From owner-chemistry@ccl.net Wed Mar 7 03:01:00 2007
From: "Sten Nilsson Lill stenil*o*chem.gu.se" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL:G: G03 Optimization problem
Message-Id: <-33755-070306210626-9989-zAtfsLsAXu3fKNehdoFjMw~!~server.ccl.net>
X-Original-From: "Sten Nilsson Lill" <stenil(_)chem.gu.se>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Wed, 7 Mar 2007 02:10:28 +0100 (CET)
MIME-Version: 1.0
Sent to CCL by: "Sten Nilsson Lill" [stenil{=}chem.gu.se]
Dear Aniel,
you can try to increase the accuracy in the early phase of the scf by
using scf=novaracc. If it doesn't work, let the program make a new guess,
i.e. take guess=read away from your input and include also scf=novaracc.
If you are running unrestricted DFT just be careful to check that your
spin distribution doesn't change too much from your current values when
the program makes a new guess.
Hope this gives some help!
Regards,
Sten Nilsson Lill
>
> Hi All,
> I have one problem and one question; first on "optimization" and second on
> "IOps".
>
> 1) I was trying to optimize a small metallic clusters (6-8 atoms) using
> SDD basis set and PBE1PBE using G03. However, I encounter some problems
> with the optimization and quit the calculation with the following error.
> Error termination request processed by link 9999.
>
> The energy is very close to converge, but the Maximum Force and RMS Force
> do not converge.
> The error message is:
> Item Value Threshold
> Converged?
> Maximum Force 0.002180 0.000450 NO
> RMS Force 0.000952 0.000300 NO
> Maximum Displacement 0.000010 0.001800 YES
> RMS Displacement 0.000005 0.001200 YES
> Predicted change in Energy=-2.455189D-05
> Optimization stopped.
> -- Number of steps exceeded, NStep= 31
> -- Flag reset to prevent archiving.
>
> grep "SCF D" {last 4 steps}
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 3 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 2 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917095 A.U. after 4 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 4 cycles
>
> I restarted the calculation from chk file; but again, the Max/RMS Force do
> not converge. Could you please tell me what modifications I should include
> in the "input" file?
> (input details for 6 atoms:
> #P pbe1pbe/SDD opt=(calcfc,maxstep=50) symm=(PG=Oh) geom=checkpoint
> guess=read)
>
> 2) What exactly is IOps? I checked the G03 manual, but did not understand
> the logic behind in choosing the correct numerator and denominator and
> integer after the "=" sign. How can I find out the correct/proper
> values/numbers to use in IOps? For example, Does the following IOp
> statement has any special meaning?
> IOp(5/42=10000428,5/43=05720572,5/44=10001000)
>
> I would really take any feedback from you. Thanks in advance.
>
> Sincerely,
> Aniel
>
>
>
>
>
> Send instant messages to your online friends http://uk.messenger.yahoo.com
Ph. D. Sten Nilsson Lill
Dep. of Chemistry
G�teborg University
Kemig�rden 4
S-412 96 G�teborg, Sweden
Phone: +46-31-772 2901
Fax: +46-31-772 3840
E-mail: stenil]^[chem.gu.se
Alternative e-mail: slill1]^[lsu.edu
From owner-chemistry@ccl.net Wed Mar 7 05:47:00 2007
From: "Ioan SILAGHI-DUMITRESCU isi*_*chem.ubbcluj.ro" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL:G: G03 Optimization problem
Message-Id: <-33756-070307051945-862-vuw0iiSFXXZWZYxzEDJfdg.@.server.ccl.net>
X-Original-From: Ioan SILAGHI-DUMITRESCU <isi[*]chem.ubbcluj.ro>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Wed, 7 Mar 2007 12:09:12 +0200 (EET)
MIME-Version: 1.0
Sent to CCL by: Ioan SILAGHI-DUMITRESCU [isi*chem.ubbcluj.ro]
Aniel,
Reducing the symmetry of the system might solve the first problem. I
encountered similar sitations when the cluster have a C5 axes and small
deviations of the coordinates from the perfect symmetry lead to normal
tremination of the optimization.
