, and also because of a (weak) absorption at 2000 nm, due to a flip flop of beta spinorbitals. Is TDDFT doubtfull for organic cations, or B3LYP? Is there articles on this issue? Many thanks in advance, P. Archirel LCP Orsay France pierre.archirel::u-psud.fr From owner-chemistry@ccl.net Thu Jun 5 11:55:00 2014 From: "singh singh^_^yamanashi.ac.jp" To: CCL Subject: CCL: TDDFT for organic cations Message-Id: <-50170-140605115353-10418-ESZT2ZcAMNC+6f6mVT3d/w=server.ccl.net> X-Original-From: singh Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 5 Jun 2014 15:53:41 +0000 MIME-Version: 1.0 Sent to CCL by: singh [singh.(~).yamanashi.ac.jp] Please use LC-DFT (for example- LC-BLYP) for the TDDFT computation. B3LYP discourages. Regards-Raman ________________________________________ > From: owner-chemistry+singh==yamanashi.ac.jp(~)ccl.net on behalf of Pierre Archirel pierre.archirel .. u-psud.fr Sent: Thursday, June 5, 2014 10:09 PM To: singh Subject: CCL: TDDFT for organic cations Sent to CCL by: "Pierre Archirel" [pierre.archirel===u-psud.fr] Dear colleagues, I have calculated the UV-visible absorption spectrum of an organic (conjugated) molecule and its cation, both in solution in water. I have used TDDFT and B3LYP. The spectrum of the neutral fits rather well with the measured spectrum. The spectrum of the cation has not been measured, but I suspect that my calculated spectrum is poor, because of a large spin contamination in the excited states, and also because of a (weak) absorption at 2000 nm, due to a flip flop of beta spinorbitals. Is TDDFT doubtfull for organic cations, or B3LYP? Is there articles on this issue? Many thanks in advance, P. Archirel LCP Orsay France pierre.archirel::u-psud.frhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jun 5 14:44:01 2014 From: "Partha Sengupta anapspsmo(~)gmail.com" To: CCL Subject: CCL: drawing tools of ribbon structure (secondary) of protein for Amber calculation Message-Id: <-50171-140605132857-8568-lpRQCuaQAG0QhC413CUmYA[]server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=089e014947b42492cd04fb1a1431 Date: Thu, 5 Jun 2014 22:58:52 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo#gmail.com] --089e014947b42492cd04fb1a1431 Content-Type: text/plain; charset=UTF-8 Friends, I want to calculate the interaction of some protein fragments with one or two biomolecules by Density Functional Theory and MM/QM methods. Let the protein fragment are Ala 321, Met 274, and Asp 272 have been used as reaction center. Now how can I draw the ribbon structure creating the link between the amino acids (link between Ala 321with Met 274 and Asp 272) showing secondary structure for DFT and MM/QM calculation? Is there any free software ? Waiting for your response Partha -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --089e014947b42492cd04fb1a1431 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Friends, I want to calculate the interaction of = some protein fragments with one or two biomolecules by Density Functional T= heory and=C2=A0 MM/QM methods. Let the prote= in=C2=A0 fragment are=C2=A0 Ala 321, Met 274, and Asp 272 have been used as reaction center. = Now how can I draw the ribbon structure creating the link between=C2=A0the amino acids (link between Ala 321with Met 2= 74 and Asp 272)=C2=A0 =C2=A0 showing secondary structure for DFT an= d MM/QM calculation?=C2=A0 Is there any free software ?
Waiting for your response
Partha

