From owner-chemistry@ccl.net Thu Jun 14 02:04:00 2007
From: "Kaci Tizi_Ouzou kaci.tiziouzou---gmail.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Basis set
Message-Id: <-34480-070614004812-4070-SFYChSIiUjPQW0OF3FaRXA[A]server.ccl.net>
X-Original-From: "Kaci Tizi_Ouzou" <kaci.tiziouzou]_[gmail.com>
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Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou]_[gmail.com]
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Hi Folks,

This is a basic question but not being used with Gaussian, I'm sort of
stuck!!

I have generated a large basis set by fitting a 1S orbital (Hydrogen atom)
with 10 Gaussian.

I have an input file of the form:

#HF/GEN

Hydrogen atom

0 2
H    0.0    0.0    0.0

H 0
S   15   1.00

Exponent#1  Coeff #1
Exponent#2  Coeff #2
And the list goes on


However, when I ran gaussian, I got an energy : 5.51 which obviously is
incorrect since it is positive!!

Can anybody point me where did I screw up the definition of the basis for
Gaussian.

Thnaks for your time and help,

Kass

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<div>Hi Folks,</div>
<div>&nbsp;</div>
<div>This is a basic question but not being used with Gaussian, I&#39;m sort of stuck!!</div>
<div>&nbsp;</div>
<div>I have generated a large basis set by fitting a 1S orbital (Hydrogen atom) with 10 Gaussian. </div>
<div>&nbsp;</div>
<div>I have an input file of the form:</div>
<div>&nbsp;</div>
<div>#HF/GEN </div>
<div>&nbsp;</div>
<div>Hydrogen atom</div>
<div>&nbsp;</div>
<div>0 2</div>
<div>H&nbsp;&nbsp;&nbsp; 0.0&nbsp;&nbsp;&nbsp; 0.0&nbsp;&nbsp;&nbsp; 0.0</div>
<div>&nbsp;</div>
<div>H 0</div>
<div>S&nbsp;&nbsp; 15&nbsp;&nbsp; 1.00</div>
<div>&nbsp;</div>
<div>Exponent#1&nbsp; Coeff #1</div>
<div>Exponent#2&nbsp; Coeff #2</div>
<div>And the list goes on</div>
<div>&nbsp;</div>
<div>&nbsp;</div>
<div>However, when I ran gaussian, I got an energy : 5.51 which obviously is incorrect since it is positive!! </div>
<div>&nbsp;</div>
<div>Can anybody point me where did I screw up the definition of the basis for Gaussian.</div>
<div>&nbsp;</div>
<div>Thnaks for your time and help,</div>
<div>&nbsp;</div>
<div>Kass</div>

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From owner-chemistry@ccl.net Thu Jun 14 04:38:01 2007
From: "Anselm.Horn**chemie.uni-erlangen.de" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: Problems about AMBER
Message-Id: <-34481-070613170143-3805-fcIp3GgMp+OCm9qOfA95ZA.:.server.ccl.net>
X-Original-From: Anselm.Horn-*-chemie.uni-erlangen.de
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Date: Wed, 13 Jun 2007 22:11:02 +0200 (CEST)
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Sent to CCL by: Anselm.Horn{=}chemie.uni-erlangen.de

Dear Yu-hui Fang,

although you were very specific about the energy calculation, you did not
mention how you prepared your Amber (what version?) input files.

PDB entry 1L5G is a crystal structure with a resolution of 3.2 A and thus
lacks any hydrogen atom information. Therefore I assume that you have
added the missing hydrogen atoms with the Amber-suite tool leap and then
calculated the vdW energy between the atoms of interest. However, the
hydrogen addition with leap, although sophisticated, will create steric
clashes. You therefore have to run at least a geometry optimization to
remove these clashes, or even better, perform a molecular dynamics
simulation and look at the mean interaction energies.

Concerning your scaling factor question: The manual says, that the scaling
factor 1/2.0 was changed to 1/1.2 for parm94.dat.

If you have further questions regarding Amber, better send them to the
Amber mail (see http://amber.scripps.edu) reflector directly.

Regards,

Anselm Horn


From owner-chemistry@ccl.net Thu Jun 14 08:34:00 2007
From: "Savita Pundlik psavita:crlindia.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: parallel nwchem
Message-Id: <-34482-070613081952-29890-XJqhZl2QNAfWPRksmtnE9g(!)server.ccl.net>
X-Original-From: "Savita Pundlik" <psavita _ crlindia.com>
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Sent to CCL by: "Savita Pundlik" [psavita.:.crlindia.com]

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Dear Sir,

            We could compile and run NWCHEM on a single node. But there is a
problem running the code on a cluster with LINUX64 and mpi. It simple hangs.