For the second question the Technical Support Information of Gaussian.com
(http://www.gaussian.com/iops.htm)
Hope this helps,
isi
---------------------------------------------------------------------
Prof.dr. Ioan Silaghi-Dumitrescu
Department of Chemistry | Facultatea de Chimie si Inginerie Chimica
Babes-Bolyai University | Universitatea Babes-Bolyai
1, Kogalniceanu str. | str. Kogalniceanu, nr.1
RO-400084 Cluj-Napoca, | RO-400084 Cluj-Napoca
Roumania | Romania
e-mail: isi.:.chem.ubbcluj.ro
Fax: +40-264-590818
Tel: +40-264-593833 ext.5665
On Tue, 6 Mar 2007, Aniel Aron anisamron+*+yahoo.com wrote:
>
Hi All,
I have one problem and one question; first on "optimization" and second on "IOps".
1) I was trying to optimize a small metallic clusters (6-8 atoms) using SDD basis set and PBE1PBE using G03. However, I encounter some problems with the optimization and quit the calculation with the following error.
Error termination request processed by link 9999.
The energy is very close to converge, but the Maximum Force and RMS Force do not converge.
The error message is:
Item Value Threshold Converged?
Maximum Force 0.002180 0.000450 NO
RMS Force 0.000952 0.000300 NO
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000005 0.001200 YES
Predicted change in Energy=-2.455189D-05
Optimization stopped.
-- Number of steps exceeded, NStep= 31
-- Flag reset to prevent archiving.
grep "SCF D" {last 4 steps}
SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 3 cycles
SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 2 cycles
SCF Done: E(UPBE+HF-PBE) = -1017.54917095 A.U. after 4 cycles
SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 4 cycles
I restarted the calculation from chk file; but again, the Max/RMS Force do not converge. Could you please tell me what modifications I should include in the "input" file?
(input details for 6 atoms:
#P pbe1pbe/SDD opt=(calcfc,maxstep=50) symm=(PG=Oh) geom=checkpoint guess=read)
2) What exactly is IOps? I checked the G03 manual, but did not understand the logic behind in choosing the correct numerator and denominator and integer after the "=" sign. How can I find out the correct/proper values/numbers to use in IOps? For example, Does the following IOp statement has any special meaning?
IOp(5/42=10000428,5/43=05720572,5/44=10001000)
I would really take any feedback from you. Thanks in advance.
Sincerely,
Aniel
Send instant messages to your online friends http://uk.messenger.yahoo.com
From owner-chemistry@ccl.net Wed Mar 7 08:33:01 2007
From: "Ulrike Salzner salzner(-)fen.bilkent.edu.tr" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL:G: G03 Optimization problem
Message-Id: <-33757-070307063139-25745-npaEEgkIzIjXbLvJfIMzTQ,,server.ccl.net>
X-Original-From: Ulrike Salzner <salzner a fen.bilkent.edu.tr>
Content-Transfer-Encoding: 7bit
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Date: Wed, 07 Mar 2007 13:31:13 +0200
MIME-Version: 1.0
Sent to CCL by: Ulrike Salzner [salzner++fen.bilkent.edu.tr]
Hi,
it looks to me like you have an extremly flat energy potential energy
surface. Your total energy is not changing anymore and the forces are
small while there are significant displacements. You can increase the
number of steps by defining "MAXCYCLE=N" and choose N larger than 31.
Maybe the optimization will converge at Step 35 or so. However, in your
case this might lead nowhere since the molecule is floppy. I would check
the geometry changes and if they are not very big I would just stop the
calculation and accept the physics. The threshold values in the program
are reasonable for most cases but might not be suitable for every molecule.
Tegards,
Ulrike Salzner
> Hi All,
> I have one problem and one question; first on "optimization" and
> second on "IOps".
>
> 1) I was trying to optimize a small metallic clusters (6-8 atoms)
> using SDD basis set and PBE1PBE using G03. However, I encounter some
> problems with the optimization and quit the calculation with the
> following error. Error termination request processed by link 9999.
>
> The energy is very close to converge, but the Maximum Force and RMS
> Force do not converge.
