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From: Sheng Cai <scai$at$umich.edu>
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Subject: curvilinear step not converged in G98
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Dear CCL'ers

I am runing OPT jobs (on a peptide with a few water molecules bound) with
Gaussian98. I used some constrains on water (fixed distances, angles, etc)
to fix the position of water. Whenever I used these constrains, I got
error message "Curvilinear step not converged, Error imposing
constaraints" and the jobs stoped before the first SCF. I tried many different
constraints (I need the position of water fixed), but none of them work.
Does anybody know how to solve this problem? Thanks.

Sincerely

Sheng Cai
Biophysics Research Division
University of Michigan
email: scai$at$umich.edu




From chemistry-request@ccl.net Fri Aug 22 04:11:44 2003
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In-Reply-To:  <Law15-F70m9ezrmjZ7z00001f9e^at^hotmail.com>
From: noel.oboyle2^at^mail.dcu.ie
Subject: RE: CCL:software for extracting first solvent shell
To: "Irene Newhouse" <einew^at^hotmail.com>
Cc: chemistry^at^ccl.net
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Hello again,
Please find attached the first and last tcl script I've ever written. This
sort of script only works with the latest version of Hyperchem (I think).

You can open the script with Notepad to see how it works and to change some
of the built-in parameters. The script assumes the solute molecule is molecule
1, and that every other molecule is solvent. It defines the first solvation
shell as every solvent molecule with an atom within 3 Angstroms of an atom
of the solute molecule. I invented that definition so feel free to change
that value.

To 'run' the script, you just go to Script/Open Script/File of Type Tcl.

Oh oh, I've just noticed - the script only works for solvent molecules with
three atoms. You should change the number 3 in the following line to the
number of atoms in each solvent molecule.

	while { $j <= 3 } {

Tell me if you have any problems,
Noel

>-- Original Message --
>From: "Irene Newhouse" <einew^at^hotmail.com>
>To: noel.oboyle2^at^mail.dcu.ie
>Subject: RE: CCL:software for extracting first solvent shell
>Date: Thu, 21 Aug 2003 06:42:51 -1000
>
>
>Well, first off, I'd like to have a LOOK at it, so your script sounds just
>
>like what I'd like.  My molecule destabilizes the solvent I'm using, you
>
>see, so there's some hope that looking at the first solvent shell may lead
>
>to some sort of insight.
>
>Yes, Hyperchem will open pdb files.  Correctly if they have CONECT records,
>
>as isolated atoms if not.  My solute/solvent files don't contain CONECT

>records, but once I've saved the results, I can look at them with VMD or
>
>PyMol, which can draw bonds w/out CONECT records.
>
>Thanks a lot!
>
>Irene
>
>>Hello
>>
>>What is it exactly you wish to do with the shell when you find it?
>>
>>I wrote a script for Hyperchem 7 (available free for 30-days) which selects
>>the first solvation shell. You may need to modify it for your purposes
(I
>>can help). Hyperchem (I think) will open .pdb files.
>>
>>When the shell is selected, you can display only the shell, the shell
plus
>>the molecule, etc. You could also remove all the other solvent molecules
>>and save the file.
>>
>>Like I said, if this is sufficient I can help.
>>
>>Noel
>>
>> >-- Original Message --
>> >Date: Wed, 20 Aug 2003 11:16:54 -1000
>> >From: Irene Newhouse <einew^at^hotmail.com>
>> >To: chemistry^at^ccl.net
>> >Subject: CCL:software for extracting first solvent shell
>> >
>> >
>> >I'm interested in examining the first solvent shell around a solute
in
>> >simulation snapshot files; mine happen to be in pdb format.  Can anyone
>> >point me toward software that does this [preferably free or cheap]?
>> >
>> >Thanks!
>> >Irene Newhouse
>> >

Noel O'Boyle
Han Vos Research Group
School of Chemical Sciences
Dublin City University

http://www.dcu.ie/~chemist/Staffpages/han_vos.htm




From chemistry-request@ccl.net Fri Aug 22 09:47:37 2003
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Date: Fri, 22 Aug 2003 15:53:23 +0200
From: Roel Hoefnagels <roelh^at^uia.ua.ac.be>
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Hi,

A question about a CASSCF output:
Is the final one electron symbolic density matrix about the ground
state, the first
excited state or averaged? I am doing casscf(4,4,nroot=3,stateaverage)
with
gaussian98.