Is there a compatibility problem of some kind?

 

Thanks

CRL


The information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments contained in it.

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<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:10=
.0pt;
font-family:Arial'>Dear Sir,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:10=
.0pt;
font-family:Arial'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp; We could compile and run NWCHEM on a single
node. But there is a problem running the code on a cluster with LINUX64 and
mpi. It simple hangs.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:10=
.0pt;
font-family:Arial'>Is there a compatibility problem of some kind?<o:p></o:p>=
</span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:10=
.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:10=
.0pt;
font-family:Arial'>Thanks<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:10=
.0pt;
font-family:Arial'>CRL<o:p></o:p></span></font></p>

</div>

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From owner-chemistry@ccl.net Thu Jun 14 12:49:00 2007
From: "Jozsef Csontos jozsefcsontos[a]creighton.edu" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Basis set
Message-Id: <-34483-070614114317-3722-U3OVRQEVOm6LgWdziZj/KA],[server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos+/-creighton.edu>
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Sent to CCL by: Jozsef Csontos [jozsefcsontos.++.creighton.edu]
Hi Kaci,

your empty line before the first exponent-coefficient pair is probably
unnecessary or even worse - a syntax error.

Here goes an example which works; try to compare it to your input.

beginning of the file
empty line
#p hf/gen gfinput

ccl h2

0 2
 H                0.00   0.00   0.0

H 0
S   3  1.00
    34.061341      .60251978E-02
    5.1235746      .45021094E-01
    1.1646626      .20189726
S   1  1.00
    .32723041      1.0000000
S   1  1.00
    .10307241      1.0000000
P   1  1.00
  1.40700000        1.0000000000
P   1  1.00
  0.38800000        1.0000000000
D   1  1.00
  1.05700000        1.0000000000
****
empty line
empty line
end of file

I hope it helps to solve your problem,

Jozsef
On Wed, 2007-06-13 at 22:19 -0600, Kaci Tizi_Ouzou
kaci.tiziouzou---gmail.com wrote:
> Hi Folks,
>  
> This is a basic question but not being used with Gaussian, I'm sort of
> stuck!!
>  
> I have generated a large basis set by fitting a 1S orbital (Hydrogen
> atom) with 10 Gaussian. 
>  
> I have an input file of the form:
>  
> #HF/GEN 
>  
> Hydrogen atom
>  
> 0 2
> H    0.0    0.0    0.0
>  
> H 0
> S   15   1.00
>  
> Exponent#1  Coeff #1
> Exponent#2  Coeff #2
> And the list goes on
>  
>  
> However, when I ran gaussian, I got an energy : 5.51 which obviously
> is incorrect since it is positive!! 
>  
> Can anybody point me where did I screw up the definition of the basis
> for Gaussian.
>  
> Thnaks for your time and help,
>  
> Kass
-- 
Jozsef Csontos, Ph.D.

(jozsefcsontos_at_creighton.edu)
Department of Biomedical Sciences
Creighton University,
Omaha, NE


From owner-chemistry@ccl.net Thu Jun 14 13:24:00 2007
From: "Jozsef Csontos jozsefcsontos ~ creighton.edu" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: parallel nwchem
Message-Id: <-34484-070614114318-3732-dzlbczKdcG3nj5kHKhpg/Q::server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos%%creighton.edu>
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Date: Thu, 14 Jun 2007 10:25:42 -0500
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Sent to CCL by: Jozsef Csontos [jozsefcsontos a creighton.edu]
Dear Savita,

as far as I can tell you there is no such compatibility problem. I'm
using parallel NWChem with 64bit nodes and the mpich implementation of
mpi. 

In order to solve your issues the best and fastest way is to post it on
the NWChem user's mailing list. Here, you can subscribe to that:
http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

They'll be glad to help you. However, I'm sure that they need a more
detailed specification of your problem:)

Jozsef

On Wed, 2007-06-13 at 16:55 +0530, Savita Pundlik psavita:crlindia.com
wrote:
> Dear Sir,
> 
>             We could compile and run NWCHEM on a single node. But
> there is a problem running the code on a cluster with LINUX64 and mpi.
> It simple hangs.
> 
> Is there a compatibility problem of some kind?
> 
>  
> 
> Thanks
> 
> CRL
> 
> 
> The information contained in this electronic message and any
> attachments to this message are intended for the exclusive use of the
> addressee(s) and may contain proprietary, confidential or privileged
> information. If you are not the intended recipient, you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately and destroy all copies of this message and any attachments
> contained in it. Contact your Administrator for further information.
> 
-- 
Jozsef Csontos, Ph.D.

