From owner-chemistry@ccl.net Thu Jun 5 09:23:00 2014
From: "Pierre Archirel pierre.archirel .. u-psud.fr" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: TDDFT for organic cations
Message-Id: <-50169-140605090924-11931-XA2paLI/m9kvG7tlGdeNdg-*-server.ccl.net>
X-Original-From: "Pierre Archirel" <pierre.archirel|-|u-psud.fr>
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" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: TDDFT for organic cations
Message-Id: <-50170-140605115353-10418-ESZT2ZcAMNC+6f6mVT3d/w=server.ccl.net>
X-Original-From: singh <singh]~[yamanashi.ac.jp>
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 <owner-chemistry+singh==yamanashi.ac.jp(~)ccl.net> on behalf of Pierre Archirel pierre.archirel .. u-psud.fr <owner-chemistry(~)ccl.net>
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" <owner-chemistry[]server.ccl.net>
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 <anapspsmo-*-gmail.com>
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
<div dir=3D"ltr"><div><div>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 <span style=3D"font-size:12pt;line-heigh=
t:115%;font-family:"Times New Roman","serif"">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 </span><span style=3D"font-size:12p=
t;line-height:115%;font-family:"Times New Roman","serif"=
;">creating the</span><span style=3D"font-size:12pt;line-height:115%;font-f=
amily:"Times New Roman","serif""><span style=3D"font-si=
ze:12pt;line-height:115%;font-family:"Times New Roman","seri=
f""> link between=C2=A0the amino acids (link between Ala 321with Met 2=
74 and Asp 272)=C2=A0 =C2=A0 </span> showing secondary structure for DFT an=
d MM/QM calculation?=C2=A0 Is there any free software ?<br>
</span></div><span style=3D"font-size:12pt;line-height:115%;font-family:&qu=
ot;Times New Roman","serif"">Waiting for your response<br></=
span></div><span style=3D"font-size:12pt;line-height:115%;font-family:"=
;Times New Roman","serif"">Partha<br>
</span><div><div><div><br>-- <br>Dr. Partha Sarathi Sengupta<br>Associate P=
rofessor<br>Vivekananda Mahavidyalaya, Burdwan
</div></div></div></div>
--089e014947b42492cd04fb1a1431--
From owner-chemistry@ccl.net Thu Jun 5 15:19:00 2014
From: "Ulrike Salzner salzner a gmail.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: TDDFT for organic cations
Message-Id: <-50172-140605103702-7712-v6xXTkHzr5CdUy2eDZ1Kiw|-|server.ccl.net>
X-Original-From: Ulrike Salzner <salzner]-[gmail.com>
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
<owner-chemistry:ccl.net> 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
<div dir=3D"ltr"><div><div><div><div><div><div><div>Dear Pierre,<br></div>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:<br>
</div>JPCA 2007, 3, 1143<br></div>JPCA 2008, 112, 5458<br></div>JPCA 2010, =
114, 10997<br></div>JCTC 2011, 7 2568<br><br></div>Greetings,<br></div>Ulri=
ke<br></div><div class=3D"gmail_extra"><br><br><div class=3D"gmail_quote">O=
n Thu, Jun 5, 2014 at 4:09 PM, Pierre Archirel pierre.archirel .. <a href=
=3D"http://u-psud.fr">u-psud.fr</a> <span dir=3D"ltr"><<a href=3D"mailto=
:owner-chemistry:ccl.net" target=3D"_blank">owner-chemistry:ccl.net</a>>=
</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><br>
Sent to CCL by: "Pierre =C2=A0Archirel" [pierre.archirel=3D=3D=3D=
<a href=3D"http://u-psud.fr" target=3D"_blank">u-psud.fr</a>]<br>
Dear colleagues,<br>
I have calculated the UV-visible absorption spectrum of an organic (conjuga=
ted) molecule and its cation, both in solution in water.<br>
I have used TDDFT and B3LYP.<br>
<br>
The spectrum of the neutral fits rather well with the measured spectrum.<br=
>
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.<br>
<br>
Is TDDFT doubtfull for organic cations, or B3LYP?<br>
Is there articles on this issue?<br>
Many thanks in advance,<br>
P. Archirel<br>
LCP Orsay France<br>
pierre.archirel::<a href=3D"http://u-psud.fr" target=3D"_blank">u-psud.fr</=
a><br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Assoc. Prof. Ulrike Sal=
zner<br>Department of Chemistry<br>Bilkent University<br>06800 Bilkent, Ank=
ara
</div>
--001a11c2c5a6fb5a6804fb17acf2--
From owner-chemistry@ccl.net Thu Jun 5 16:40:00 2014
From: "David A Case case~~biomaps.rutgers.edu" <owner-chemistry * server.ccl.net>
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 <case%%biomaps.rutgers.edu>
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" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: CYP2B4
Message-Id: <-50174-140605133944-9650-GNor3OvCB0AJzpnE4p0KDw^-^server.ccl.net>
X-Original-From: Partha Sengupta <anapspsmo..gmail.com>
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
<div dir=3D"ltr"><div>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?<br></div>Regards,<br>=C2=
=A0Partha</div>
<div class=3D"gmail_extra"><br><br><div class=3D"gmail_quote">On Fri, May 2=
3, 2014 at 12:00 AM, brupalf brupalf:<a href=3D"http://umich.edu">umich.edu=