> The error message is:
> Item Value Threshold
> Converged?
> Maximum Force 0.002180 0.000450 NO
> RMS Force 0.000952 0.000300 NO
> Maximum Displacement 0.000010 0.001800 YES
> RMS Displacement 0.000005 0.001200 YES
> Predicted change in Energy=-2.455189D-05
> Optimization stopped.
> -- Number of steps exceeded, NStep= 31
> -- Flag reset to prevent archiving.
>
> grep "SCF D" {last 4 steps}
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 3 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 2 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917095 A.U. after 4 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 4 cycles
>
> I restarted the calculation from chk file; but again, the Max/RMS
> Force do not converge. Could you please tell me what modifications I
> should include in the "input" file?
> (input details for 6 atoms: #P pbe1pbe/SDD opt=(calcfc,maxstep=50)
> symm=(PG=Oh) geom=checkpoint guess=read)
>
> 2) What exactly is IOps? I checked the G03 manual, but did not
> understand the logic behind in choosing the correct numerator and
> denominator and integer after the "=" sign. How can I find out the
> correct/proper values/numbers to use in IOps? For example, Does the
> following IOp statement has any special meaning?
> IOp(5/42=10000428,5/43=05720572,5/44=10001000)
>
> I would really take any feedback from you. Thanks in advance.
>
> Sincerely,
> Aniel
>
>
>
>
>
> Send instant messages to your online friends
> http://uk.messenger.yahoo.comhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>
>
>
From owner-chemistry@ccl.net Wed Mar 7 10:27:01 2007
From: "Taye Beyene Demisse sene3095.:.yahoo.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Sever error message2070
Message-Id: <-33758-070307102159-9521-3Bnb3hT/gN+1MDQz5EXzkg^_^server.ccl.net>
X-Original-From: "Taye Beyene Demisse" <sene3095(~)yahoo.com>
Date: Wed, 7 Mar 2007 10:21:56 -0500
Sent to CCL by: "Taye Beyene Demisse" [sene3095%x%yahoo.com]
Dear subscribers, when I am calculating frequency for a molecule containing 227 alpha and 227 beta electrons, it terminates by reporting "severe error message2070". What is this message? is there any material that clarify error message types? Please help.
Thanks.
Taye
From owner-chemistry@ccl.net Wed Mar 7 11:01:01 2007
From: "Stradella, Omar omar.stradella{=}intel.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: calculating titration state distributions for multiprotic acids with coupled sites
Message-Id: <-33759-070303113411-16175-BtWA30TPkRyyKhhiK5KjLw*_*server.ccl.net>
X-Original-From: "Stradella, Omar" <omar.stradella*intel.com>
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charset="us-ascii"
Date: Sat, 3 Mar 2007 10:58:57 -0500
MIME-Version: 1.0
Sent to CCL by: "Stradella, Omar" [omar.stradella .. intel.com]
On Fri, Feb 23, 2007, Seth Olsen s.olsen1,,uq.edu.au wrote:
>
> I have been trying to find references or algorithms which can estimate
> equilibrium distributions of different protonation states of a
> multiprotic acid where the sites may be coupled. Can anyone point me
in
> the right direction?
In the past I've used MCCE (Multi-Conformation Continuum Electrostatics)
> from Marilyn Gunner at CUNY with very good results.
http://www.sci.ccny.cuny.edu/~mcce/
Omar
--------------------
Omar Stradella, PhD
Life Sciences Applications Engineer
Intel Corp.
77 Reed Rd.
Hudson, MA 01749
Email: omar.stradella*o*intel.com
Phone: +1 978-553-5388
From owner-chemistry@ccl.net Wed Mar 7 11:36:01 2007
From: "Soren Eustis soren _ jhu.edu" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL:G: G03 Optimization problem
Message-Id: <-33760-070307112435-14737-zP4Of7hiYRzip7Yg9i7+iw_._server.ccl.net>
X-Original-From: "Soren Eustis" <soren##jhu.edu>
Content-language: en-us
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charset="iso-8859-1"
Date: Wed, 7 Mar 2007 10:24:06 -0500
MIME-Version: 1.0
Sent to CCL by: "Soren Eustis" [soren]|[jhu.edu]
This does not look like an SCF convergence problem, rather it is an
optimization convergence problem. You need to increase the number of
optimization cycles. Add OPT=MAXCYCLE=100 to your input. Also, You can try
OPT=(NRScale,Maxcycle=100) if you still have issues.
Soren N. Eustis
Graduate Research Assistant
Department of Chemistry
Johns Hopkins University
Remsen Hall
3400 N Charles Street
Baltimore, MD 21218
(410) 516-4675 (office)
(410) 925-5167 (cell)
(410) 516-8420 (fax)
soren() jhu.edu
-----Original Message-----
> From: owner-chemistry() ccl.net [mailto:owner-chemistry() ccl.net]
Sent: Tuesday, March 06, 2007 8:10 PM
To: Eustis, Soren
Subject: CCL:G: G03 Optimization problem
Sent to CCL by: "Sten Nilsson Lill" [stenil{=}chem.gu.se]
Dear Aniel,
you can try to increase the accuracy in the early phase of the scf by
using scf=novaracc. If it doesn't work, let the program make a new guess,
i.e. take guess=read away from your input and include also scf=novaracc.
If you are running unrestricted DFT just be careful to check that your
spin distribution doesn't change too much from your current values when
the program makes a new guess.
Hope this gives some help!
Regards,
Sten Nilsson Lill
>
> Hi All,
> I have one problem and one question; first on "optimization" and second on
> "IOps".
>
> 1) I was trying to optimize a small metallic clusters (6-8 atoms) using
> SDD basis set and PBE1PBE using G03. However, I encounter some problems
> with the optimization and quit the calculation with the following error.
> Error termination request processed by link 9999.
>
> The energy is very close to converge, but the Maximum Force and RMS Force
> do not converge.
> The error message is:
> Item Value Threshold
> Converged?
> Maximum Force 0.002180 0.000450 NO
> RMS Force 0.000952 0.000300 NO
> Maximum Displacement 0.000010 0.001800 YES
> RMS Displacement 0.000005 0.001200 YES
> Predicted change in Energy=-2.455189D-05
> Optimization stopped.
> -- Number of steps exceeded, NStep= 31
> -- Flag reset to prevent archiving.
>
> grep "SCF D" {last 4 steps}
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 3 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 2 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917095 A.U. after 4 cycles
> SCF Done: E(UPBE+HF-PBE) = -1017.54917094 A.U. after 4 cycles
>
> I restarted the calculation from chk file; but again, the Max/RMS Force do
> not converge. Could you please tell me what modifications I should include
> in the "input" file?
> (input details for 6 atoms:
> #P pbe1pbe/SDD opt=(calcfc,maxstep=50) symm=(PG=Oh) geom=checkpoint
> guess=read)
>
> 2) What exactly is IOps? I checked the G03 manual, but did not understand
> the logic behind in choosing the correct numerator and denominator and
> integer after the "=" sign. How can I find out the correct/proper
> values/numbers to use in IOps? For example, Does the following IOp
> statement has any special meaning?
> IOp(5/42=10000428,5/43=05720572,5/44=10001000)
>
> I would really take any feedback from you. Thanks in advance.
>
> Sincerely,
> Aniel
>
>
>
>
>
> Send instant messages to your online friends http://uk.messenger.yahoo.com
Ph. D. Sten Nilsson Lill
Dep. of Chemistry
G�teborg University
Kemig�rden 4
S-412 96 G�teborg, Sweden
Phone: +46-31-772 2901
Fax: +46-31-772 3840
E-mail: stenil|*|chem.gu.se
Alternative e-mail: slill1|*|lsu.eduhttp://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 Wed Mar 7 12:11:00 2007
From: "Shobe, David David.Shobe!^!sud-chemie.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Sever error message2070
Message-Id: <-33761-070307113231-18408-9N2ibROBQDE+5nCBqjQjIg#,#server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe===sud-chemie.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
charset="iso-8859-1"
Date: Wed, 7 Mar 2007 17:32:17 +0100
MIME-Version: 1.0
Sent to CCL by: "Shobe, David" [David.Shobe^sud-chemie.com]
What comp-chem program and operating system are you using?