--
Dr. Partha Sarathi Sengupta
Associate P= rofessor
Vivekananda Mahavidyalaya, Burdwan
--089e014947b42492cd04fb1a1431-- From owner-chemistry@ccl.net Thu Jun 5 15:19:00 2014 From: "Ulrike Salzner salzner a gmail.com" To: CCL Subject: CCL: TDDFT for organic cations Message-Id: <-50172-140605103702-7712-v6xXTkHzr5CdUy2eDZ1Kiw|-|server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary=001a11c2c5a6fb5a6804fb17acf2 Date: Thu, 5 Jun 2014 17:36:51 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner*|*gmail.com] --001a11c2c5a6fb5a6804fb17acf2 Content-Type: text/plain; charset=UTF-8 Dear Pierre, I have investigated spectra of conjugated radicals with hybrid functionals and the results looked always reasonable. I found spin contamination mainly for alpha excitations and very little for beta. I am enclosing some references: JPCA 2007, 3, 1143 JPCA 2008, 112, 5458 JPCA 2010, 114, 10997 JCTC 2011, 7 2568 Greetings, Ulrike On Thu, Jun 5, 2014 at 4:09 PM, Pierre Archirel pierre.archirel .. u-psud.fr wrote: > > Sent to CCL by: "Pierre Archirel" [pierre.archirel===u-psud.fr] > Dear colleagues, > I have calculated the UV-visible absorption spectrum of an organic > (conjugated) molecule and its cation, both in solution in water. > I have used TDDFT and B3LYP. > > The spectrum of the neutral fits rather well with the measured spectrum. > The spectrum of the cation has not been measured, but I suspect that my > calculated spectrum is poor, because of a large spin contamination in the > excited states, and also because of a (weak) absorption at 2000 nm, due to > a flip flop of beta spinorbitals. > > Is TDDFT doubtfull for organic cations, or B3LYP? > Is there articles on this issue? > Many thanks in advance, > P. Archirel > LCP Orsay France > pierre.archirel::u-psud.fr> > > -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara --001a11c2c5a6fb5a6804fb17acf2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Pierre,
I= have investigated spectra of conjugated radicals with hybrid functionals a= nd the results looked always reasonable. I found spin contamination mainly = for alpha excitations and very little for beta. I am enclosing some referen= ces:
JPCA 2007, 3, 1143
JPCA 2008, 112, 5458
JPCA 2010, = 114, 10997
JCTC 2011, 7 2568

Greetings,
Ulri= ke


O= n Thu, Jun 5, 2014 at 4:09 PM, Pierre Archirel pierre.archirel .. u-psud.fr <owner-chemistry:ccl.net>= wrote:

Sent to CCL by: "Pierre =C2=A0Archirel" [pierre.archirel=3D=3D=3D= u-psud.fr]
Dear colleagues,
I have calculated the UV-visible absorption spectrum of an organic (conjuga= ted) molecule and its cation, both in solution in water.
I have used TDDFT and B3LYP.

The spectrum of the neutral fits rather well with the measured spectrum. The spectrum of the cation has not been measured, but I suspect that my cal= culated spectrum is poor, because of a large spin contamination in the exci= ted states, and also because of a (weak) absorption at 2000 nm, due to a fl= ip flop of beta spinorbitals.

Is TDDFT doubtfull for organic cations, or B3LYP?
Is there articles on this issue?
Many thanks in advance,
P. Archirel
LCP Orsay France
pierre.archirel::u-psud.fr



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--
Assoc. Prof. Ulrike Sal= zner
Department of Chemistry
Bilkent University
06800 Bilkent, Ank= ara
--001a11c2c5a6fb5a6804fb17acf2-- From owner-chemistry@ccl.net Thu Jun 5 16:40:00 2014 From: "David A Case case~~biomaps.rutgers.edu" To: CCL Subject: CCL: pdb curation, standardization for MM calculations? Message-Id: <-50173-140604145446-25329-643ytHOW4tC3a6kk8RD7ag * server.ccl.net> X-Original-From: David A Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 4 Jun 2014 19:54:38 +0100 MIME-Version: 1.0 Sent to CCL by: David A Case [case ~~ biomaps.rutgers.edu] > On Wed, 2014-06-04 at 08:25 -0600, Matt Challacombe wrote: > > > > I have somewhat unconventional pdb files, eg from neutron calculations, > > involving D instead of H and etc. Are there simple scripts available to > > clean up a pbd for these sorts of non-standard differences (ie make > > recognizable for force field calculations)? For a lot of these sorts of thing, I use the simple perl script below. This parses ATOM/HETATM cards, allowing you to make any modifcations you want, then writes them back out. Records other than ATOM/HETATM are passed through unchanged. This is especially useful for "one-off" conversions, or unusual changes that would not pre-programmed in other packages (e.g. the need to change residue numbers, add TER cards, put some other info into the b-factor column, etc.etc.) Reads a pdb file on stdin, writes out the modified version on stdout. YMMV...dave case ----------------------------------------------------------------------------- #!/usr/bin/env perl -n # # first, read in a pdb file line and unpack # if( $_ =~ /^ATOM|^HETATM/){ ( $label $atno, $atname, $alt, $resname, $chainId, $resno, $iCode, $x, $y, $z, $occ, $bfact, $element, $charge ) = unpack("a6 x a4 x a4 a a3 x a a4 a x3 a8 a8 a8 a6 a6 x10 a2 a2",$_); # # do modifications necessary here: # # # write back out # printf "%6s %4s %-4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s\n", $label, $atno,$atname,$alt, $resname,$chainId, $resno, $iCode, $x,$y,$z, $occ, $bfact, $element, $charge; } else { print; } ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Jun 5 17:59:00 2014 From: "Partha Sengupta anapspsmo=-=gmail.com" To: CCL Subject: CCL: CYP2B4 Message-Id: <-50174-140605133944-9650-GNor3OvCB0AJzpnE4p0KDw^-^server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=047d7bd7526a9fbd4004fb1a3aca Date: Thu, 5 Jun 2014 23:09:38 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo- -gmail.com] --047d7bd7526a9fbd4004fb1a3aca Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Sir, Is there any free software for drawing of ribbon structure of protein for DFT and QM/MM study using AMBER/ othe quantum mechanical calculation? Is there any free software? Regards, Partha On Fri, May 23, 2014 at 12:00 AM, brupalf brupalf:umich.edu < owner-chemistry-,-ccl.net> wrote: > Yes: > Danni L. Harris, > Jin-Young Park, > Larry Gruenke and > Lucy Waskell (2004) "Theoretical study of the ligand=E2=80=93CYP2B4 compl= exes: > Effect of structure on binding free energies and heme spin state", > Proteins, 55, 895 - 914 > > ciao, > Bruce > > Bruce A. Palfey > Associate Professor of Biological Chemistry & > Associate Director, Program in Chemical Biology > Department of Biological Chemistry > University of Michigan Medical School > 5220E MSRB III > 1150 W. Medical Center Drive > Ann Arbor, MI 48109-0606 > (734) 615-2452 > brupalf(a)umich.edu > > http://www.biochem.med.umich.edu/?q=3Dpalfey > http://www.chembio.umich.edu/people/palfey.html > http://tinyurl.com/webzyme > > > > On May 22, 2014, at 11:11 AM, "Partha Sengupta anapspsmo|gmail.com" < > owner-chemistry(a)ccl.net> wrote: > > Dear Friends, Is it possible to model Cytochrome 450, CYP2B4 for DFT > calculation? > Help. > Partha Sarathi Sengupta > > -- > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan > > > --=20 Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --047d7bd7526a9fbd4004fb1a3aca Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Sir, Is there any free software for drawing of ribbon= structure of protein for DFT and QM/MM study using AMBER/ othe quantum mec= hanical calculation? Is there any free software?
Regards,
=C2= =A0Partha