</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry-,-ccl.net" targe=
t=3D"_blank">owner-chemistry-,-ccl.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><div style=3D"word-wrap:break-word"><div>Yes=
: =C2=A0<li style=3D"font-family:Arial,'Lucida Grande',Geneva,Verda=
na,Helvetica,'Lucida Sans Unicode',sans-serif;margin:0px 5px 0px 0p=
x;padding:0px;border:0px;outline:0px;vertical-align:baseline;display:inline=
;line-height:1.5em;float:none">
Danni L. Harris,=C2=A0</li><li style=3D"font-family:Arial,'Lucida Grand=
e',Geneva,Verdana,Helvetica,'Lucida Sans Unicode',sans-serif;ma=
rgin:0px 5px 0px 0px;padding:0px;border:0px;outline:0px;vertical-align:base=
line;display:inline;line-height:1.5em;float:none">
Jin-Young Park,=C2=A0</li><li style=3D"font-family:Arial,'Lucida Grande=
',Geneva,Verdana,Helvetica,'Lucida Sans Unicode',sans-serif;mar=
gin:0px 5px 0px 0px;padding:0px;border:0px;outline:0px;vertical-align:basel=
ine;display:inline;line-height:1.5em;float:none">
Larry Gruenke=C2=A0and</li><li style=3D"font-family:Arial,'Lucida Grand=
e',Geneva,Verdana,Helvetica,'Lucida Sans Unicode',sans-serif;ma=
rgin:0px 5px 0px 0px;padding:0px;border:0px;outline:0px;vertical-align:base=
line;display:inline;line-height:1.5em;float:none">
Lucy Waskell (2004) </li><span style=3D"background-color:rgb(255,255,255);f=
ont-family:Arial,'Lucida Grande',Geneva,Verdana,Helvetica,'Luci=
da Sans Unicode',sans-serif;line-height:14px">"Theoretical study o=
f the ligand=E2=80=93CYP2B4 complexes: Effect of structure on binding free =
energies and heme spin state</span><span style=3D"font-family:Arial,'Lu=
cida Grande',Geneva,Verdana,Helvetica,'Lucida Sans Unicode',san=
s-serif;line-height:1.5em">", Proteins, 55, 895 - 914</span></div>
<br><div>
<div><div style=3D"font-size:12px">ciao,</div><div style=3D"font-size:12px"=
>Bruce</div><div style=3D"font-size:12px"><br></div><div style=3D"font-size=
:12px">Bruce A. Palfey<br>Associate Professor=C2=A0of Biological Chemistry=
=C2=A0&</div>
<div style=3D"font-size:12px">Associate Director, Program in Chemical Biolo=
gy<br>Department of Biological Chemistry<br>University of Michigan Medical =
School<br>5220E MSRB III<br>1150 W. Medical Center Drive<br>Ann Arbor, MI 4=
8109-0606<br>
(734) 615-2452<br><a href=3D"mailto:brupalf(a)umich.edu" target=3D"_blank">=
brupalf(a)umich.edu</a><br><br><a href=3D"http://www.biochem.med.umich.edu/=
?q=3Dpalfey" target=3D"_blank">http://www.biochem.med.umich.edu/?q=3Dpalfey=
</a><br>
<a href=3D"http://www.chembio.umich.edu/people/palfey.html" target=3D"_blan=
k">http://www.chembio.umich.edu/people/palfey.html</a><br></div><div style=
=3D"font-size:12px"><a href=3D"http://tinyurl.com/webzyme" target=3D"_blank=
">http://tinyurl.com/webzyme</a></div>
</div><div><br></div><br>
</div><div class=3D"">
<br><div><div>On May 22, 2014, at 11:11 AM, "Partha Sengupta anapspsmo=
|<a href=3D"http://gmail.com" target=3D"_blank">gmail.com</a>" <<a =
href=3D"mailto:owner-chemistry(a)ccl.net" target=3D"_blank">owner-chemistry=
(a)ccl.net</a>> wrote:</div>
<br><blockquote type=3D"cite"><div dir=3D"ltr"><div><div>Dear Friends, Is i=
t possible to model Cytochrome 450, <span style=3D"font-size:10pt;line-heig=
ht:115%;font-family:Tahoma,sans-serif">CYP2B4 for DFT calculation?<br>
</span></div><span style=3D"font-size:10pt;line-height:115%;font-family:Tah=
oma,sans-serif">Help.<br></span></div><span style=3D"font-size:10pt;line-he=
ight:115%;font-family:Tahoma,sans-serif">Partha Sarathi Sengupta<br>
</span><div><br>-- <br>Dr. Partha Sarathi Sengupta<br>Associate Professor<b=
r>Vivekananda Mahavidyalaya, Burdwan
</div></div>
</blockquote></div><br></div></div></blockquote></div><br><br clear=3D"all"=
><br>-- <br>Dr. Partha Sarathi Sengupta<br>Associate Professor<br>Vivekanan=
da Mahavidyalaya, Burdwan
</div>
--047d7bd7526a9fbd4004fb1a3aca--
From owner-chemistry@ccl.net Thu Jun 5 18:34:00 2014
From: "Jason Swails jason.swails*gmail.com" <owner-chemistry.@.server.ccl.net>
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 <jason.swails _ gmail.com>
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]
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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
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<div dir=3D"ltr"><div class=3D"gmail_default" style=3D"color:#000000"><br><=
/div><div class=3D"gmail_extra"><br><br><div class=3D"gmail_quote">On Thu, =
Jun 5, 2014 at 1:28 PM, Partha Sengupta anapspsmo(~)<a href=3D"http://gmail=
.com">gmail.com</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry=
],[ccl.net" target=3D"_blank">owner-chemistry],[ccl.net</a>></span> wrote:<b=
r>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><div dir=3D"ltr"><div><div>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 <span sty=
le=3D"font-size:12pt;line-height:115%;font-family:"Times New Roman&quo=
t;,"serif"">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 </span><span style=3D"font-size:12p=
t;line-height:115%;font-family:"Times New Roman","serif"=
;">creating the</span><span style=3D"font-size:12pt;line-height:115%;font-f=
amily:"Times New Roman","serif""><span style=3D"font-si=
ze:12pt;line-height:115%;font-family:"Times New Roman","seri=
f""> link between=C2=A0the amino acids (link between Ala 321with Met 2=
74 and Asp 272)=C2=A0 =C2=A0 </span> showing secondary structure for DFT an=
d MM/QM calculation?=C2=A0 Is there any free software ?<br>
</span></div></div></div></blockquote><div><br></div><div class=3D"gmail_de=
fault" style=3D"color:rgb(0,0,0)">=E2=80=8BVMD. =C2=A0PyMol. =C2=A0Chimera.=
=C2=A0Several others, too, I'm sure.</div><div class=3D"gmail_default"=
style=3D"color:rgb(0,0,0)">
<br></div></div>-- <br><div dir=3D"ltr">Jason M. Swails<br>BioMaPS,<br>Rutg=
ers University<br>Postdoctoral Researcher</div>
</div></div>
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From owner-chemistry@ccl.net Thu Jun 5 19:09:00 2014
From: "David Gallagher gallagher.da=-=gmail.com" <owner-chemistry]*[server.ccl.net>
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 <gallagher.da/./gmail.com>
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Date: Thu, 05 Jun 2014 14:32:18 -0700
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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
<mailto:Workshop-#-CACheResearch.com>, and include name, affiliation, and
location.
URL: http://www.cacheresearch.com/aiche.html#training
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<font style="font-style: normal; font-variant: normal; font-weight:
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rgb(255, 255, 255);" face="Arial"><font style="font-style: normal;
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normal; line-height: normal; orphans: auto; text-align:
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white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; font-size: 13px;
background-color: rgb(255, 255, 255);" face="Arial">During the
ACS meeting in San Francisco t</font>here 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.<br>
<br>
<b>Time and venue:</b><br>
10am - noon, Wednesday 13th March 2014,<br>
Room 206, Moscone South (</font><font style="font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: auto; text-align: -webkit-left;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
font-size: 13px; background-color: rgb(255, 255, 255);"
face="Arial">San Francisco ACS)</font><font style="font-style:
normal; font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: auto; text-align:
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</font><font style="font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height: normal;
orphans: auto; text-align: -webkit-left; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size:
13px; background-color: rgb(255, 255, 255);" face="Arial"><font
style="font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal; orphans:
auto; text-align: -webkit-left; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size:
13px; background-color: rgb(255, 255, 255);" face="Arial"><br>
</font><b>Registration:</b> The workshop is free but seats are
limited so please email your registration to<span
class="Apple-converted-space"> </span><a
href="mailto:Workshop-#-CACheResearch.com">Workshop-#-CACheResearch.com</a>,
and include name, affiliation, and location.</font><br>
<font style="font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal; orphans:
auto; text-align: -webkit-left; text-indent: 0px; text-transform:
none; white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; font-size: 13px; background-color:
rgb(255, 255, 255);" color="#808080" face="Arial"><font
style="font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal; orphans:
auto; text-align: -webkit-left; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size:
13px; background-color: rgb(255, 255, 255);" color="#000000"
face="Arial">URL: </font><font color="#000000"><a
href="http://www.cacheresearch.com/aiche.html#training"><font
style="font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: -webkit-left;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width:
0px; font-size: 13px; background-color: rgb(255, 255, 255);"
face="Arial"><font style="font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: auto; text-align:
-webkit-left; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; font-size: 13px;
background-color: rgb(255, 255, 255);" face="Arial">http://www.cacheresearch.com/aiche.html#training</font></font></a></font><br>
</font>
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From owner-chemistry@ccl.net Thu Jun 5 21:12:00 2014
From: "Gustavo L.C. Moura gustavo.moura*_*ufpe.br" <owner-chemistry++server.ccl.net>
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" <gustavo.moura^ufpe.br>
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