Regards,
--David Shobe
S�d-Chemie, Inc.
Attention to detial is essentail.
-----Original Message-----
> From: owner-chemistry : ccl.net [mailto:owner-chemistry : ccl.net]
Sent: Wednesday, March 07, 2007 10:22 AM
To: Shobe, David
Subject: CCL: Sever error message2070
Sent to CCL by: "Taye Beyene Demisse" [sene3095%x%yahoo.com] Dear subscribers, when I am calculating frequency for a molecule containing 227 alpha and 227 beta electrons, it terminates by reporting "severe error message2070". What is this message? is there any material that clarify error message types? Please help.
Thanks.
Tayehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message.
Thank you.
From owner-chemistry@ccl.net Wed Mar 7 13:36:00 2007
From: "Jose Gamez joseantonio.gamez|a|uam.es" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL:G: Restart a scan from a point not converged
Message-Id: <-33762-070307112957-17253-8q9ITy1fTy7pnOdSkMNtgg],[server.ccl.net>
X-Original-From: "Jose Gamez" <joseantonio.gamez.:.uam.es>
Date: Wed, 7 Mar 2007 11:29:54 -0500
Sent to CCL by: "Jose Gamez" [joseantonio.gamez,uam.es]
Hi, everyone. I would like to ask for some help.
I was doing a scan to follow the reaction path of a reaction with Gaussian 03. The eighth point didn't converge as it exceeded the limit number of optimisation cycles, having then the ninth and so forth really wierd strucutres. Is there any way in which i could restart the scan from the eighth point? I mean, could i choose the point from which i can restart it? That makes me think if there is some options or anywith to tell Gaussian to stop a scan when one of the points is not fully converged
Thanks for your help
Cheers
Jos A. Gmez
joseantonio.gamez<at>uam.es
Departamento de Qumica. Universidad Autnoma de Madrid.
Spain
From owner-chemistry@ccl.net Wed Mar 7 14:11:00 2007
From: "Peeter Burk peeter.burk ~ ut.ee" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: NH4NO3 Structure
Message-Id: <-33763-070304033107-16631-me43TqNcOclUSZPuJTISnQ-*-server.ccl.net>
X-Original-From: Peeter Burk <peeter.burk-,-ut.ee>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Sun, 4 Mar 2007 09:54:45 +0200 (EET)
MIME-Version: 1.0
Sent to CCL by: Peeter Burk [peeter.burk]~[ut.ee]
Hi,
It seems that HNO3 is a too weak acid (and NH3 is too weak base) to give
you proton transfered product (i.e. salt). That means, if the hydrogen
bonded acid-base pair is more stable than ion pair, thats what you get.
The suggestion of adding some explicit water molecules might help as it
usually stabilizes both anion and cation...
Best regards
Peeter
On Fri, 2 Mar 2007, Cory Pye cpye|*|crux.smu.ca wrote:
>
> Sent to CCL by: Cory Pye [cpye]~[crux.smu.ca]
> Hi,
>
> My quess is either that you will need to add a few explicit water molecules to
> solvate the cluster and allow the ions to form, or to implicitly add a solvent
> using a variant of PCM, perhaps. Glycine zwitterion has the same problem in
> vacuo.
>
> -Cory Pye
>
> On Fri, 2 Mar 2007, Young Leh youngleh * gmail.com wrote:
>
> >
> > Sent to CCL by: "Young Leh" [youngleh*|*gmail.com]
> > Dear CCLer,
> >
> > I have problem while optimizing the structure of NH4NO3. It looks like no matter what my initial structure is, the structure always ends up with CH3 & HNO3. Could somebody please provide me some help on this, a xyz or pdb file will greatly help?
> >
> > Thanks all
> >
> > Young Leh
> >
>
> ************* ! Dr. Cory C. Pye
> ***************** ! Associate Professor
> *** ** ** ** ! Theoretical and Computational Chemistry
> ** * **** ! Department of Chemistry, Saint Mary's University
> ** * * ! 923 Robie Street, Halifax, NS B3H 3C3
> ** * * ! cpye++crux.stmarys.ca http://apwww.stmarys.ca/~cpye
> *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104
> ***************** !
> ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans)>
>
>
>
>
> --
> This message was scanned for spam and viruses by BitDefender.
> For more information please visit http://linux.bitdefender.com/
>
>
---
Peeter Burk Jakobi 2, 51014 Tartu, Estonia
Institute of Chemical Physics Phone (372-7) 375-258
Tartu University Fax (372-7) 375-264
Estonia E-mail peeter..chem.ut.ee
--
This message was scanned for spam and viruses by BitDefender.
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From owner-chemistry@ccl.net Wed Mar 7 14:47:01 2007
From: "Michael Potter potterm]|[verachem.com" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: Free tools for conformer generation and partial charge assignment
Message-Id: <-33764-070307114150-25619-kiEfkebHFd61QOx/G0NPzQ|server.ccl.net>
X-Original-From: "Michael Potter" <potterm]-[verachem.com>
Date: Wed, 7 Mar 2007 11:41:47 -0500
Sent to CCL by: "Michael Potter" [potterm^^verachem.com]
VeraChem is pleased to announce the release of three new products. All VeraChem products are now licensed free of charge to academic and other non-profit users!
Vconf, conformational search for drug-like molecules. In "prep" mode, Vconf quickly generates 3D structures suitable for docking and other torsional search applications, with multiple outputs for distinct ring-puckers. In "search" model, Vconf carries out thorough conformational searches and provides high-quality, low-energy conformations. Special features include:
- filtering to remove repeat conformations from the output, accounting for internal molecular symmetries
- option to hold a set of atoms rigidly fixed in the input conformation
- detailed control of chiral centers and double bond geometries.
For more information and download, go to http://www.verachem.com/vconf.html.
Vfilter, conformational filtering for drug-like molecules. Processes the output of Vconf or any other conformational analysis program to remove repeat conformations based upon energy or RMSD, accounting for symmetry. For more information and download, go to http://www.verachem.com/vfilter.html.
Vrms, calculation of RMSDs of conformations of a drug-like molecule, accounting for symmetries. RMSD with superposition is suitable for free ligands in solution; RMSD without superposition is suitable for docked ligands. For more information and download, go to http://www.verachem.com/vrms.html
Vcharge, rapid generation of RESP-like partial charges, is also available. For more information and download, go to http://www.verachem.com/vcharge.html.
Please feel free to contact me for additional information.
Regards,
Michael J. Potter
VeraChem LLC
potterm()verachem.com
From owner-chemistry@ccl.net Wed Mar 7 19:38:00 2007
From: "=?UTF-8?B?w5Zkw7ZuIEZhcmthcw==?= farkas!=!chem.elte.hu" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL:G: G03 Optimization problem
Message-Id: <-33765-070307130645-15135-wsnrIz4h9JBtcKiA0WIDVg|*|server.ccl.net>
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Date: Wed, 7 Mar 2007 19:04:36 +0100
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Dear Aniel,
=20
My guess is different from what the others suggested, the rest of the =
output may contain the real answer. It is really unusual that the step =
size converges in an optimiyation but the gradient not, so I think this =
problem is related to symmetry. You might have indication that the =
wavefunction breaks symmetry during the SCF. If this is the case, than =
the optimization will still produce a symmetric step, so you should turn =
of symmetry and try if it converges or not.
=20
The IOps are integer arrays to control the Gaussian links. At the =
beginning of the output you can find the route table. Containing the =
sequence of links and the assigned IOps, which is created automatically =
> from your command line. Using IOps you can alter these values or even =
run Gaussian using a non-standard route table (NonStd command).
=20
Best wishes,
=20
=C3=96d=C3=B6n
=20
=C3=96d=C3=B6n Farkas
Associate professor
Deparment of Organic Chemistry, Institute of Chemistry,
E=C3=B6tv=C3=B6s Lor=C3=A1nd University, Budapest
Address: 1/A P=C3=A1zm=C3=A1ny P=C3=A9ter s=C3=A9t=C3=A1ny, H-117 =
Budapest, Hungary
Phone: +36-1-372-2570
Cell phone: +36-30-255-3111
Fax: +36-1-372-2620
URL: http://organ.elte.hu/farkas
=20
-----Original Message-----
> From: owner-chemistry-,-ccl.net [mailto:owner-chemistry-,-ccl.net]=20
Sent: Tuesday, March 06, 2007 11:07 PM
To: Farkas, XdXXn
Subject: CCL:G: G03 Optimization problem
=20
Hi All,
I have one problem and one question; first on "optimization" and second =
on "IOps".
1) I was trying to optimize a small metallic clusters (6-8 atoms) using =
SDD basis set and PBE1PBE using G03. However, I encounter some problems =
with the optimization and quit the calculation with the following error. =
=20
Error termination request processed by link 9999.
The energy is very close to converge, but the Maximum Force and RMS =
Force do not converge.
The error message is:=20
Item Value Threshold =
Converged?
Maximum Force 0.002180 0.000450 NO
RMS Force 0.000952 0.000300 NO
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000005 0.001200 YES
Predicted change in Energy=3D-2.455189D-05
Optimization stopped.
-- Number of steps exceeded, NStep=3D 31
-- Flag reset to prevent archiving.
grep "SCF D" {last 4 steps}
SCF Done: E(UPBE+HF-PBE) =3D -1017.54917094 A.U. after 3 =
cycles
SCF Done: E(UPBE+HF-PBE) =3D -1017.54917094 A.U. after 2 =
cycles
SCF Done: E(UPBE+HF-PBE) =3D -1017.54917095 A.U. after 4 =
cycles
SCF Done: E(UPBE+HF-PBE) =3D -1017.54917094 A.U. after 4 =
cycles
I restarted the calculation from chk file; but again, the Max/RMS Force =
do not converge. Could you please tell me what modifications I should =
include in the "input" file?
(input details for 6 atoms:=20
#P pbe1pbe/SDD opt=3D(calcfc,maxstep=3D50) symm=3D(PG=3DOh) =
geom=3Dcheckpoint guess=3Dread)
2) What exactly is IOps? I checked the G03 manual, but did not =
understand the logic behind in choosing the correct numerator and =
denominator and integer after the "=3D" sign. How can I find out the =
correct/proper values/numbers to use in IOps? For example, Does the =
following IOp statement has any special meaning?
IOp(5/42=3D10000428,5/43=3D05720572,5/44=3D10001000)
I would really take any feedback from you. Thanks in advance.
Sincerely,
Aniel
Send instant messages to your online friends =
http://uk.messenger.yahoo.com=20
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<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Dear Aniel,</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>M</span></font><font size=3D2 =
color=3Dnavy
face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:Arial;
color:navy'>y guess is different from what the others suggested, the =
rest of
the output may contain the real answer. It is really unusual that the =
step size
converges in an optimiyation but the gradient not, so I think this =
problem is
related to symmetry. You might have indication that the wavefunction =
breaks symmetry
during the SCF. If this is the case, than the optimization will still =
produce a
symmetric step, so you should turn of symmetry and try if it converges =
or not.</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:navy'> </span></fo=
nt></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:navy'>The IOps are =
integer
arrays to control the Gaussian links. At the beginning of the output you =
can
find the route table. Containing the sequence of links and the assigned =
IOps, which
is created automatically from your command line. Using IOps you can =
alter these
values or even run Gaussian using a non-standard route table (NonStd =
command).</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:navy'> </span></fo=
nt></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:navy'>Best =
wishes,</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:navy'> </span></fo=
nt></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>=C3=96d=C3=B6n</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Arial;color:navy'> </span></fo=
nt></p>
<div>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>=C3=96d=C3=B6n =
