From owner-chemistry@ccl.net Thu Jul 21 00:21:21 2005
From: "CCL" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: W:molecular orbitals and potential energy scan
Message-Id: <-28909-050721002010-7812-eSc6C2yCCSce8pLLLmWjCA[A]server.ccl.net>
X-Original-From: "Bryan Wong" <usagi01[A]gmail.com>
Sent to CCL by: "Bryan Wong" <usagi01[A]gmail.com>
Hi!
Does anyone know if there is an IOP keyword in Gaussian that will print out the molecular orbital coefficients for every single point in a potential energy scan?
Bryan
From owner-chemistry@ccl.net Thu Jul 21 04:08:54 2005
From: "CCL" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: W:molecular orbitals and potential energy scan
Message-Id: <-28910-050721025023-499-eSc6C2yCCSce8pLLLmWjCA%x%server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= <nicolas.ferre%x%up.univ-mrs.fr>
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Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= <nicolas.ferre%x%up.univ-mrs.fr>
Hi, IOp(5/33=2) should print MOs as long as density matrices.
CCL a �crit :
> Sent to CCL by: "Bryan Wong" <usagi01[A]gmail.com>
> Hi!
>
> Does anyone know if there is an IOP keyword in Gaussian that will print out the molecular orbital coefficients for every single point in a potential energy scan?
>
> Bryan>
>
>
>
>
--
*********** Dr. Nicolas Ferre' ***********
Laboratoire de Chimie Theorique et de Modelisation Moleculaire
UMR 6517 - CNRS Universites Aix-Marseille Case 521
Centre de Saint-Jerome 13397 - Marseille Cedex 20, France
Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58
http://www.up.univ-mrs.fr/cbrl/lctmm
**************************************************************
From owner-chemistry@ccl.net Thu Jul 21 04:43:04 2005
From: "CCL" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: CCSD convergence in g03
Message-Id: <-28911-050721043851-23271-eSc6C2yCCSce8pLLLmWjCA(_)server.ccl.net>
X-Original-From: Gert von Helden <helden(_)fhi-berlin.mpg.de>
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Sent to CCL by: Gert von Helden <helden(_)fhi-berlin.mpg.de>
Dear all,
I am trying to do a single point calculation of a molecular complex at
the CCSD(T) level using g03 rev C.02, 64 bit on an Opteron. I am using
the 6-311++G(2d,p) basis, resulting in 408 BFs. The problem is that the
CCSD does not converge. The convergence of the wavefunction ("Norm of
the A-vectors") oscillates between 1E-3 and 1E-4 and convergence, even
after 50 iterations, is nowhere in sight. Delta E oscillates between
1E-6 and 1E-8.
Would a different basis set help? The disk is to small for the
aug-cc-pvtz basis.
I would appreciate any suggestions.
Thanks,
Gert von Helden
-------------------------------------
Gert von Helden
Fritz-Haber-Institut der Max-Planck-Gesellschaft
Faradayweg 4-6
14195 Berlin
tel.: +49-30-8413 5615
fax: +49-30-8413 5603
From owner-chemistry@ccl.net Thu Jul 21 06:39:57 2005
From: "CCL" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: PCM error termination Gaussian03
Message-Id: <-28912-050721055937-15738-eSc6C2yCCSce8pLLLmWjCA[#]server.ccl.net>
X-Original-From: Sofia Godinho <godinho.sofia[#]gmail.com>
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Sent to CCL by: Sofia Godinho <godinho.sofia[#]gmail.com>
Dear CCL member,
while running a PCM calculation with Gaussian03 I got an error
message. This happens both when I try to optimise with IEFPCM or to
run just a PCM SinglePoint. And not just with one conformation. I
tried two different for the same molecule.
The last part of one the output files is as follows:
---------------------------------------------------------------------------------------------------------------------------
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UAHF (United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.200 OFac=0.890).
Default sphere list used, NSphG= 13.
Tesserae with average area of 0.200 Ang**2.
Solvent : Water, Eps = 78.390000
Eps(inf)= 1.776000
RSolv = 1.385000 Ang.
------------------------------------------------------------------------------
AdVTs1: ISph= 648 is engulfed by JSph= 649 but Ae( 648) is not yet zero!