(jozsefcsontos_at_creighton.edu)
Department of Biomedical Sciences
Creighton University,
Omaha, NE


From owner-chemistry@ccl.net Thu Jun 14 14:00:00 2007
From: "Richard Wood rwoodphd(0)msn.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL: Phase Force Fields
Message-Id: <-34485-070614132935-31957-VlJhEXrF7nvzjll+gSwWuA()server.ccl.net>
X-Original-From: "Richard  Wood" <rwoodphd(a)msn.com>
Date: Thu, 14 Jun 2007 13:29:32 -0400


Sent to CCL by: "Richard  Wood" [rwoodphd:-:msn.com]
Hi all,

We're trying to do pharmacophore modeling of a series of peptidomimetics
using the program Phase. According to the Phase manual, the force field choices when doing the generation of conformers are MMFFs and OPLS 2005. We'd like to use the MMFFs force field, but we have noticed that the program uses MacroModel atom types, as our nitrogens come out being typed wrong (N2 when they should be amide nitrogens). No matter what one does, you can't get away from the MacroModel atom types.  We'd like to use the NC=O type for the amide nitrogens, but that type isn't defined in the file atom.typ. There is a file called sybyl.typ that seems to convert N.am to N.2, but there is no way to get around this, even if one uses a file format other than mol2 (ie, like a maestro file).  

We have two questions: How do we implement this atom type (NC=O) in our
calculations, and secondly, how do we assure ourselves that we are indeed
using the MMFFs force field, and not some hybrid using MacroModel atom types and functionals from the MMFFs force field?

Thanks in advance,
Richard

Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
woodx278^_^umn.edu


From owner-chemistry@ccl.net Thu Jun 14 14:34:00 2007
From: "Chunyi Sung juneyi1%a%yahoo.com.tw" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: TS calculation with PCM
Message-Id: <-34486-070614133409-3425-3tDZH26rhFP0Dh/vg3Nv3A,+,server.ccl.net>
X-Original-From: "Chunyi  Sung" <juneyi1^^yahoo.com.tw>
Date: Thu, 14 Jun 2007 13:34:06 -0400


Sent to CCL by: "Chunyi  Sung" [juneyi1[*]yahoo.com.tw]
Hi,

   I am studying a gas phase reaction using PCM model 
to see how the reaction goes in the presence of a solvent. 
When I tried to find the transtion state structure with 
PCM model (started with the transition state structure found 
in gas phase), I got an error like this before getting any 
SCF cycle done: 

United Atom Topological Model (UA0  parameters set).
UA0: Hydrogen 2 is unbound. Keep it explicit at all point on the
UA0: potential energy surface to get meaningful results.
 
This step is actually about a hydrogen transferring from 
a carbon to oxygen, so the hydrogen was not closely bound
to any atoms in the initial geometry (the transition state
structure in gas phase). 

So, what do I do to keep the hydrogen explicit? 
or this error is just telling me that this reaction is actually
not going to happen in the solvent?    

thanks

Chunyi


From owner-chemistry@ccl.net Thu Jun 14 15:09:00 2007
From: "Gilles Frapper gilles.frapper-*-univ-poitiers.fr" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: diffusion in zeolite
Message-Id: <-34487-070614132152-25783-51OREEfjObt2LmqMQY0OFA,+,server.ccl.net>
X-Original-From: Gilles Frapper <gilles.frapper-x-univ-poitiers.fr>
Content-Type: multipart/alternative;
 boundary="------------050900070203040605080009"
Date: Thu, 14 Jun 2007 18:28:42 +0200
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Sent to CCL by: Gilles Frapper [gilles.frapper__univ-poitiers.fr]
This is a multi-part message in MIME format.
--------------050900070203040605080009
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Bonjour,

We are looking for a FREE program in MM or QM/MM to study:
- the diffusion of organic molecules in zeolites (FAU X or Y: Si, O, Al, 
Na or Cs, H)
- the desorption of organic molecules from zeolite to water or organic 
solvant such as n-heptane (interface solid/liquid).

Music http://zeolites.cqe.northwestern.edu/Music seems appropriate.

What else ? References ?

