From owner-chemistry@ccl.net Wed Jan 16 08:53:00 2013 From: "Leonardo Viana Lima leo.vlima(-)hotmail.com" To: CCL Subject: CCL: (Gamess) SCF DID NOT CONVERGE Message-Id: <-48071-130115190215-29399-4FCZf+o18et87gL/qlDHkQ-#-server.ccl.net> X-Original-From: "Leonardo Viana Lima" Date: Tue, 15 Jan 2013 19:02:13 -0500 Sent to CCL by: "Leonardo Viana Lima" [leo.vlima###hotmail.com] Dear CCL Members, I was trying to run an Opt and Hessian job in Gamess software as stated below (input file): $CONTRL SCFTYP=RHF MPLEVL=2 RUNTYP=OPTIMIZE ICHARG=0 MULT=1 COORD=ZMT NZVAR=0 EXETYP=RUN $END $SYSTEM MWORDS=300 MEMDDI=1200 $END $BASIS GBASIS=N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.TRUE. DIFFS=.TRUE. $END $STATPT HSSEND=.TRUE. $END $DATA For some molecules (all of them disubstituted ciclohexane) I end up with the following error (output file): ...... END OF PROPERTY EVALUATION ...... CPU 0: STEP CPU TIME= 0.12 TOTAL CPU TIME= 4.4 ( 0.1 MIN) TOTAL WALL CLOCK TIME= 2014.7 SECONDS, CPU UTILIZATION IS 0.22% SCF DID NOT CONVERGE...NO MPLEVL=2 CALCULATION EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Wed Jan 9 00:44:52 2013 768674 WORDS OF DYNAMIC MEMORY USED CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 4.4 ( 0.1 MIN) TOTAL WALL CLOCK TIME= 2014.8 SECONDS, CPU UTILIZATION IS 0.22% DDI Process 0: error code 911 application called MPI_Abort(MPI_COMM_WORLD, 911) - process 0 EXIT STRING: Killed (signal 9) unset echo I found somewhere else that this error arises from linear dependency in basis set [6-311++G(d,p)] but I am not sure about how to solve this (using the ISPHERE keyword? Using QMTTOL keyword, with which new threshold? In which level does this affect the results?) without changing the basis set. Does anybody knows some solution for this error in Gamess software or another possible cause for this? Thanks in advance. Leonardo. Chemistry graduation student. leonardovc.lima-*-gmail.com From owner-chemistry@ccl.net Wed Jan 16 09:28:00 2013 From: "iksha singh ikshasingh9:+:gmail.com" To: CCL Subject: CCL:G: error in optimizing a geometry Message-Id: <-48072-130116062813-13376-w7RyEMaYdOsAaLg5KAa0Bw-#-server.ccl.net> X-Original-From: "iksha singh" Date: Wed, 16 Jan 2013 06:28:11 -0500 Sent to CCL by: "iksha singh" [ikshasingh9(-)gmail.com] I am getting the following error while optimizing the fe metal with MP4 technique- Error termination via Lnk1e in /home1/raj/gaussian09//g09/l913.exe can anybody help me out?? Iksha From owner-chemistry@ccl.net Wed Jan 16 10:03:00 2013 From: "Edilson Beserra Filho edilsonbeserra{}gmail.com" To: CCL Subject: CCL: E-Dragon error Message-Id: <-48073-130116063238-13547-WCoZlSTutogKldQ9mJKrVA_+_server.ccl.net> X-Original-From: "Edilson Beserra Filho" Date: Wed, 16 Jan 2013 06:32:37 -0500 Sent to CCL by: "Edilson Beserra Filho" [edilsonbeserra * gmail.com] I'm calculating molecular parameters with the E-Dragon plataform. For some analogues with para-nitro group the calculations presents error with values of -999 for all descriptors. Only a few molecules presents this. What's happening? The structures are in .sdf format and the program works well for many others structures. Thanks for attention, Prof. Edilson Beserra From owner-chemistry@ccl.net Wed Jan 16 11:43:00 2013 From: "partha kundu partha1kundu,gmail.com" To: CCL Subject: CCL:G: error in optimizing a geometry Message-Id: <-48074-130116112626-25457-lBhT2yEEg1DIZLWeRlgp1g^_^server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=0015174c3b2c40c41a04d36a569c Date: Wed, 16 Jan 2013 21:55:33 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu###gmail.com] --0015174c3b2c40c41a04d36a569c Content-Type: text/plain; charset=ISO-8859-1 The following link is very helpful http://docs.notur.no/application-support/chemistry-applications/gaussian-1/troubleshooting-gaussian-calculations Partha On Wed, Jan 16, 2013 at 4:58 PM, iksha singh ikshasingh9:+:gmail.com < owner-chemistry ~ ccl.net> wrote: > > Sent to CCL by: "iksha singh" [ikshasingh9(-)gmail.com] > I am getting the following error while optimizing the fe metal with MP4 > technique- > > Error termination via Lnk1e in /home1/raj/gaussian09//g09/l913.exe > > can anybody help me out?? > > Iksha> > > --0015174c3b2c40c41a04d36a569c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
The following link is very helpful
http://docs.notur.no/applic= ation-support/chemistry-applications/gaussian-1/troubleshooting-gaussian-ca= lculations