Error termination via Lnk1e in /usr/local/chem/g03.C02/g03/l301.exe
at Sat Jul 16 17:39:50 2005.
-----------------------------------------------------------------------------------------------------------------------------------
What does this means?...How to get around it?
Could you kindly help me to solve the problem?
Many thanks!
Sofia Godinho
godinho.sofia at gmail.com
From owner-chemistry@ccl.net Thu Jul 21 06:40:39 2005
From: "CCL" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: W:All electron basis set for La-Ac
Message-Id: <-28913-050721063527-18579-eSc6C2yCCSce8pLLLmWjCA]~[server.ccl.net>
X-Original-From: "Jordi Cirera" <jordi.cirera]~[qi.ub.es>
Sent to CCL by: "Jordi Cirera" <jordi.cirera]~[qi.ub.es>
We are trying to do calculations in organometallic systems with Lantanide elements,and we
want to do it with all electron basis set. We have found the ANO-RCC basis set that is all
electron, but is decontracted (and really big), and we are interested in know if someone knows
if there is another basis set for those elementes contracted. Thanks in advance to all of you.
Jordi Cirera
From owner-chemistry@ccl.net Thu Jul 21 07:43:47 2005
From: "CCL" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: photoabsorbtion/photodetachment
Message-Id: <-28914-050721074215-17742-eSc6C2yCCSce8pLLLmWjCA|*|server.ccl.net>
X-Original-From: may abdelghani <may01dz|*|yahoo.fr>
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Sent to CCL by: may abdelghani <may01dz|*|yahoo.fr>
Hello, CCLers
what is the diference between photoabsorbtion and
photodetachment, and how we can modelate them
theoriticaly?
best regards
___________________________________________________________________________
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From owner-chemistry@ccl.net Thu Jul 21 14:06:25 2005
From: "CCL" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: PMF drug-docking scoring function
Message-Id: <-28915-050721132854-24413-eSc6C2yCCSce8pLLLmWjCA[a]server.ccl.net>
X-Original-From: Mark Thompson <mark[a]arguslab.com>
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Sent to CCL by: Mark Thompson <mark[a]arguslab.com>
I would like to hear from anyone who has an implementation of Ingo
Muegge's PMF scoring function in a commercial or non-commercial product.
I am interested in comparing some results.
Thanks in advance,
Mark Thompson
mark[a]arguslab.com
http://www.arguslab.com
From owner-chemistry@ccl.net Thu Jul 21 16:02:59 2005
From: "CCL" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: CCL smiles
Message-Id: <-28916-050721151732-10176-eSc6C2yCCSce8pLLLmWjCA^-^server.ccl.net>
X-Original-From: "Robinson, James" <James.Robinson^-^evotec.com>
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Sent to CCL by: "Robinson, James" <James.Robinson^-^evotec.com>
Smiles are a good choice for storing and sorting textual information.
However, ring closure reaction are often stereospecific as one must
decide between thermodynamic and kinetic products. Smiles strings may
not be the best choice for storing stereoisomers. To find the preferred
outcome from a ring closure you might use a script that allows for
Baldwins rules of ring closure. It took me a few years with b3lyp to
sort out a set of ring closures. Also gas phase calcs may yield stable
zwitterions whereas solvated calcs may not indicate stable zwitterions.
James
-----Original Message-----
> From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net]
Sent: 17 July 2005 17:49
To: Robinson, James
Subject: CCL: W:SMILES AND MODELLING
Sent to CCL by: "Antonio Starcevic" <astar{:}pbf.hr> Dear All;
We are a academic group working on a bioinformatics application written
in Java, that involves certain chemistry solutions. That's the part we
need some help solving. We are storing our molecules in SMILES format,
and at the end our goal is to turn linear structures into cyclisized.
FIRST QUESTION: are SMILES the best choice for database entries and
computation
of new structres???
SECOND QUESTION: if you model spontaneous cyclization from a linear
compound, how can you determine which product out of all possible ones
is most likely to be the real thing
THIRD QUESTION: is there a software that can help us solve "second
question", and could you recomend us some(it should cooperate with
SMILES "Daylight toolkit" if possible)
P.S. are there any Java libraries for this stuff???
Thanks for all suggestions!