Farkas</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>Associate =
professor</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>Deparment of Organic Chemistry, =
Institute
of Chemistry,</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>E=C3=B6tv=C3=B6s Lor=C3=A1nd =
University, Budapest</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>Address: 1/A P=C3=A1zm=C3=A1ny =
P=C3=A9ter s=C3=A9t=C3=A1ny, H-117
Budapest, Hungary</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>Phone: =
+36-1-372-2570</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>Cell phone: =
+36-30-255-3111</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>Fax: =
+36-1-372-2620</span></font></p>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>URL: =
http://organ.elte.hu/farkas</span></font></p>
</div>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
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<p class=3DMsoNormal style=3D'margin-left:35.4pt'><font size=3D2 =
face=3DTahoma><span
style=3D'font-size:10.0pt;font-family:Tahoma'>-----Original =
Message-----<br>
<b><span style=3D'font-weight:bold'>From:</span></b> =
owner-chemistry-,-ccl.net [mailto:owner-chemistry-,-ccl.net]
<br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Tuesday, March 06, =
2007
11:07 PM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> Farkas, XdXXn =
<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> CCL:G: G03 =
Optimization
problem</span></font></p>
<p class=3DMsoNormal style=3D'margin-left:35.4pt'><font size=3D3
face=3D"Times New Roman"><span =
style=3D'font-size:12.0pt'> </span></font></p>
<div>
<div>
<p class=3DMsoNormal =
style=3D'margin-right:0cm;margin-bottom:12.0pt;margin-left:
35.4pt'><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:12.0pt'><br>
Hi All,<br>
I have one problem and one question; first on "optimization" =
and
second on "IOps".<br>
<br>
1) I was trying to optimize a small metallic clusters (6-8 atoms) using =
SDD
basis set and PBE1PBE using G03. However, I encounter some problems with =
the
optimization and quit the calculation with the following error. =
<br>
<i><span style=3D'font-style:italic'>Error termination request processed =
by link
9999</span></i>.<br>
<br>
The energy is very close to converge, but the Maximum Force and RMS =
Force do
not converge.<br>
The error message is: <br>
<i><span style=3D'font-style:italic'> =
Item
Value =
Threshold
Converged?<br>
Maximum =
Force
0.002180 =
0.000450
NO<br>
RMS
Force =
0.000952 0.000300
NO<br>
Maximum Displacement
0.000010 0.001800 =
YES<br>
RMS
Displacement
0.000005 0.001200 =
YES<br>
Predicted change in Energy=3D-2.455189D-05<br>
Optimization stopped.<br>
-- Number of steps exceeded, NStep=3D =
31<br>
-- Flag reset to prevent archiving.</span></i><br>
<br>
grep "SCF D" {last 4 steps}<br>
<i><span style=3D'font-style:italic'> SCF Done: =
E(UPBE+HF-PBE) =3D
-1017.54917094 A.U. after 3 =
cycles<br>
SCF Done: E(UPBE+HF-PBE) =3D
-1017.54917094 A.U. after 2 =
cycles<br>
SCF Done: E(UPBE+HF-PBE) =3D
-1017.54917095 A.U. after 4 =
cycles<br>
SCF Done: E(UPBE+HF-PBE) =3D
-1017.54917094 A.U. after 4 =
cycles</span></i><br>
<br>
I restarted the calculation from chk file; but again, the Max/RMS Force =
do not
converge. Could you please tell me what modifications I should include =
in the
"input" file?<br>
(input details for 6 atoms: <br>
<i><span style=3D'font-style:italic'>#P pbe1pbe/SDD =
opt=3D(calcfc,maxstep=3D50)
symm=3D(PG=3DOh) geom=3Dcheckpoint guess=3Dread</span></i>)<br>
<br>
2) What exactly is IOps? I checked the G03 manual, but did not =
understand the
logic behind in choosing the correct numerator and denominator and =
integer
after the "=3D" sign. How can I find out the correct/proper
values/numbers to use in IOps? For example, Does the following IOp =
statement
has any special meaning?<br>
IOp(5/42=3D10000428,5/43=3D05720572,5/44=3D10001000)<br>
<br>
I would really take any feedback from you. Thanks in advance.<br>
<br>
Sincerely,<br>
Aniel<br>
<br>
</span></font></p>
</div>
</div>
<p class=3DMsoNormal style=3D'margin-left:35.4pt'><font size=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'><br>
Send instant messages to your online friends =
http://uk.messenger.yahoo.com </span></font></p>
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