Partha

<= div class=3D"gmail_quote">On Wed, Jan 16, 2013 at 4:58 PM, iksha singh iksh= asingh9:+:gmail.com <owner-chemistry ~ ccl.net> wrote:

Sent to CCL by: "iksha =A0singh" [ikshasingh9(-)gmail.com]
I am getting the following error while optimizing the fe metal with MP4 tec= hnique-

=A0Error termination via Lnk1e in /home1/raj/gaussian09//g09/l913.exe

can anybody help me out??

Iksha



-=3D This is automatically added to each message by the mailing script =3D-=
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--0015174c3b2c40c41a04d36a569c-- From owner-chemistry@ccl.net Wed Jan 16 12:44:01 2013 From: "Mehdi Esrafili m_esrafili-x-yahoo.com" To: CCL Subject: CCL: (Gamess) SCF DID NOT CONVERGE Message-Id: <-48075-130116123821-21112-2hLDh7u04jEruw34i9QWMg:_:server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="-613093590-2131777586-1358357894=:91770" Date: Wed, 16 Jan 2013 09:38:14 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili,,yahoo.com] ---613093590-2131777586-1358357894=:91770 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Leonardo:=0Ayou can simply use MAXIT=3D200 in $contrl. This is for inc= rease scf iteration in the GAMESS calculations. But, I suggest you to chang= e algorithm for scf calculations. you may use following command =0A=A0$SCF = DAMP=3D.T. SOSCF=3D.F. DIIS=3D.T. $end=0AFor my computations, this command = works very well in many cases.=0A=0A=0A=A0=0A=A0=0A------------------------= ---------------------------------------------------------------------------= ---------------------------=A0=A0=0A`The man who makes no mistakes does not= usually make anything.'=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Edward John Phelps (182= 2-1900)=0A-----------------------------------------------------------------= ------------------------------------------------------------- =0AMehdi D. E= srafili, Ph.D.=0AAssistant Professor of Physical Chemistry=A0=0ACurrent add= ress:=A0Department of Chemistry, =0AFaculty of Basic Sciences,University of= =0AMaragheh, Iran. =0AE-mail 1:m_esrafili[-]yahoo.com=0AE-mail 2: esrafili[-]ma= ragheh.ac.ir=0A------------------------------------------------------------= ------------------------------------------------------------------ =0A=0A= =0A________________________________=0A From: Leonardo Viana Lima leo.vlima(= -)hotmail.com =0ATo: "Esrafili, Mehdi D " = =0ASent: Wednesday, January 16, 2013 3:32 AM=0ASubje= ct: CCL: (Gamess) SCF DID NOT CONVERGE=0A =0A=0ASent to CCL by: "Leonardo V= iana Lima" [leo.vlima###hotmail.com]=0ADear CCL Members,=0A=0AI was trying = to run an Opt and Hessian job in Gamess software as stated below =0A(input = file):=0A=0A$CONTRL SCFTYP=3DRHF MPLEVL=3D2 RUNTYP=3DOPTIMIZE ICHARG=3D0 MU= LT=3D1=0ACOORD=3DZMT NZVAR=3D0 EXETYP=3DRUN $END=0A$SYSTEM MWORDS=3D300 MEM= DDI=3D1200 $END=0A$BASIS GBASIS=3DN311 NGAUSS=3D6 NDFUNC=3D1 NPFUNC=3D1 DIF= FSP=3D.TRUE. DIFFS=3D.TRUE. =0A$END=0A$STATPT HSSEND=3D.TRUE. $END=0A$DATA= =0A=0AFor some molecules (all of them disubstituted ciclohexane) I end up w= ith the =0Afollowing error (output file):=0A=0A...... END OF PROPERTY EVALU= ATION ......