From owner-chemistry@ccl.net Tue Jun  1 05:22:00 2010
From: "Cyril Bauvais cyril.bauvais()bioquanta.net" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: how to build the protein loop
Message-Id: <-42031-100601042643-24761-6EqsngVLsLFsrJAkf4dZRw{}server.ccl.net>
X-Original-From: Cyril Bauvais <cyril.bauvais|-|bioquanta.net>
Content-Type: multipart/alternative; boundary=0016e6470cc00d6a6c0487f3bb44
Date: Tue, 1 Jun 2010 10:26:31 +0200
MIME-Version: 1.0


Sent to CCL by: Cyril Bauvais [cyril.bauvais],[bioquanta.net]
--0016e6470cc00d6a6c0487f3bb44
Content-Type: text/plain; charset=GB2312
Content-Transfer-Encoding: quoted-printable

i-tasser server from Zhang lab can di this for you.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/

best,

cb

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

2010/5/27 jeffle07 jeffle07[]163.com <owner-chemistry\a/ccl.net>

> Dear all,
>         We are going to build a protein model for MD simulation.
> But several loop regions (about 50 residues in each missed loop) are miss=
ed
> in the crystal structure. Could someone know how to build these regions
> properly? Is there any package or webserver that can do the job?
>
> Many thanks.
>
> Jeff. Yang
>
>
> ------------------------------
> =CD=F8=D2=D7=CE=AA=D6=D0=D0=A1=C6=F3=D2=B5=C3=E2=B7=D1=CC=E1=B9=A9=C6=F3=
=D2=B5=D3=CA=CF=E4=A3=A8=D7=D4=D6=F7=D3=F2=C3=FB=A3=A9 <http://ym.163.com/?=
> from=3Dod3>

--0016e6470cc00d6a6c0487f3bb44
Content-Type: text/html; charset=GB2312
Content-Transfer-Encoding: quoted-printable

i-tasser server from Zhang lab can di this for you.<br><a href=3D"http://zh=
anglab.ccmb.med.umich.edu/I-TASSER/">http://zhanglab.ccmb.med.umich.edu/I-T=
ASSER/</a><br><br>best,<br><br>cb<br><br><a href=3D"http://zhanglab.ccmb.me=
d.umich.edu/I-TASSER/">http://zhanglab.ccmb.med.umich.edu/I-TASSER/</a><br>
<br><div class=3D"gmail_quote">2010/5/27 jeffle07 jeffle07[]<a href=3D"http=
://163.com">163.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemi=
stry\a/ccl.net">owner-chemistry\a/ccl.net</a>&gt;</span><br><blockquote class=
=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, 204, 204); margin=
: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Dear all,</div>
<div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;We are going to build =
a protein model for MD simulation. But&nbsp;several loop regions (about 50 =
residues in each missed loop) are missed in the crystal structure.&nbsp;Cou=
ld someone know how to build these regions properly? Is there any&nbsp;pack=
age or webserver that can do the&nbsp;job?</div>

<div>&nbsp;</div>
<div>Many thanks.</div>
<div>&nbsp;</div>
<div>Jeff. Yang&nbsp;&nbsp;</div><br><br><span title=3D"neteasefooter"></sp=
an><hr>
<a href=3D"http://ym.163.com/?from=3Dod3" target=3D"_blank">=CD=F8=D2=D7=CE=
=AA=D6=D0=D0=A1=C6=F3=D2=B5=C3=E2=B7=D1=CC=E1=B9=A9=C6=F3=D2=B5=D3=CA=CF=E4=
=A3=A8=D7=D4=D6=F7=D3=F2=C3=FB=A3=A9</a>
</blockquote></div><br>

--0016e6470cc00d6a6c0487f3bb44--


From owner-chemistry@ccl.net Tue Jun  1 10:06:00 2010
From: "santhanamoorthi N santhanamoorthi[#]rediffmail.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: To perform constrained Optimization.
Message-Id: <-42032-100601050350-2885-rXia8BH+rVdq9qlwJXAGtQ{=}server.ccl.net>
X-Original-From: "santhanamoorthi  N" <santhanamoorthi(-)rediffmail.com>
Date: Tue, 1 Jun 2010 05:03:49 -0400


Sent to CCL by: "santhanamoorthi  N" [santhanamoorthi]-[rediffmail.com]
Is it Possible to fix the two unbonded atoms at a particular distance while optimization? For example, in Dipeptide, i want to fix the Two oxygen atoms at a particular distance. Is it possible in Gaussian? 