Bonne journée

Gilles Frapper
groupe chimie quantique appliquée
UMR CNRS 6503 - LACCO - Université de Poitiers
40, av. recteur Pineau 86022 Poitiers cedex
tel : 05 49 45 35 74 - mel : gilles.frapper%x%univ-poitiers.fr
site : http://labo.univ-poitiers.fr/yargla


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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<big><font size="-1"><big><tt>Bonjour,<br>
<br>
We are looking for a FREE program in MM or QM/MM to study:<br>
- the diffusion of organic molecules in zeolites (FAU X or Y: Si, O,
Al, Na or Cs, H) <br>
- the desorption </tt></big></font><font size="-1"><big><tt>of organic
molecules </tt></big></font><font size="-1"><big><tt>from zeolite to
water or organic solvant such as n-heptane (interface solid/liquid).<br>
<br>
Music </tt></big></font><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;;"><a
 href="http://zeolites.cqe.northwestern.edu/Music">http://zeolites.cqe.northwestern.edu/Music</a>
</span><font size="-1"><big><tt>seems appropriate. <br>
<br>
What else ? References ?<br>
<br>
Bonne journ&eacute;e</tt></big></font></big><br>
<pre class="moz-signature" cols="72">Gilles Frapper
groupe chimie quantique appliqu&eacute;e
UMR CNRS 6503 - LACCO - Universit&eacute; de Poitiers
40, av. recteur Pineau 86022 Poitiers cedex
tel : 05 49 45 35 74 - mel : <a class="moz-txt-link-abbreviated" href="mailto:gilles.frapper%x%univ-poitiers.fr">gilles.frapper%x%univ-poitiers.fr</a>
site : <a class="moz-txt-link-freetext" href="http://labo.univ-poitiers.fr/yargla">http://labo.univ-poitiers.fr/yargla</a>
</pre>
</body>
</html>

--------------050900070203040605080009--


From owner-chemistry@ccl.net Thu Jun 14 15:44:00 2007
From: "Atul Agarwal aagarwal---achillion.com" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: Negative frequency problem
Message-Id: <-34488-070614132108-25340-uW8tJsodiG5mKwm9lWnHFA],[server.ccl.net>
X-Original-From: "Atul Agarwal" <aagarwal .. achillion.com>
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Date: Thu, 14 Jun 2007 12:46:20 -0400
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Sent to CCL by: "Atul Agarwal" [aagarwal**achillion.com]
Hi,

I am faced with the same issue of multiple negative frequencies.  I used
Jaguar for TS calculations.  Does anyone know of tricks in Jaguar to
eliminate additional negative frequencies?

Thanks,
Atul

-----Original Message-----
> From: owner-chemistry_+_ccl.net [mailto:owner-chemistry_+_ccl.net] 
Sent: Wednesday, June 13, 2007 3:38 AM
To: Atul Agarwal
Subject: CCL: Negative frequency problem


Sent to CCL by: "Jos   I. Garc  a" [jig _ unizar.es]
Hi Gary,

If your system and/or your computational resources allow it, try the
old, but usually effective OPT=(TS,CalcAll,...). A second, small,
negative frequency, associated to a low-energy torsion is really a
pain in the neck, and if we could simply ignore it, it would be great.
However, try to eliminate it first. You'll feel better after...

Jos I. Garca
CSIC Research Professor
Instituto de Ciencia de Materiales de Aragon
CSIC-Universidad de Zaragoza
E-50009 Zaragoza (Spain)http://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 14 16:29:00 2007
From: "Sten Nilsson Lill stenil[A]chem.gu.se" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: TS calculation with PCM
Message-Id: <-34489-070614162618-32106-F7JWvtaVvBygSrJ0Tcblwg(0)server.ccl.net>
X-Original-From: "Sten Nilsson Lill" <stenil---chem.gu.se>
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Date: Thu, 14 Jun 2007 21:33:29 +0200 (CEST)
MIME-Version: 1.0


Sent to CCL by: "Sten Nilsson Lill" [stenil|,|chem.gu.se]
Dear Chunyi,

by assuming you are using Gaussian you can add a sphere on a specific
hydrogen by adding the keyword "SPHEREONH=N" in the route card of your pcm
calculation. Here, N is the position of that hydrogen in your atom
coordinate list. In the Gaussian manual you can read about this and also
how to add keywords to the scrf calculation.

Hope this helps!

Regards,

Sten Nilsson Lill




>
> Sent to CCL by: "Chunyi  Sung" [juneyi1[*]yahoo.com.tw]
> Hi,
>
>    I am studying a gas phase reaction using PCM model
> to see how the reaction goes in the presence of a solvent.
> When I tried to find the transtion state structure with
> PCM model (started with the transition state structure found
> in gas phase), I got an error like this before getting any
> SCF cycle done:
>
> United Atom Topological Model (UA0  parameters set).
> UA0: Hydrogen 2 is unbound. Keep it explicit at all point on the
> UA0: potential energy surface to get meaningful results.
>
> This step is actually about a hydrogen transferring from
> a carbon to oxygen, so the hydrogen was not closely bound
> to any atoms in the initial geometry (the transition state
> structure in gas phase).
>
> So, what do I do to keep the hydrogen explicit?
> or this error is just telling me that this reaction is actually
> not going to happen in the solvent?
>
> thanks
>
> Chunyi>
>
>
>