Thanks in advance,

Roel Hoefnagels
University of Antwerpen
Belgium
roelh^at^uia.ua.ac.be



From chemistry-request@ccl.net Fri Aug 22 06:48:30 2003
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On behalf of Dave Marriott, AstraZeneca, Charnwood, UK

- - - - - - - - - - - - - - - - 

Hello,

This is to announce the upcoming 7th European Catalyst User Group Meeting 
to be hosted by Dr Dave Marriott and Dr Andy Davis, at AstraZeneca, 
located at Charnwood, UK. This meeting will be held on Tuesday October 
28th, 2003 at this venue.  Registration and agenda for this event has been 
posted at the URL below:

http://www.accelrys.com/usergroups/catalyst/2003/eu/index.html

The agenda is still being updated as more speakers are added to the list. 
The past success of these meetings has been based on the diverse 
scientific contributions from the Catalyst user community and invited 
speakers. Please register for this event so that we can determine the 
numbers of attendees and speakers, and continue the successful tradition 
of the Catalyst UGM.

An important aspect of this meeting will be discussions centred on (a) 
in-depth overview of the major changes within the Catalyst 4.8 release, 
(b) Catalyst on Linux, SGI and IBM server platforms, (c) Accelrys' 
integrated modelling and simulation platform - Discovery Studio - and the 
migration plan for Catalyst, (d) new and future technologies within the 
Catalyst product line, and (e) input into future enhancements to the 
Catalyst program.  As you can all see, there will be plenty of issues to 
discuss and it looks to be a very rewarding event for everyone coming. 

Thanks and looking forward to seeing many of you in Charnwood in October.

Dave Marriott
AstraZeneca

- - - - - - - - - - - - - - - - 
--=_alternative 003B5A4C80256D8A_=
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<br><font size=2 face="sans-serif">On behalf of Dave Marriott, AstraZeneca,
Charnwood, UK</font>
<br>
<br><font size=2 face="sans-serif">- - - - - - - - - - - - - - - - </font>
<br>
<div>
<br><font size=2 face="sans-serif">Hello,</font>
<br>
<br><font size=2 face="sans-serif">This is to announce the upcoming 7th
European Catalyst User Group Meeting to be hosted by Dr Dave Marriott and
Dr Andy Davis, at AstraZeneca, located at Charnwood, UK. This meeting will
be held on Tuesday October 28th, 2003 at this venue. &nbsp;Registration
and agenda for this event has been posted at the URL below:</font>
<br>
<br><font size=2 face="sans-serif">http://www.accelrys.com/usergroups/catalyst/2003/eu/index.html</font>
<br>
<br><font size=2 face="sans-serif">The agenda is still being updated as
more speakers are added to the list. The past success of these meetings
has been based on the diverse scientific contributions from the Catalyst
user community and invited speakers. Please register for this event so
that we can determine the numbers of attendees and speakers, and continue
the successful tradition of the Catalyst UGM.</font>
<br>
<br><font size=2 face="sans-serif">An important aspect of this meeting
will be discussions centred on (a) in-depth overview of the major changes
within the Catalyst 4.8 release, (b) Catalyst on Linux, SGI and IBM server
platforms, (c) Accelrys' integrated modelling and simulation platform -
Discovery Studio - and the migration plan for Catalyst, (d) new and future
technologies within the Catalyst product line, and (e) input into future
enhancements to the Catalyst program. &nbsp;As you can all see, there will
be plenty of issues to discuss and it looks to be a very rewarding event
for everyone coming. </font>
<br>
<br><font size=2 face="sans-serif">Thanks and looking forward to seeing
many of you in Charnwood in October.</font>
<br>
<br><font size=2 face="sans-serif">Dave Marriott</font>
<br><font size=2 face="sans-serif">AstraZeneca</font>
<br>
<br><font size=2 face="sans-serif">- - - - - - - - - - - - - - - - </font></div>
--=_alternative 003B5A4C80256D8A_=--


From chemistry-request@ccl.net Fri Aug 22 13:35:04 2003
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From: "Grady Scott Weston" <gscottweston<<at>>hotmail.com>
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Subject: Spartan vs. Jaguar for DFT
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CCLers,

Has anyone done (or seen) any head-to-head comparisons between Spartan and 
Jaguar for DFT calculations on standard Linux boxes?

Thanks,

Scott Weston

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From chemistry-request@ccl.net Fri Aug 22 14:02:50 2003
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From: "Martijn Zwijnenburg" <M.A.Zwijnenburg=at=tnw.tudelft.nl>
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To: chemistry=at=ccl.net
Date: Fri, 22 Aug 2003 20:02:41 +0200
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Subject: ccl: TD/G98 and CIS wavefunction symmetry could not be determined.
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Hi,

I'm doing time dependent DFT in g98 using the TD keyword and the 
calculation seem to finish fine. However, there seems to be a problem 
with determining the symmetry of the wavefunctions of the excited 
states. For every excited state the program reports:

CIS wavefunction symmetry could not be determined.
 Excited State   1:   Triplet-?Sym    3.3120 eV  374.35 nm  f=0.0000
     105 ->106         0.70550

Is this normal, and if not how should I fix it? The header of my 
input file looks like this:

%chk=Si7O14_TD
#P trackio
# GFINPUT IOP(6/7=3)
# TD(50-50,Nstates=4)
# B3LYP/6-31G*
# SCF(restart,tight,maxcycle=200)
# density=current
# fcheck=all
# guess=check
# symm=loose
# integral(grid=ultrafine)

Gaussian job
Si7O14_TD

0 1

Thanx in advance,

Martijn --------------------------------------------------------------
-----------
Martijn Zwijnenburg
Lab. of Applied Organic Chemistry and Catalysis
Delft University of Technology
Julianalaan 136
2628 BL Delft
The Netherlands
Tel: 0031-(0)152782691
Fax: 0031-(0)152784700
e-mail: M.A.Zwijnenburg=at=tnw.tudelft.nl
web page: http://come.to/tock




From chemistry-request@ccl.net Fri Aug 22 13:54:45 2003
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From: "William Wei" <william.wei=at=utoronto.ca>
To: "CCLers" <CHEMISTRY=at=ccl.net>
Subject: Open Babel with g98
Date: Fri, 22 Aug 2003 13:42:59 -0500
Message-ID: <MDEIKEJBFAGCDMAAIPIBIEIGCEAA.william.wei=at=utoronto.ca>
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Hi Friends,

I am trying to get the molecular configurations during Gaussian
optimizations using open babel. Babel can get them and transfer (g94) to
sybyl mol2 file, but the molecules are 2-D, the connections are not correct.
But seems Open babel donot support g98 output file as its' input? Please
tell me I am wrong, and give me a suggestion. I really need the different
configurations of the molecules, like the "SCAN" in Gaussian.

Thank you and have a good day,
William

PS. I am still trying the other ways.

-------------------------
William Wei
Molecular Design and Information Technology (MDIT) center
Faculty of Pharmacy, University of Toronto
19 Russell Street, Toronto, ON. M5S 2S2
Tel: 1-416-946-8469
Fax: 1-416-978-8511
Email: william.wei=at=utoronto.ca
       william=at=phm.utoronto.ca




From chemistry-request@ccl.net Fri Aug 22 13:51:51 2003
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	 <chemistry-.at.-ccl.net>
Subject: CCL: MP2 Freq memory problem
Date: Fri, 22 Aug 2003 14:53:42 -0300
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Dear CCLers,
I'm sorry if this is going over old ground for many of you.

The following edited  GW98 output shows a failed MP2 Freq analysis claiming
lack of memory and/or disk space where according to me I have plenty of
space and memory (25GB and 780 MB). I'm I doing something wrong here and
what would be the minimum windows based machine configuartion for this
stubbon molecule.

TIA
Ian

%chk=propylbenzene radical1.chk
 %mem=9MW
 %nproc=1
 Will use up to    1 processors via shared memory.
 
%rwf=a.rwf,236MW,b.rwf,236MW,c.rwf,236MW,d.rwf,236MW,e.rwf,236MW,f.rwf,236MW
 Default route:  MaxDisk=25GB
 -----------------------------------------------
 # freq=noraman ump2/6-31+g(d) geom=connectivity
 -----------------------------------------------
 1/10=4,30=1,38=1,57=2/1,3;
 2/17=6,18=5,40=1/2;
 3/5=1,6=6,7=11,11=2,25=1,30=1/1,2,3;
 4/7=2/1;
 5/5=2,38=4/2;
 8/6=3,8=1,10=1,19=11,23=2,27=-939524096,30=-1/1;
 9/15=3,16=-3,27=-939524096/6;
 11/6=1,8=1,15=11,17=12,24=-1,27=1,28=-2,29=300,32=6,42=1/1,2,10;
 10/6=2,21=1/2;
 8/6=4,8=1,10=1,19=11,23=2,27=-939524096,30=-1/11,4;
 10/5=1,20=4/2;
 11/12=2,14=11,16=11,17=2,28=-2,42=1/2,10,12;
 6/7=2,8=2,9=2,10=2/1;
 7/8=1,10=1,12=2,25=1,44=2/1,2,3,16;
 1/10=4,30=1/3;
 99//99;
 -------------------------------------
 propylbenzene radical 
 -------------------------------------
 Symbolic Z-matrix:
 Charge =  0 Multiplicity = 2
 C
 C                    1     1.39852 
 C                    2     1.4032   1     120.91975 
 C                    3     1.40339  2     118.44627  1    -0.30121  0
 C                    4     1.39839  3     120.92068  2     0.32748  0
 C                    1     1.3989   2     120.05045  3     0.37461  0
 H                    1     1.08846  2     119.86509  3    -179.63861  0
 H                    2     1.09018  1     119.68215  6     179.67626  0
 H                    4     1.09028  3     119.42579  2     179.54814  0
 H                    5     1.08846  4     119.87177  3     179.59903  0
 H                    6     1.08806  1     120.19419  2    -179.84125  0
 C                    3     1.50618  2     120.71153  1    -176.73938  0
 H                    12    1.09828  3     109.7884  2    -149.09095  0
 H                    12    1.09717  3     109.85076  2    -31.68602  0
 C                    12    1.53862  3     111.7057  2     89.62474  0
 H                    15    1.09756  12    109.1265  3    -58.45023  0
 H                    15    1.10366  12    108.06691  3     56.02172  0
 C                    15    1.49185  12    112.90762  3     178.61052  0
 H                    18    1.08362  15    121.20449  12    152.42788  0
 H                    18    1.08472  15    120.30301  12   -39.04474  0

---------------Cut----------------------Cut--------------------

There are   193 symmetry adapted basis functions of A   symmetry.
 Crude estimate of integral set expansion from redundant integrals=1.000.
 Integral buffers will be    262144 words long.
 Raffenetti 2 integral format.
 Two-electron integral symmetry is turned on.
   193 basis functions      332 primitive gaussians
    33 alpha electrons       32 beta electrons
       nuclear repulsion energy       400.4988053437 Hartrees.
 One-electron integrals computed using PRISM.
 NBasis=   193 RedAO= T  NBF=   193
 NBsUse=   192 1.00D-04 NBFU=   192
 Projected INDO Guess.
 <S**2> of initial guess= 0.7590
 Requested convergence on RMS density matrix=1.00D-08 within  64 cycles.
 Requested convergence on MAX density matrix=1.00D-06.
 Restarting incremental Fock formation.
 SCF Done:  E(UHF) =  -347.185140465     A.U. after   23 cycles
             Convg  =    0.7367D-08             -V/T =  2.0018
             S**2   =   0.7627
 Annihilation of the first spin contaminant:
 S**2 before annihilation     0.7627,   after     0.7501
 Range of M.O.s used for correlation:    10   192
 NBasis=   193 NAE=    33 NBE=    32 NFC=     9 NFV=     0
 NROrb=    183 NOA=    24 NOB=    23 NVA=   159 NVB=   160

 **** Warning!!: The largest alpha MO coefficient is  0.12935817D+03


 **** Warning!!: The largest beta MO coefficient is  0.13628298D+03

 Not enough disk for semidirect, minimum=    13896525
 Not enough memory for fully direct, minimum=     4191877.
 Not enough resources for E2 calculation.
 Error termination via Lnk1e in C:\G98W\l906.exe.
 Job cpu time:  0 days  0 hours 17 minutes 14.0 seconds.
 File lengths (MBytes):  RWF= 2513 Int=    0 D2E=    0 Chk=    7 Scr=    1

Ian Hovell - Ph.D. 
NUCLEO DE MODELAGEM MOLECULAR-NMM 
Centro de Tecnologia Mineral - CETEM 
Ministerio da Cijncia e da Tecnologia- MCT 
Avenida Ipj, No 900 - Cidade Universitaria 
Ilha do Fundco Rio de Janeiro RJ Brasil 
CEP 21941-590 
tel 00 55 (xx) 3865 - 7216 
Fax 00 55 (xx) 22602837 ou 2290-4286 
e-mail hovell-.at.-cetem.gov.br


From chemistry-request@ccl.net Fri Aug 22 15:34:09 2003
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From: "Ferber, Steven D" <sferber!at!howard.edu>
To: "'CHEMISTRY!at!ccl.net'" <CHEMISTRY!at!ccl.net>
Subject: re: CCL:curvilinear step not converged in G98
Date: Fri, 22 Aug 2003 15:33:41 -0400
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The problem is you need to have your input in redundant internal coordinate 
in order for the "freeze" option to work in the Geom(modredundant) keyword.
A trick I've found works is to perform a 1-step "Optimization" in order to
generate such coordinates, written to a checkpoint file which can then be
used to start-up your real optimization. < Opt(MaxCycle=1) >

        Steven Ferber
        Howard University Chemistry (Doctoral candidate)
        sferber!at!howard.edu
        202/806-4231


From chemistry-request@ccl.net Fri Aug 22 18:32:14 2003
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Date: Fri, 22 Aug 2003 18:31:38 -0400
From: Fan.Huajun/at/epamail.epa.gov
Subject: calculated H-Bond energy
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Hi,

I was wondering if anyone has a good reference to a calculated H-Bond
energies, say using DFT methods (B3lyp etc with relative decent basis
set).

Many thanks.

Have a good weekend.

huajun