On Fri, May 2= 3, 2014 at 12:00 AM, brupalf brupalf:umich.edu= <owner-chemistry-,-ccl.net> wrote:
Yes= : =C2=A0
  • Danni L. Harris,=C2=A0
  • Jin-Young Park,=C2=A0
  • Larry Gruenke=C2=A0and
  • Lucy Waskell (2004)
    • "Theoretical study o= f the ligand=E2=80=93CYP2B4 complexes: Effect of structure on binding free = energies and heme spin state", Proteins, 55, 895 - 914

    ciao,
    Bruce

    Bruce A. Palfey
    Associate Professor=C2=A0of Biological Chemistry= =C2=A0&
    Associate Director, Program in Chemical Biolo= gy
    Department of Biological Chemistry
    University of Michigan Medical = School
    5220E MSRB III
    1150 W. Medical Center Drive
    Ann Arbor, MI 4= 8109-0606
    (734) 615-2452
    = brupalf(a)umich.edu

    http://www.biochem.med.umich.edu/?q=3Dpalfey=
    http://www.chembio.umich.edu/people/palfey.html



    On May 22, 2014, at 11:11 AM, "Partha Sengupta anapspsmo= |gmail.com" <owner-chemistry= (a)ccl.net> wrote:

    Dear Friends, Is i= t possible to model Cytochrome 450, CYP2B4 for DFT calculation?
    Help.
    Partha Sarathi Sengupta

    --
    Dr. Partha Sarathi Sengupta
    Associate ProfessorVivekananda Mahavidyalaya, Burdwan




    --
    Dr. Partha Sarathi Sengupta
    Associate Professor
    Vivekanan= da Mahavidyalaya, Burdwan
    --047d7bd7526a9fbd4004fb1a3aca-- From owner-chemistry@ccl.net Thu Jun 5 18:34:00 2014 From: "Jason Swails jason.swails*gmail.com" To: CCL Subject: CCL: drawing tools of ribbon structure (secondary) of protein for Amber calculation Message-Id: <-50175-140605153618-9206-W30/KHsYu3Lb8/rvJed+Ng.@.server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=089e0122a546856e6f04fb1bdbbd Date: Thu, 5 Jun 2014 15:36:12 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [jason.swails : gmail.com] --089e0122a546856e6f04fb1bdbbd Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On Thu, Jun 5, 2014 at 1:28 PM, Partha Sengupta anapspsmo(~)gmail.com < owner-chemistry],[ccl.net> wrote: > Friends, I want to calculate the interaction of some protein fragments > with one or two biomolecules by Density Functional Theory and MM/QM > methods. Let the protein fragment are Ala 321, Met 274, and Asp 272 > have been used as reaction center. Now how can I draw the ribbon structur= e creating > the link between the amino acids (link between Ala 321with Met 274 and > Asp 272) showing secondary structure for DFT and MM/QM calculation? > Is there any free software ? > =E2=80=8BVMD. PyMol. Chimera. Several others, too, I'm sure. --=20 Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher --089e0122a546856e6f04fb1bdbbd Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