=0ACPU=A0 =A0 0: STEP CPU TIME=3D=A0 =A0 0.12 TOTAL CPU TIME= =3D=A0 =A0 =A0 =A0 4.4 (=A0 =A0 0.1 MIN)=0ATOTAL WALL CLOCK TIME=3D=A0 =A0 = 2014.7 SECONDS, CPU UTILIZATION IS=A0 0.22%=0A=0ASCF DID NOT CONVERGE...N= O MPLEVL=3D2 CALCULATION=0AEXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT W= ed Jan=A0 9 00:44:52 2013=0A=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 768674=A0 WORDS= OF DYNAMIC MEMORY USED=0ACPU=A0 =A0 0: STEP CPU TIME=3D=A0 =A0 0.00 TOTA= L CPU TIME=3D=A0 =A0 =A0 =A0 4.4 (=A0 =A0 0.1 MIN)=0ATOTAL WALL CLOCK TIME= =3D=A0 =A0 2014.8 SECONDS, CPU UTILIZATION IS=A0 0.22%=0ADDI Process 0: e= rror code 911=0Aapplication called MPI_Abort(MPI_COMM_WORLD, 911) - process= 0=0AEXIT STRING: Killed (signal 9)=0Aunset echo=0A=0AI found somewhere els= e that this error arises from linear dependency in basis =0Aset [6-311++G(d= ,p)] but I am not sure about how to solve this (using the =0AISPHERE keywor= d? Using QMTTOL keyword, with which new threshold? In which =0Alevel does t= his affect the results?) without changing the basis set. Does =0Aanybody kn= ows some solution for this error in Gamess software or another =0Apossible = cause for this?=0A=0AThanks in advance.=0ALeonardo.=0AChemistry graduation = student.=0Aleonardovc.lima(0)gmail.com=0A=0A=0A=0A-=3D This is automaticall= y added to each message by the mailing script =3D-=0ATo recover the email a= ddress of the author of the message, please change=0Athe strange characters= on the top line to the [-] sign. You can also=0Alook up the X-Original-From:= line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY[-]ccl.net or = use:=0A=A0 =A0 =A0=0A=0AE-m= ail to administrators: CHEMISTRY-REQUEST[-]ccl.net or use=0A=A0 =A0 =A0 http:= //www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0A=0A= =A0 =A0 =A0=0A=0ABefore postin= g, check wait time at: http://www.ccl.net=0A=0AJob: http://www.ccl.net/jobs= =0A= =0A=0A= =0A=0A=0A=A0 =A0 =A0 ==0A=0ARTFI: http://www.ccl.net/chemistry/abo= utccl/instructions/ ---613093590-2131777586-1358357894=:91770 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Leonardo:
y= ou can simply use MAXIT=3D200 in $contrl. This is for increase scf iteratio= n in the GAMESS calculations. But, I suggest you to change algorithm for sc= f calculations. you may use following command
 $SCF DAMP=3D.T. SOS= CF=3D.F. DIIS=3D.T. $end
For my computations, this command works very we= ll in many cases.

 
&nbs= p;
-----------------------------------------------------------------------= -------------------------------------------------------  <= /div>
`The man who makes no mistakes does not usually make anything.'
          &nb= sp;            =            Edward John Ph= elps (1822-1900)
--------------------------------------------------= ---------------------------------------------------------------------------= -
Mehdi D. Esrafili, Ph.D.
Assistant Professor of Physical Chem= istry 
Current address: Department of Chemistry,
Faculty of Basic Sciences,University of
Maragheh, Iran. <= /div>
E-mail 1: m_esrafili[-]yahoo.com
E-mail 2: esrafi= li[-]maragheh.ac.ir
----------------------------------------------------------------------= --------------------------------------------------------

From: Leonardo Viana Lima leo.vlima(-)hotmail.com <own= er-chemistry[-]ccl.net>
To: "Esrafili, Mehdi D -i= d#3za-" <m_esrafili[-]yahoo.com>
Sent: Wednesday, January 16, 2013 3:32 AM
Subject: CCL: (Gamess) SCF DID NOT CONV= ERGE

=0A
Sent to CCL by: "Leonardo Viana Lima" [l= eo.vlima###hotmail.com]
Dear CCL Members,