Ph. D. Sten Nilsson Lill
Dep. of Chemistry
Göteborg University
Kemigården 4
S-412 96 Göteborg, Sweden
Phone: +46-31-772 2901
Fax: +46-31-772 3840
E-mail: stenil|a|chem.gu.se
Alternative e-mail: slill1|a|lsu.edu


From owner-chemistry@ccl.net Thu Jun 14 17:03:00 2007
From: "Sena Jr, D. M. dnz[-]fisica.ufc.br" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Yet a Basis Set Question
Message-Id: <-34490-070614164950-15298-1dQQruvhX9oH8YpCgNXf7Q-#-server.ccl.net>
X-Original-From: "Sena Jr, D. M." <dnz%x%fisica.ufc.br>
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Date: Thu, 14 Jun 2007 16:47:17 -0300
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Sent to CCL by: "Sena Jr, D. M." [dnz.##.fisica.ufc.br]
Dear CCL members,
  I´m having some difficulty formatting the bases Z2Pol / Z3Pol so
that GAMESS will understand. For example, for Carbon we have in Z2Pol:
************************************************************************
/C.Z2Pol.Sadlej.10s6p2d.4s3p1d.
Z.Benkova,A.J.Sadlej,R.E.Oakes,S.E.Bell:
J. Comput. Chem. 26, 145-153 (2005)
************************************************************************
          6.0
* s-functions
  10
5240.6353 782.20480 178.35083 50.815942 16.823562 6.175776 2.418049
0.511900 0.156590 0.047900
 0.00093698  -0.00019825  0.0  0.0
 0.00722784  -0.00156289  0.0  0.0
 0.03634144  -0.00774345  0.0  0.0
 0.13061168  -0.03018300  0.0  0.0
 0.31888429  -0.07680492  0.0  0.0
 0.43887954  -0.16109835  0.0  0.0
 0.21474143  -0.09444475  0.0  0.0
 0.00953294   0.56455725  0.0  0.0
 0.0          0.0         1.0  0.0
 0.0          0.0         0.0  1.0
* p-functions
   6
18.84180 4.159240 1.206710 0.385540 0.121940 0.038568
 0.01386672  0.0  0.0
 0.08641841  0.0  0.0
 0.28783731  0.0  0.0
 0.50267179  0.0  0.0
 0.0         1.0  0.0
 0.0         0.0  1.0
* d-functions
   2
0.121940 0.038568
 1.00000000
 0.26402653

---------------------------------------------------------
Could someone explain how (or send an example) this should be
formatted for GAMESS?
Regards,
        Diniz Maciel


From owner-chemistry@ccl.net Thu Jun 14 17:39:00 2007
From: "Christopher Cramer cramer,,chem.umn.edu" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Negative frequency problem
Message-Id: <-34491-070614165439-18031-hCtCYJtpARj6C3rljWVD0g^server.ccl.net>
X-Original-From: Christopher Cramer <cramer###chem.umn.edu>
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Sent to CCL by: Christopher Cramer [cramer..chem.umn.edu]

--Apple-Mail-22--463697818
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    There have been several posts recently with questions and  
proposed solutions to the problem of "too many negative frequencies"  
for transition-state (TS) structures.

    First, at the risk of sounding needlessly didactic, the  
frequencies are not "negative," they are imaginary. It is the  
computed force constant that is negative. In the quantum mechanical  
harmonic oscillator (QMHO) approximation, the frequency is related to  
the square root of the force constant, and hence it is imaginary. It  
is a historical curiosity, probably relating to the difference  
between FORTRAN floating point and character variables, that most  
codes print the specific frequencies as negative numbers rather than  
appending Euler's "i" after the magnitude.

    On a more substantial front, several posters have offered  
suggestions for removing the "minor" imaginary frequency by  
perturbing geometries along the predicted normal mode, reoptimizing,  
generally jiggling structures, etc. Such procedures can indeed be  
effective, but only if the imaginary frequency is really there...  
Left unaddressed (at least in the most recent iteration of this  
thread -- I have vague memories that others may have posted to CCL on  
this point before) is the possibility that the unwanted imaginary  
frequency is an artifact of the quadrature grid used in a DFT  
calculation (recent posters have not actually specified their level  
of electronic structure theory, but given the prevalence of DFT in  
modern calculations, one suspects this was indeed their choice).

    Most (if not all) modern DFT functionals do NOT permit an  
analytic evaluation of the necessary volume integrals of the exchange- 
correlation potential. Instead, the integrals are solved via a  
quadrature procedure over a 3-dimensional grid. The so-called  
analytic derivatives and second derivatives are thus NOT analytic  
derivatives of the correct integrals, they are analytic derivatives  
of the quadrature schemes for these integrals. The accuracy of any  
quadrature approach depends on the density of the grid points, and,  
of course, the cost of the integral evaluation also goes up with the  
number of grid points. So, codes like Gaussian, Jaguar, ADF, NWChem,  
ORCA, etc. (sorry if I left out your favorite) have come up with  
default integration grids that represent good compromises for speed  
and accuracy. However, the demands on grid size increase as one  
becomes interested in not just the value of an integral, but also in  
the value of its first and second derivatives with respect to atomic  
positions. Thus, it is not at all uncommon with default grids to find  
a geometry that seems by all accounts to be, say, a local minimum,  
but gives a small imaginary frequency even though it has no symmetry  
and all attempts to rotate methyl groups (for instance) fail to  
eliminate the problem. TS structures can certainly suffer from  
exactly the same phenomenon. The problem is that the force constant  
is not being computed accurately enough by the quadrature scheme, NOT  
that there really is a negative curvature on the potential energy  
surface.

    So, what can one do? Some codes permit one to choose a finer  
quadrature grid, and this often does solve the problem. Of course,  
one can then worry about whether one should go back and recompute  
one's full set of stationary points with this finer grid (it's only  
computer time...) but at least one knows that the issue is not a  
chemical one. Another option is to compute the frequencies by finite  
difference of the first derivatives (probably even MORE expensive and  
not really an ideal option). Lastly, one can boldly rely on one's  
chemical intuition to know when one is being plagued by this problem  
and attempt to sleep well while blithely ignoring the issue (after  
all, the mode in question will have a "true" frequency that will  
contribute negligibly to zero-point vibrational energy, and  
negligibly to enthalpy, and will be so small that the correct value  
should not be used on the QMHO approximation for entropy in any case).

    For those wishing for a more complete discussion of these issues,  
I believe that Fritz Schaefer and co-workers recently published a  
paper or two comparing the convergence of default quadrature grids  
for various properties in various codes, but I'm too lazy to do the  
literature search for these inquiring individuals. Happy hunting.

Chris Cramer
--

Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone:  (612) 624-0859 || FAX:  (612) 626-2006
Mobile: (952) 297-2575
cramer(0)pollux.chem.umn.edu
http://pollux.chem.umn.edu/~cramer
(website includes information about the textbook "Essentials
     of Computational Chemistry:  Theories and Models, 2nd Edition")


--Apple-Mail-22--463697818
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<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; ">=A0 =A0There have been several =
posts recently with questions and proposed solutions to the problem of =
"too many negative frequencies" for transition-state (TS) =
structures.<DIV><BR class=3D"khtml-block-placeholder"></DIV><DIV>=A0 =
=A0First, at the risk of sounding needlessly didactic, the frequencies =
are not "negative," they are imaginary. It is the computed force =
constant that is negative. In the quantum mechanical harmonic oscillator =
(QMHO) approximation, the frequency is related to the square root of the =
force constant, and hence it is imaginary. It is a historical curiosity, =
probably relating to the difference between FORTRAN floating point and =
character variables, that most codes print the specific frequencies as =
negative numbers rather than appending Euler's "i" after the =
magnitude.</DIV><DIV><BR class=3D"khtml-block-placeholder"></DIV><DIV>=A0 =
=A0On a more substantial front, several posters have offered suggestions =
for removing the "minor" imaginary frequency by perturbing geometries =
along the predicted normal mode, reoptimizing, generally jiggling =
structures, etc. Such procedures can indeed be effective, but only if =
the imaginary frequency is really there... Left unaddressed (at least in =
the most recent iteration of this thread -- I have vague memories that =
others may have posted to CCL on this point before) is the possibility =
that the unwanted imaginary frequency is an artifact of the quadrature =
grid used in a DFT calculation (recent posters have not actually =
specified their level of electronic structure theory, but given the =
prevalence of DFT in modern calculations, one suspects this was indeed =
their choice).</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>=A0 =A0Most (if not all) =
modern DFT functionals do NOT permit an analytic evaluation of the =
necessary volume integrals of the exchange-correlation potential. =
Instead, the integrals are solved via a quadrature procedure over a =
3-dimensional grid. The so-called analytic derivatives and second =
derivatives are thus NOT analytic derivatives of the correct integrals, =
they are analytic derivatives of the quadrature schemes for these =
integrals. The accuracy of any quadrature approach depends on the =
density of the grid points, and, of course, the cost of the integral =
evaluation also goes up with the number of grid points. So, codes like =
Gaussian, Jaguar, ADF, NWChem, ORCA, etc. (sorry if I left out your =
favorite) have come up with default integration grids that represent =
good compromises for speed and accuracy. However, the demands on grid =
size increase as one becomes interested in not just the value of an =
integral, but also in the value of its first and second derivatives with =
respect to atomic positions. Thus, it is not at all uncommon with =
default grids to find a geometry that seems by all accounts to be, say, =
a local minimum, but gives a small imaginary frequency even though it =
has no symmetry and all attempts to rotate methyl groups (for instance) =
fail to eliminate the problem. TS structures can certainly suffer from =
exactly the same phenomenon. The problem is that the force constant is =
not being computed accurately enough by the quadrature scheme, NOT that =
there really is a negative curvature on the potential energy =
surface.</DIV><DIV><BR class=3D"khtml-block-placeholder"></DIV><DIV>=A0 =
=A0So, what can one do? Some codes permit one to choose a finer =
quadrature grid, and this often does solve the problem. Of course, one =
can then worry about whether one should go back and recompute one's full =
set of stationary points with this finer grid (it's only computer =
time...) but at least one knows that the issue is not a chemical one. =
Another option is to compute the frequencies by finite difference of the =
first derivatives (probably even MORE expensive and not really an ideal =
option). Lastly, one can boldly rely on one's chemical intuition to know =
when one is being plagued by this problem and attempt to sleep well =
while blithely ignoring the issue (after all, the mode in question will =
have a "true" frequency that will contribute negligibly to zero-point =
vibrational energy, and negligibly to enthalpy, and will be so small =
that the correct value should not be used on the QMHO approximation for =
entropy in any case).</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>=A0 =A0For those wishing =
for a more complete discussion of these issues, I believe that Fritz =
Schaefer and co-workers recently published a paper or two comparing the =
convergence of default quadrature grids for various properties in =
various codes, but I'm too lazy to do the literature search for these =
inquiring individuals. Happy hunting.</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Chris Cramer<BR><DIV> <P =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">--</FONT></P> <P =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; =
min-height: 14.0px"><BR></P> <P style=3D"margin: 0.0px 0.0px 0.0px =
0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">Christopher J. Cramer</FONT></P> <P style=3D"margin: 0.0px =
0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica">University of Minnesota</FONT></P> <P style=3D"margin: =
0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" size=3D"3" =
style=3D"font: 12.0px Helvetica">Department of Chemistry</FONT></P> <P =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">207 Pleasant St. =
SE</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">Minneapolis, MN 55455-0431</FONT></P> <P style=3D"margin: =
0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" size=3D"3" =
style=3D"font: 12.0px Helvetica">--------------------------</FONT></P> =
<P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">Phone:<SPAN =
class=3D"Apple-converted-space">=A0 </SPAN>(612) 624-0859 || FAX:<SPAN =
class=3D"Apple-converted-space">=A0 </SPAN>(612) 626-2006</FONT></P> <P =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">Mobile: (952) =
297-2575</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica"><A =
href=3D"mailto:cramer(0)pollux.chem.umn.edu">cramer(0)pollux.chem.umn.edu</A><=
/FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica"><A =
href=3D"http://pollux.chem.umn.edu/~cramer">http://pollux.chem.umn.edu/~cr=
amer</A></FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica">(website =
includes information about the textbook "Essentials</FONT></P> <P =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica"><SPAN =
class=3D"Apple-converted-space">=A0 =A0 </SPAN>of Computational =
Chemistry:<SPAN class=3D"Apple-converted-space">=A0 </SPAN>Theories and =
Models, 2nd Edition")</FONT></P>  </DIV><BR></DIV></BODY></HTML>=

--Apple-Mail-22--463697818--


From owner-chemistry@ccl.net Thu Jun 14 18:49:00 2007
From: "ALBERT POATER TEIXIDOR albert.poater-x-udg.edu" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: TS calculation with PCM
Message-Id: <-34492-070614165951-21332-h3+8LACW4f12LiGw3m5arA#,#server.ccl.net>
X-Original-From: "ALBERT POATER TEIXIDOR" <albert.poater**udg.edu>
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Date: Thu, 14 Jun 2007 20:52:50 +0200 (CEST)
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Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater(~)udg.edu]
Dear PCM users,
Just in the SCRF keywork include READ, so: SCRF=(pcm,read) and at the end
of the input
SPHEREONH=2
Hope this helps,
Albert


>
> Sent to CCL by: "Chunyi  Sung" [juneyi1[*]yahoo.com.tw]
> Hi,
>
>    I am studying a gas phase reaction using PCM model
> to see how the reaction goes in the presence of a solvent.
> When I tried to find the transtion state structure with
> PCM model (started with the transition state structure found
> in gas phase), I got an error like this before getting any
> SCF cycle done:
>
> United Atom Topological Model (UA0  parameters set).
> UA0: Hydrogen 2 is unbound. Keep it explicit at all point on the
> UA0: potential energy surface to get meaningful results.
>
> This step is actually about a hydrogen transferring from
> a carbon to oxygen, so the hydrogen was not closely bound
> to any atoms in the initial geometry (the transition state
> structure in gas phase).
>
> So, what do I do to keep the hydrogen explicit?
> or this error is just telling me that this reaction is actually
> not going to happen in the solvent?
>
> thanks
>
> Chunyi>
>
>
>


Albert Poater Teixidor
University of Salerno


From owner-chemistry@ccl.net Thu Jun 14 19:24:00 2007
From: "Quentin McDonald dqmcdonald+/-mac.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Phase Force Fields
Message-Id: <-34493-070614172839-11070-ZHIaj59raBfnasBYgIVd8Q/./server.ccl.net>
X-Original-From: Quentin McDonald <dqmcdonald,+,mac.com>
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Date: Fri, 15 Jun 2007 08:41:45 +1200
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Sent to CCL by: Quentin McDonald [dqmcdonald]![mac.com]
>
Hi Richard,

> We're trying to do pharmacophore modeling of a series of  
> peptidomimetics
> using the program Phase. According to the Phase manual, the force  
> field choices when doing the generation of conformers are MMFFs and  
> OPLS 2005. We'd like to use the MMFFs force field, but we have  
> noticed that the program uses MacroModel atom types, as our  
> nitrogens come out being typed wrong (N2 when they should be amide  
> nitrogens). No matter what one does, you can't get away from the  
> MacroModel atom types.  We'd like to use the NC=O type for the  
> amide nitrogens, but that type isn't defined in the file atom.typ.  
> There is a file called sybyl.typ that seems to convert N.am to N.2,  
> but there is no way to get around this, even if one uses a file  
> format other than mol2 (ie, like a maestro file).
>
> We have two questions: How do we implement this atom type (NC=O) in  
> our
> calculations, and secondly, how do we assure ourselves that we are  
> indeed
> using the MMFFs force field, and not some hybrid using MacroModel  
> atom types and functionals from the MMFFs force field?

N2 is the appropriate type for amides in MacroModel and conformer  
generation in Phase. If you run with MMFFs the correct parameters  
should be assigned and used in the calculation. Do you have any  
reason to think this is not happening?


Quentin


From owner-chemistry@ccl.net Thu Jun 14 22:44:01 2007
From: "Qing Shao shaoqingfly1981,gmail.com" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: diffusion in zeolite
Message-Id: <-34494-070614223109-26030-6wKlPeCehOBljORFADvong_+_server.ccl.net>
X-Original-From: "Qing Shao" <shaoqingfly1981_._gmail.com>
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Sent to CCL by: "Qing Shao" [shaoqingfly1981..gmail.com]
Hi Frapper:
 The diffusion of molecules is calculated according to the MD simulation. 
There are several free MD program such as Gromacs (http://www.gromacs.org) and NAMD (http://www.ks.uiuc.edu/Research/namd/) which you may download freely from their websits.
The desorption and adsorption are usually treated with GCMC and GEMC simulation. You could find Towhee (http://towhee.sourceforge.net/) and several availabel package from CCP5(http://www.ccp5.ac.uk/)
The Music is the package which combine all the codes for MD and MC. However, you may do the separated simulations with the different package. It is the same, i guess.
Good Luck.




Qing Shao
2007-06-15



·¢¼þÈË£º Gilles Frapper gilles.frapper-*-univ-poitiers.fr
·¢ËÍʱ¼ä£º 2007-06-15 03:38:56
ÊÕ¼þÈË£º Shao, Qing 
³­ËÍ£º 
Ö÷Ì⣺ CCL: diffusion in zeolite

Bonjour,

We are looking for a FREE program in MM or QM/MM to study:
- the diffusion of organic molecules in zeolites (FAU X or Y: Si, O, Al, Na or Cs, H) 
- the desorption of organic molecules from zeolite to water or organic solvant such as n-heptane (interface solid/liquid).

Music http://zeolites.cqe.northwestern.edu/Music seems appropriate. 

What else ? References ?

Bonne journ¨¦e

Gilles Frapper
groupe chimie quantique appliqu¨¦e
UMR CNRS 6503 - LACCO - Universit¨¦ de Poitiers
40, av. recteur Pineau 86022 Poitiers cedex
tel : 05 49 45 35 74 - mel : gilles.frapper(~)univ-poitiers.fr
site : http://labo.univ-poitiers.fr/yargla