Thanks in Advance


From owner-chemistry@ccl.net Tue Jun  1 11:10:00 2010
From: "Rinderspacher, Berend (Cont, ARL/WMRD) berend.rinderspacher%x%us.army.mil" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL:G: To perform constrained Optimization. (UNCLASSIFIED)
Message-Id: <-42033-100601110713-28503-MrP5wa/v1F23WsCLRbxLFA]~[server.ccl.net>
X-Original-From: "Rinderspacher, Berend (Cont, ARL/WMRD)" <berend.rinderspacher%%us.army.mil>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset="us-ascii"
Date: Tue, 1 Jun 2010 11:06:43 -0400
MIME-Version: 1.0


Sent to CCL by: "Rinderspacher, Berend (Cont, ARL/WMRD)" [berend.rinderspacher]~[us.army.mil]
Classification: UNCLASSIFIED
Caveats: NONE

On Gaussian's webpage read about=20

	Opt=3Dmodredund

This should take care of all your needs. Alternatively define your
Z-matrix such that the interatomic distance is an internal coordinate
and user opt=3Dz-matrix.

-----Original Message-----
Subject: CCL:G: To perform constrained Optimization.


Sent to CCL by: "santhanamoorthi  N" [santhanamoorthi]-[rediffmail.com]
Is it Possible to fix the two unbonded atoms at a particular distance
while optimization? For example, in Dipeptide, i want to fix the Two
oxygen atoms at a particular distance. Is it possible in Gaussian?=20

Thanks in Advance



-=3D This is automatically added to each message by the mailing script =
=3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txtClassification: UNCLASSIFIED
Caveats: NONE


From owner-chemistry@ccl.net Tue Jun  1 12:53:00 2010
From: "Ol Ga eurisco1^^pochta.ru" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL:G: To perform constrained Optimization.
Message-Id: <-42034-100601125147-13861-jFnM7p2V4sBIyngYkhxRug|*|server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1_._pochta.ru>
Date: Tue, 1 Jun 2010 12:51:46 -0400


Sent to CCL by: "Ol  Ga" [eurisco1|*|pochta.ru]
Dear santhanamoorthi,

Yes, sure. You can freeze distance between two atoms.

# method/basis popt(modredundant)

comment

0 1
z-mat

X number_1_atom F
X number_2_atom F 

Sincerely,
Ol ga


--------------------------------------------------
> From: "santhanamoorthi N santhanamoorthi[#]rediffmail.com" <owner-chemistry _ ccl.net>
Sent: Tuesday, June 01, 2010 1:03 PM
To: "Ga, Ol " <eurisco1 _ pochta.ru>
Subject: CCL:G: To perform constrained Optimization.

> 
> 
> Sent to CCL by: "santhanamoorthi  N" [santhanamoorthi]-[rediffmail.com]
> Is it Possible to fix the two unbonded atoms at a particular distance while optimization? For example, in Dipeptide, i want to fix the Two oxygen atoms at a particular distance. Is it possible in Gaussian? 
> 
> Thanks in Advance
> 
> 
>


From owner-chemistry@ccl.net Tue Jun  1 13:27:00 2010
From: "DIEGOI GOMEZ darkego21-x-yahoo.com" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: To perform constrained Optimization.
Message-Id: <-42035-100601115537-31794-uJA5NQpAfWyHKpeRthLrzg(_)server.ccl.net>
X-Original-From: DIEGOI GOMEZ <darkego21%a%yahoo.com>
Content-Type: multipart/alternative; boundary="0-1251447893-1275407727=:71904"
Date: Tue, 1 Jun 2010 08:55:27 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: DIEGOI GOMEZ [darkego21]*[yahoo.com]
--0-1251447893-1275407727=:71904
Content-Type: text/plain; charset=us-ascii



Dear Subscribers

A Single doub.

I would like to know if there are cc-pVDZ auxilirary basis set for RI-MP2 calculations for the Sc-Zn elements.

I have done a search in the EMLS data base and in Prof. Peterson's web Page (http://tyr0.chem.wsu.edu/~kipeters/basis.html). There are only cc-pVTZ auxiliary RI basis set for this elements.

Thanks for any reply.

Diego


      
--0-1251447893-1275407727=:71904
Content-Type: text/html; charset=us-ascii

<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div><br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">Dear Subscribers<br><br>A Single doub.<br><br>I would like to know if there are cc-pVDZ auxilirary basis set for RI-MP2 calculations for the Sc-Zn elements.<br><br><span>I have done a search in the EMLS data base and in Prof. Peterson's web Page (<a target="_blank" href="http://tyr0.chem.wsu.edu/%7Ekipeters/basis.html">http://tyr0.chem.wsu.edu/~kipeters/basis.html</a>). There are only cc-pVTZ auxiliary RI basis set for this elements</span><meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">.<br><br>Thanks for any reply.<br><br>Diego<br><title></title>
	<meta name="GENERATOR" content="OpenOffice.org 3.1  (Linux)">
	<style>
		<!-- 
		BODY,DIV,TABLE,THEAD,TBODY,TFOOT,TR,TH,TD,P { font-family:"Arial"; font-size:x-small</style><meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8">
	<title></title>
	<meta name="GENERATOR" content="OpenOffice.org 3.1  (Linux)">
	<style>
		<!-- 
		BODY,DIV,TABLE,THEAD,TBODY,TFOOT,TR,TH,TD,P { font-family:"Arial"; font-size:x-small }
		 --></style></div>
</div><br>

      </body></html>
--0-1251447893-1275407727=:71904--


From owner-chemistry@ccl.net Tue Jun  1 14:02:00 2010
From: "Esteban Gabriel Vega Hissi egvega-x-gmail.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL:G: To perform constrained Optimization.
Message-Id: <-42036-100601134749-2512-d/wH0Lt4Jgjp6vwyQeVkaw||server.ccl.net>
X-Original-From: Esteban Gabriel Vega Hissi <egvega+*+gmail.com>
Content-Type: multipart/alternative; boundary=0016e65aef96cacec60487fb91f9
Date: Tue, 1 Jun 2010 19:47:19 +0200
MIME-Version: 1.0


Sent to CCL by: Esteban Gabriel Vega Hissi [egvega-#-gmail.com]
--0016e65aef96cacec60487fb91f9
Content-Type: text/plain; charset=ISO-8859-1

Hi,
I think that you have to define redundant coordinates and put them as
constants.

Hope this help

Esteban G. Vega-Hissi
UNSL
--

On Tue, Jun 1, 2010 at 11:03 AM, santhanamoorthi N santhanamoorthi[#]
rediffmail.com <owner-chemistry(_)ccl.net> wrote:

>
> Sent to CCL by: "santhanamoorthi  N" [santhanamoorthi]-[rediffmail.com]
> Is it Possible to fix the two unbonded atoms at a particular distance while
> optimization? For example, in Dipeptide, i want to fix the Two oxygen atoms
> at a particular distance. Is it possible in Gaussian?
>
> Thanks in Advance>
>
>

--0016e65aef96cacec60487fb91f9
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi,<br>I think that you have to define redundant coordinates and put them a=
s constants.<br><br>Hope this help<br><br>Esteban G. Vega-Hissi<br>UNSL<br>=
--<br><br><div class=3D"gmail_quote">On Tue, Jun 1, 2010 at 11:03 AM, santh=
anamoorthi N santhanamoorthi[#]<a href=3D"http://rediffmail.com">rediffmail=
.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry(_)ccl.net">o=
wner-chemistry(_)ccl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: &quot;santhanamoorthi =A0N&quot; [santhanamoorthi]-[<a href=
=3D"http://rediffmail.com" target=3D"_blank">rediffmail.com</a>]<br>
Is it Possible to fix the two unbonded atoms at a particular distance while=
 optimization? For example, in Dipeptide, i want to fix the Two oxygen atom=
s at a particular distance. Is it possible in Gaussian?<br>
<br>
Thanks in Advance<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY(_)ccl.net">CHEMISTRY(_)ccl.n=
et</a> or use:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST(_)ccl.net">CHEM=
ISTRY-REQUEST(_)ccl.net</a> or use<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
Subscribe/Unsubscribe:<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=
=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">h=
ttp://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br>

--0016e65aef96cacec60487fb91f9--


From owner-chemistry@ccl.net Tue Jun  1 14:38:00 2010
From: "Ol Ga eurisco1^pochta.ru" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: aux-basis set fro cc-pVDZ-PP (was "To perform constrained")
Message-Id: <-42037-100601140901-22120-ZDrWjlNuGbnrwDgijc0iSQ{}server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1-#-pochta.ru>
Date: Tue, 1 Jun 2010 14:09:00 -0400


Sent to CCL by: "Ol  Ga" [eurisco1|,|pochta.ru]
Dear DIEGOI GOMEZ ,

You can find both cc-pVDZ-PP and corresponding cc-pVDZ-PP-RI aux-basis set on https://bse.pnl.gov/bse/portal.