    <= /div>


    On Thu, = Jun 5, 2014 at 1:28 PM, Partha Sengupta anapspsmo(~)gmail.com <owner-chemistry],[ccl.net> wrote:
    Friends, I want t= o calculate the interaction of some protein fragments with one or two biomo= lecules by Density Functional Theory and=C2=A0 MM/QM methods. Let the protein=C2=A0 fragment are=C2=A0 Ala 321, Met 274, and Asp 272 have been used as reaction center. = Now how can I draw the ribbon structure creating the link between=C2=A0the amino acids (link between Ala 321with Met 2= 74 and Asp 272)=C2=A0 =C2=A0 showing secondary structure for DFT an= d MM/QM calculation?=C2=A0 Is there any free software ?

    =E2=80=8BVMD. =C2=A0PyMol. =C2=A0Chimera.= =C2=A0Several others, too, I'm sure.

    --
    Jason M. Swails
    BioMaPS,
    Rutg= ers University
    Postdoctoral Researcher
    --089e0122a546856e6f04fb1bdbbd-- From owner-chemistry@ccl.net Thu Jun 5 19:09:00 2014 From: "David Gallagher gallagher.da=-=gmail.com" To: CCL Subject: CCL: Turbomole Training, San Francisco, 13 Aug 2014 Message-Id: <-50176-140605173209-19903-Da1lRH/V6BEsWLXv7NJeOw]*[server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="------------060901060906010000020300" Date: Thu, 05 Jun 2014 14:32:18 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da[*]gmail.com] This is a multi-part message in MIME format. --------------060901060906010000020300 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit During the ACS meeting in San Francisco there will be a Turbomole hands-on training session for chemists who want to learn more about this popular quantum chemistry package and it's capabilities. No prior Turbomole experience necessary. An evaluation copy of Turbomole will be provided, but please bring your own laptop. *Time and venue:* 10am - noon, Wednesday 13th March 2014, Room 206, Moscone South (San Francisco ACS) *Registration:* The workshop is free but seats are limited so please email your registration toWorkshop-#-CACheResearch.com , and include name, affiliation, and location. URL: http://www.cacheresearch.com/aiche.html#training --------------060901060906010000020300 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit During the ACS meeting in San Francisco there will be a Turbomole hands-on training session for chemists who want to learn more about this popular quantum chemistry package and it's capabilities.  No prior Turbomole experience necessary.  An evaluation copy of Turbomole will be provided, but please bring your own laptop.

    Time and venue:
    10am - noon, Wednesday 13th March 2014,
    Room 206, Moscone South (    San Francisco ACS)

    Registration:  The workshop is free but seats are limited so please email your registration to Workshop-#-CACheResearch.com, and include name, affiliation, and location.
    URL: http://www.cacheresearch.com/aiche.html#training
     --------------060901060906010000020300-- From owner-chemistry@ccl.net Thu Jun 5 21:12:00 2014 From: "Gustavo L.C. Moura gustavo.moura*_*ufpe.br" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50177-140605183036-24726-9YFt8eIIbd3XL1X0y7xicA++server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Thu, 5 Jun 2014 18:30:34 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura=ufpe.br] Dear CCL community, I have been searching for a conformer generator program that can handle acyclic compounds (none of my molecules have flexible rings, yet). I have already tested a few programs, and so far, none has worked to my satisfaction. The program I am looking for should obey some requirements. The requirements are: 1) The program should use the RMSD of the coordinates to check for equivalent conformers. The first program that I tested employed only the energy to differentiate conformers and was unable to differentiate non-superimposable conformers that happen to have the same energy. 2) I am not overly concerned with the quality of the molecular mechanics forcefield that will be employed by the program to optimize the geometries of the conformers because I will reoptimize them with quantum chemical methods. However, I need to have a forcefield that is able to handle selenium atoms. 3) The program should be capable of generating conformers resulting from the rotation around C-OH and C-NH2 bonds. My interest is in the spectroscopic properties (UV-VIS and NMR) of my molecules and rotations around such bonds are very important to me. So, does anyone on the list know of a conformer generator program that has the characteristics above? Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura