From owner-chemistry@ccl.net Thu Oct 28 00:36:01 2010
From: "xunlei ding dingxunlei-,-gmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL:G: freezing angle Error in internal coordinate system
Message-Id: <-43024-101028003445-17635-FJWZI1aTdbEjVGPzaO0pJQ:server.ccl.net>
X-Original-From: xunlei ding <dingxunlei a gmail.com>
Content-Type: multipart/alternative; boundary=0016e6570eae1b853c0493a5dc8e
Date: Thu, 28 Oct 2010 12:34:38 +0800
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Sent to CCL by: xunlei ding [dingxunlei!=!gmail.com]
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Hi All,

If doing a full optimization, I think the best way  is to use
opt(cartesian).
But for partical optimization, this does not work.
Sometimes this error may be solved by using G03 instead of G09, but I don't
think this is a good way.

Ding



2010/9/27 Decai Yu decaiyu23]![yahoo.com <owner-chemistry{=}ccl.net>

>   Dear All,
>
> I am trying to do a partial  geometry optimization.
> In my structures, I have a number of atoms fixed and I also have one angle
> fixed.
> When I changed the value of the fixed angle from 135 to 180, the smaller
> angle runs are finished without error.
> But for angle value larger than 175, it can only run one step (a full SCF
> relaxation).
>
> The program ends with the following error:
>
>  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
>  Berny optimization.
>  NTrRot=   421 NTRed=   574 NAtoms=    51 NSkip=   421 IsLin=F
>  Error in internal coordinate system.
>
> I would appreciate any help or advice.
>
> Best Regards,
>
> Decai
>
>
>
>
>

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<div>Hi All,</div>
<div>
<div>=A0</div>
<div>If doing a full optimization, I think the best way=A0 is to use opt(ca=
rtesian).</div></div>
<div>But for partical optimization, this does not work.</div>
<div>Sometimes this error may be solved by using G03 instead of G09, but I =
don&#39;t think this is a good way.</div>
<div>=A0</div>
<div>Ding</div>
<div><br><br>=A0</div>
<div class=3D"gmail_quote">2010/9/27 Decai Yu decaiyu23]![<a href=3D"http:/=
/yahoo.com">yahoo.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-che=
mistry{=}ccl.net">owner-chemistry{=}ccl.net</a>&gt;</span><br>
<blockquote class=3D"gmail_quote" style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0=
px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0">
<tbody>
<tr>
<td valign=3D"top">
<div>Dear All,</div>
<div>=A0</div>
<div>I am trying to do a partial=A0 geometry optimization.</div>
<div>In my structures, I have a number of atoms fixed and I also have one a=
ngle fixed.</div>
<div>When I changed the value of the fixed angle from 135 to 180, the small=
er angle runs are finished without error.</div>
<div>But for angle value larger than 175, it can only run one step (a full =
SCF relaxation). </div>
<div>=A0</div>
<div>The program=A0ends with the following error:</div>
<div>=A0</div>
<div>=A0GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGra=
dGrad<br>=A0Berny optimization.<br>=A0NTrRot=3D=A0=A0 421 NTRed=3D=A0=A0 57=
4 NAtoms=3D=A0=A0=A0 51 NSkip=3D=A0=A0 421 IsLin=3DF<br>=A0Error in interna=
l coordinate system.<br><br>I would appreciate any help or advice.</div>

<div>=A0</div>
<div>Best Regards,</div>
<div>=A0</div>
<div>Decai<br></div>
<blockquote style=3D"PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(=
16,16,255) 2px solid">
<div>=A0</div></blockquote></td></tr></tbody></table><br></blockquote></div=
><br>

--0016e6570eae1b853c0493a5dc8e--


From owner-chemistry@ccl.net Thu Oct 28 04:05:00 2010
From: "Lars Goerigk lars.goerigk#,#uni-muenster.de" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL:G: Double hybrid functionals for excited states with Gaussian09
Message-Id: <-43025-101028040035-16019-/vR4robuXdGjEygBcI0W0Q^^server.ccl.net>
X-Original-From: Lars Goerigk <lars.goerigk++uni-muenster.de>
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Date: Thu, 28 Oct 2010 10:00:27 +0200
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Sent to CCL by: Lars Goerigk [lars.goerigk _ uni-muenster.de]
TD-B2PLYP works as follows:
First, you perform a ground state B2LYP calculation. The perturbative 
correction  is not needed if you are not interested in any ground state 
properties, because you are just interested in the resulting KS-orbitals.
Then a standard TD-DFT treatment (i.e. TD-B2LYP) is carried out, which gives 
you excitation energies and transition moments of TD-BHLYP quality.

The B2LYP orbitals and TD-B2LYP excitation energies and amplitudes are then 
used for a CIS(D) type treatment to correct the TD-B2LYP energies.

I do not know if such a treatment is possible in Gaussian by adjusting some 
IOPs. I assume that the CIS(D) routine will crash if TD-DFT results are used 
as an input.

However, the routine may not fail with an CIS like input. The Tamm-Dancoff-
Approximation is basically CIS. I do not know if Gaussian does TDA-DFT.
Basically you can then carry out the CIS(D) correction based on your TDA-B2LYP 
result. This gives you TDA-B2PLYP energies. This was also discussed in the 
2007 Grimme/Neese paper. TDA-DFT usually gives you very similar energies to 
TD-DFT. But again, I do not know whether Gaussian can handle this with IOPs, 
but it's worth testing it.
Maybe the Gaussian people can help you with the IOPs if you contact them; 
maybe it's even possible to do full TD-B2PLYP.

Another option would be ORCA, which is freely available. It does TDA-B2PLYP, 
but not full TD-B2PLYP.

I hope these information are somehow useful for you.

Cheers,
Lars



On Wednesday 27 October 2010 05:08:27 pm you wrote:
> Sent to CCL by: "Lara Martinez Fernandez" [lara.martinez*o*uam.es]
> I am trying to run some TD-DFT calculation (for excited states) using
>  double hybrid functionals with Gaussian09. I have some doubts about how
>  TD-B2PLYP,TD-B2GP-PLYP work. If I dont misunderstood, first I have to run
>  a B2LYP calculation for the ground state and then use this orbitals and
>  amplitudes to run the CIS(D) correction for the rest of excited states. I
>  dont know if this procedure is possible with Gaussian09. Do anyone know
>  how to do that? I guess there must be any keyword to read the B2LYP (of
>  the ground state) orbitals and not optimise them in the CIS(D)
>  calculation.
> 
> 
> Thanks in advance, Lara>


From owner-chemistry@ccl.net Thu Oct 28 06:59:01 2010
From: "makowskm!^!chemia.uj.edu.pl" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL:G: MP2 Calculation
Message-Id: <-43026-101028063634-27985-nzeXCRrDdzyEbVeo7mHnaw]|[server.ccl.net>
X-Original-From: makowskm#chemia.uj.edu.pl
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Date: Thu, 28 Oct 2010 12:36:26 +0200 (CEST)
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Sent to CCL by: makowskm^^chemia.uj.edu.pl

>
> Sent to CCL by: "Leonardo Moreira da Costa" [leomdcosta a yahoo.com.br]
> I have a very simple doubt.
>
> It is said in the Gaussian help (C:\G03W\help\k_maxdisk.htm), about
> maxDisk,  that MP2 energies and gradients obey MaxDisk, which must be at
> least 2ON2.
>
> It is said that, but they do not specify what are the ''O'' and ''N''
> parameters of the formula.
>
> Anyone can, please, explain me what are these two parameters? I have
> looked for it in many resources, but I did not obatin a certain meaning
> (number of the electrons, orbitals, atoms, ...).

O denotes the number of occupied orbitals, N refers to the number of basis
functions.

Regards,
Marcin


From owner-chemistry@ccl.net Thu Oct 28 10:14:01 2010
From: "Emilio Xavier Esposito emilio.esposito=-=gmail.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: The Anaheim ACS meeting abstract deadline: November 2nd, 2010
Message-Id: <-43027-101028101232-22052-ND5QMa9A0JucFBORaK/eFA .. server.ccl.net>
X-Original-From: Emilio Xavier Esposito <emilio.esposito===gmail.com>
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Date: Thu, 28 Oct 2010 10:12:03 -0400
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Sent to CCL by: Emilio Xavier Esposito [emilio.esposito!^!gmail.com]
Hi
The abstract submission deadline for the Anaheim ACS meeting is
Tuesday, November 2nd, 2010.

Have you submitted your abstract?

Symposia include:
- Computers in Chemical & Pharmaceutical Research Award Symposium
Honoring Thom Dunning
- Chemical Computing Group Excellence Award (Graduate students; open submission)
- Hewlett-Packard Outstanding Junior Faculty Award (Open submission)
- Thomas Kuhn Paradigm Shift Award (Open submission)
- Challenges in Industrial Computational Methods (Invitation only)
- Docking & Scoring (Invitation only)
- Drug Discovery
- Molecular Mechanics
- Quantum Chemistry
- The COMP Poster Session

Abstracts can be submitted using the Program and Abstract Creation
System (PACS) at http://abstracts.acs.org .

Please feel free to contact us if you have questions about the COMP
technical programs for the upcoming meetings or if you are interested
in organizing a symposium within the COMP Division for the Fall 2011
or Spring 2012 National Meeting.

We have a great technical program planned for the Anaheim meeting and
we hope that you are able to attend.

Sincerely
Emilio Xavier Esposito, Jeffry D. Madura, and Scott Wildman
The COMP Programming Board
COMP Division of the ACS

Follow COMP on twitter! http://twitter.com/acscomp


From owner-chemistry@ccl.net Thu Oct 28 14:19:00 2010
From: "lamees hegazy lameesshams(0)yahoo.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: capping residues for charmm force field
Message-Id: <-43028-101028123028-15148-ibKYqJuzNb2h97BwLoQa4g,+,server.ccl.net>
X-Original-From: lamees hegazy <lameesshams^^yahoo.com>
Content-Type: multipart/alternative; boundary="0-240090501-1288283423=:44810"
Date: Thu, 28 Oct 2010 09:30:23 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: lamees hegazy [lameesshams%%yahoo.com]
--0-240090501-1288283423=:44810
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I am working on developing parameters for a ligand connected to my protein.=
=A0The ligand is=A0oxalyl-aspartyl anhydride=A0=A0 O-CO-CO-O-CO-ASP. As the=
 first step for optimization, I wil cut between O and CO-=A0ASP and add cap=
ping residue NH-CH3 so=A0 I will parameterize this ligand O-CO-CO-O-NH-CH3.=
 I woud like to do the parameterization accurately and I appreciate your su=
ggessions.=0A=0A=0A      
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<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><DIV>I am working on developing parameters fo=
r a ligand connected to my protein.&nbsp;The ligand is&nbsp;oxalyl-aspartyl=
 anhydride&nbsp;&nbsp; O-CO-CO-O-CO-ASP. As the first step for optimization=
, I wil cut between O and CO-&nbsp;ASP and add capping residue NH-CH3 so&nb=
sp; I will parameterize this ligand O-CO-CO-O-NH-CH3. I woud like to do the=
 parameterization accurately and I appreciate your suggessions.</DIV></td><=
/tr></table><br>=0A=0A      
--0-240090501-1288283423=:44810--


From owner-chemistry@ccl.net Thu Oct 28 14:54:00 2010
From: "Hans De Winter hans.dewinter/a\silicos.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: PIRAMID 1.0.0: Shape-based alignment of molecules
Message-Id: <-43029-101028090330-31168-HeHgdGz0wQpta+b9wjWuIQ^server.ccl.net>
X-Original-From: Hans De Winter <hans.dewinter:+:silicos.com>
Content-Type: multipart/alternative; boundary=Apple-Mail-11-726154964
Date: Thu, 28 Oct 2010 15:03:20 +0200
Mime-Version: 1.0 (Apple Message framework v936)


Sent to CCL by: Hans De Winter [hans.dewinter_._silicos.com]

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Dear,

Silicos NV is pleased to announced today the release of its new open  
source software tool called PIRAMID under the General Public License  
(GPL) v2. PIRAMID has been written on top of Open Babel's C++ API.

PIRAMID is a shape-based alignment tool for the alignment of pairs of  
molecules. It is based on Gaussian volumes for the description  
molecular shape as was originally introduced by Grant and Pickup ( J.  
Phys. Chem. 1995, 99, 3503-3510).

The software is downloadable from Silicos website ( http://www.silicos.be 
  ) or from the Open Babel related projects webpage ( http://openbabel.org/wiki/Related_Projects 
  ).

Please contact Silicos at info[at]silicos.com for more information.

Kind regards,
Hans


--Apple-Mail-11-726154964
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	charset=US-ASCII
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<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear,<div><br></div><div>Silicos NV is pleased to announced today the release of its new open source software tool called PIRAMID under the General Public License (GPL) v2. PIRAMID has been written on top of Open Babel's C++ API.</div><div><br></div><div>PIRAMID is a shape-based alignment tool for the alignment of pairs of molecules.<font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">&nbsp;It is
based on Gaussian volumes for the description molecular shape as was originally introduced by Grant and Pickup (<span class="Apple-style-span" style="font-size: medium; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">&nbsp;J.
Phys. Chem. 1995, 99, 3503-3510</span></font><span class="Apple-style-span" style="font-size: 12px; ">).</span></span></span></font></div><!--StartFragment--><!--EndFragment-->



<div><br></div><div>The software is downloadable from Silicos website ( <a href="http://www.silicos.be">http://www.silicos.be</a> ) or from the Open Babel related projects webpage ( <a href="http://openbabel.org/wiki/Related_Projects">http://openbabel.org/wiki/Related_Projects</a> ).</div><div><br></div><div>Please contact Silicos at info[at]silicos.com for more information.</div><div><br></div><div>Kind regards,</div><div>Hans</div><div><br></div></body></html>
--Apple-Mail-11-726154964--


From owner-chemistry@ccl.net Thu Oct 28 19:28:00 2010
From: "Adam Sykes admin(0)quanano.co.uk" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: capping residues for charmm force field
Message-Id: <-43030-101028180347-22636-w9w9wAyG2ckNsbf69kEQBQ-$-server.ccl.net>
X-Original-From: Adam Sykes <admin{:}quanano.co.uk>
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Date: Thu, 28 Oct 2010 23:03:59 +0100
MIME-Version: 1.0


Sent to CCL by: Adam Sykes [admin]~[quanano.co.uk]
--00221534d727d27f3f0493b4835b
Content-Type: text/plain; charset=ISO-8859-1

I would suggest taking a look at
http://mackerell.umaryland.edu/Empirical_FF_Dev.html as a starting point.



Best wishes,


Adam



Dr. Adam Sykes MChem., PhD.

*Managing Director*

*QuaNano Ltd*

e:   adam.sykes!=!quanano.co.uk

m: +44 (0)7855 379 397

t:   +44 (0)151 324 2866

w:  http://www.quanano.co.uk



*From:* owner-chemistry+adam.sykes==quanano.co.uk!=!ccl.net [mailto:
owner-chemistry+adam.sykes <owner-chemistry%2Badam.sykes>==quanano.co.uk!=!
ccl.net] *On Behalf Of *lamees hegazy lameesshams(0)yahoo.com
*Sent:* 28 October 2010 17:30
*To:* Sykes, Adam C 
*Subject:* CCL: capping residues for charmm force field



I am working on developing parameters for a ligand connected to my
protein. The ligand is oxalyl-aspartyl anhydride   O-CO-CO-O-CO-ASP. As the
first step for optimization, I wil cut between O and CO- ASP and add capping
residue NH-CH3 so  I will parameterize this ligand O-CO-CO-O-NH-CH3. I woud
like to do the parameterization accurately and I appreciate your
suggessions.

--00221534d727d27f3f0493b4835b
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<html>

<head>
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>
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<body lang=3D"EN-GB" link=3D"blue" vlink=3D"purple">

<div class=3D"WordSection1">

<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;
color:#1F497D">I would suggest taking a look at <a href=3D"http://mackerell=
.umaryland.edu/Empirical_FF_Dev.html">http://mackerell.umaryland.edu/Empiri=
cal_FF_Dev.html</a>
as a starting point.</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;
color:#1F497D">=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;
color:#1F497D">Best wishes,</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;
color:#1F497D"><br>
Adam</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;
color:#1F497D">=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;
color:#1F497D">Dr. Adam Sykes MChem., PhD.</span></p>

<p class=3D"MsoNormal"><b><span style=3D"font-size:10.0pt;font-family:&quot=
;Calibri&quot;,&quot;sans-serif&quot;;
color:#1F497D">Managing Director</span></b></p>

<p class=3D"MsoNormal"><i><span style=3D"font-size:10.0pt;font-family:&quot=
;Calibri&quot;,&quot;sans-serif&quot;;
color:#1F497D">QuaNano Ltd</span></i></p>

<p class=3D"MsoNormal"><span style=3D"font-size:9.0pt;font-family:&quot;Cal=
ibri&quot;,&quot;sans-serif&quot;;
color:#1F497D">e:=A0=A0 <a href=3D"mailto:adam.sykes!=!quanano.co.uk">adam.sy=
kes!=!quanano.co.uk</a></span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:9.0pt;font-family:&quot;Cal=
ibri&quot;,&quot;sans-serif&quot;;
color:#1F497D">m: +44 (0)7855 379 397</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:9.0pt;font-family:&quot;Cal=
ibri&quot;,&quot;sans-serif&quot;;
color:#1F497D">t:=A0=A0 +44 (0)151 324 2866</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:9.0pt;font-family:&quot;Cal=
ibri&quot;,&quot;sans-serif&quot;;
color:#1F497D">w:=A0 <a href=3D"http://www.quanano.co.uk/">http://www.quana=
no.co.uk</a>
</span><span style=3D"font-size:9.0pt;font-family:&quot;Calibri&quot;,&quot=
;sans-serif&quot;;
color:#1F497D"></span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;
color:#1F497D">=A0</span></p>

<div style=3D"border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm =
0cm 0cm">

<p class=3D"MsoNormal"><b><span lang=3D"EN-US" style=3D"font-size:10.0pt;fo=
nt-family:
&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span lang=3D"EN=
-US" style=3D"font-size:10.0pt;
font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
owner-chemistry+adam.sykes=3D=3D<a href=3D"http://quanano.co.uk">quanano.co=
.uk</a>!=!<a href=3D"http://ccl.net">ccl.net</a>
[mailto:<a href=3D"mailto:owner-chemistry%2Badam.sykes">owner-chemistry+ada=
m.sykes</a>=3D=3D<a href=3D"http://quanano.co.uk">quanano.co.uk</a>!=!<a href=
=3D"http://ccl.net">ccl.net</a>] <b>On Behalf Of </b>lamees
hegazy lameesshams(0)<a href=3D"http://yahoo.com">yahoo.com</a><br>
<b>Sent:</b> 28 October 2010 17:30<br>
<b>To:</b> Sykes, Adam C <br>
<b>Subject:</b> CCL: capping residues for charmm force field</span></p>

</div>

<p class=3D"MsoNormal">=A0</p>

<table class=3D"MsoNormalTable" border=3D"0" cellspacing=3D"0" cellpadding=
=3D"0">
 <tr>
  <td valign=3D"top" style=3D"padding:0cm 0cm 0cm 0cm">
  <div>
  <p class=3D"MsoNormal">I am working on developing parameters for a ligand
  connected to my protein.=A0The ligand is=A0oxalyl-aspartyl anhydride=A0=
=A0
  O-CO-CO-O-CO-ASP. As the first step for optimization, I wil cut between O=
 and
  CO-=A0ASP and add capping residue NH-CH3 so=A0 I will parameterize this
  ligand O-CO-CO-O-NH-CH3. I woud like to do the parameterization accuratel=
y
  and I appreciate your suggessions.</p>
  </div>
  </td>
 </tr>
</table>

<p class=3D"MsoNormal"><span style=3D"font-size:10.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;">=A0</span></p>

</div>

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