Sincerely,
Ol Ga


----------------------------------
> From: DIEGOI GOMEZ darkego21-x-yahoo.com 
Sent: Tuesday, June 01, 2010 7:55 PM
To: Ga, Ol  
Subject: CCL: To perform constrained Optimization.Dear Subscribers

A Single doub.

I would like to know if there are cc-pVDZ auxilirary basis set for RI-MP2 calculations for the Sc-Zn elements.

I have done a search in the EMLS data base and in Prof. Peterson's web Page (http://tyr0.chem.wsu.edu/~kipeters/basis.html). There are only cc-pVTZ auxiliary RI basis set for this elements.

Thanks for any reply.

Diego


From owner-chemistry@ccl.net Tue Jun  1 15:27:00 2010
From: "Alex Allardyce aa^_^chemaxon.hu" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: Call for papers: ChemAxon US UGM, Sept 14-15, Boston, M
Message-Id: <-42038-100601141340-26447-cJ33iu7WORPfWEq0nbDjDQ%%server.ccl.net>
X-Original-From: Alex Allardyce <aa(_)chemaxon.hu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Tue, 01 Jun 2010 20:13:37 +0200
MIME-Version: 1.0


Sent to CCL by: Alex Allardyce [aa%chemaxon.hu]
Excuse cross postings

We are calling for papers for ChemAxon's 2010 US User Group Meeting, to be held on Tuesday and Wednesday, September 14-15th at the Omni Parker House in Downtown Boston.

The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development.

Oral abstract submission deadline is June 30, poster abstracts September 1st. To find out more visit the meeting page (http://www.chemaxon.com/events/2010-us-ugm/), and to submit an abstract please Register (http://www.chemaxon.com/ugm.php).

To review the archives of previous meetings, including original
presentations (slides and video) and meeting reports from Yvonne Martin
and Wendy Warr visit this page (http://www.chemaxon.com/library/ugm-presentations/).

We look forward to seeing you there.
BR
Alex

Satellite meetings

User training
Preceding the meeting will be a dual track developer and end user Training Day on September 13th. To see the topics and schedule visit: Developer Training Day http://www.chemaxon.com/events/2010-us-ugm/#training--developer). End user: Application Focus Training Day (http://www.chemaxon.com/events/2010-us-ugm/#training--application-focus).

Patent professionals and Markush structure users
Following the UGM on September 16th, we have the first US meeting of the Markush Forum, an open morning for interested organizations (users and content developers) to participate in the further development of ChemAxon's tools for Markush structure enumeration and search. More information here (https://www.chemaxon.com/events/2010-us-ugm/#markush-forum).
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Alex Allardyce
Marketing Dir. ChemAxon


From owner-chemistry@ccl.net Tue Jun  1 17:05:00 2010
From: "Jonas Baltrusaitis jasius_1 a yahoo.com" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: when TDDFT fails
Message-Id: <-42039-100601170259-27389-MGVKbZWu7TYl2TKg1fYL0w#%#server.ccl.net>
X-Original-From: "Jonas  Baltrusaitis" <jasius_1]*[yahoo.com>
Date: Tue, 1 Jun 2010 17:02:45 -0400


Sent to CCL by: "Jonas  Baltrusaitis" [jasius_1{:}yahoo.com]
Dear CCLers,

I am calculating optical properties (absorption/emission) of organic molecules. I am doing that in standard way: optimizing ground state structure>calculate vertical excitation for absorption properties and then optimize 1st excited state>calculate vertical excitation for emission properties. I am doing that DFT BP or BLYP functional. The infamous problem with this approach is that excited state optimization more often than not runs into crossing of the PES and TDDFT and CI just break down and ca not be used.
While this is an infamous problem, I do not know of any way to solve it. How to work with these systems with crossing PES for molecules that are large, e.g. 50 atoms and more (hydrocarbons for now, no metal ions). I have not tried any multireference methods as I do not have experience with them, but (a) would they be able to perform adequately with 70-80 atoms and (b) do they normally have gradients implemented for excited state geometry optimization

any insight or literature references would be appreciated

Jonas