I was trying to run an = Opt and Hessian job in Gamess software as stated below
(input file):
$CONTRL SCFTYP=3DRHF MPLEVL=3D2 RUNTYP=3DOPTIMIZE ICHARG=3D0 MULT=3D1=
COORD=3DZMT NZVAR=3D0 EXETYP=3DRUN $END
$SYSTEM MWORDS=3D300 MEMDD= I=3D1200 $END
$BASIS GBASIS=3DN311 NGAUSS=3D6 NDFUNC=3D1 NPFUNC=3D1 DIF= FSP=3D.TRUE. DIFFS=3D.TRUE.
$END
$STATPT HSSEND=3D.TRUE. $END
$= DATA

For some molecules (all of them disubstituted ciclohexane) I en= d up with the
following error (output file):

...... END OF PROP= ERTY EVALUATION ......
CPU    0: STEP CPU TIME=3D  &nbs= p; 0.12 TOTAL CPU TIME=3D        4.4 (    0.= 1 MIN)
TOTAL WALL CLOCK TIME=3D    2014.7 SECONDS, CPU UTILI= ZATION IS  0.22%

SCF DID NOT CONVERGE...NO MPLEVL=3D2 CALCULA= TION
EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Wed Jan  9 00:44:52 2013
            &nb= sp;   768674  WORDS OF DYNAMIC MEMORY USED
CPU    = 0: STEP CPU TIME=3D    0.00 TOTAL CPU TIME=3D     = ;   4.4 (    0.1 MIN)
TOTAL WALL CLOCK TIME=3D  &nb= sp; 2014.8 SECONDS, CPU UTILIZATION IS  0.22%
DDI Process 0: err= or code 911
application called MPI_Abort(MPI_COMM_WORLD, 911) - process = 0
EXIT STRING: Killed (signal 9)
unset echo

I found somewhere = else that this error arises from linear dependency in basis
set [6-311+= +G(d,p)] but I am not sure about how to solve this (using the
ISPHERE k= eyword? Using QMTTOL keyword, with which new threshold? In which
level = does this affect the results?) without changing the basis set. Does
any= body knows some solution for this error in Gamess software or another
p= ossible cause for this?

Thanks in advance.
Leonardo.
Chemistry graduation student.
leonardovc.lima(= 0)gmail.com


=
-=3D This is automatically added to each message by the mailing script = =3D-
To recover the email address of the author of the message, please c= hange
E-mail to = subscribers: CHEMISTRY[-]ccl.net or use:
      http://ww= w.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST[-]ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsub= scribe:
     
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Conferences: http://server.ccl.net/chemistry/announc= ements/conferences/

Search Messages: http://www.ccl.net/chemistry/se= archccl/index.shtml

If your mail bounces from CCL with 5.7.1 error, = check:
     

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---613093590-2131777586-1358357894=:91770-- From owner-chemistry@ccl.net Wed Jan 16 13:18:01 2013 From: "Mehdi Esrafili m_esrafili^^^yahoo.com" To: CCL Subject: CCL:G: error in optimizing a geometry Message-Id: <-48076-130116124233-23259-KUl+2FlAUOCwXBlyGSh45Q..server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="1989420431-375178358-1358358147=:1279" Date: Wed, 16 Jan 2013 09:42:27 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili-#-yahoo.com] --1989420431-375178358-1358358147=:1279 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Iksha;=0AThis is most likely about your % section ( including %CHK add= ress, %mem, %RWF, %nproc) or about your route section ( method of calculati= on, basis set, and the property keyword). =0A=0A=0A=A0=0A=A0=0A------------= ---------------------------------------------------------------------------= ---------------------------------------=A0=A0=0A`The man who makes no mista= kes does not usually make anything.'=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Edward John= Phelps (1822-1900)=0A-----------------------------------------------------= ------------------------------------------------------------------------- = =0AMehdi D. Esrafili, Ph.D.=0AAssistant Professor of Physical Chemistry=A0= =0ACurrent address:=A0Department of Chemistry, =0AFaculty of Basic Sciences= ,University of=0AMaragheh, Iran. =0AE-mail 1:m_esrafili*|*yahoo.com=0AE-mail = 2: esrafili*|*maragheh.ac.ir=0A----------------------------------------------= ---------------------------------------------------------------------------= ----- =0A=0A=0A________________________________=0A From: "partha kundu part= ha1kundu,gmail.com" =0ATo: "Esrafili, Mehdi D -id#= 3za-" =0ASent: Wednesday, January 16, 2013 7:55 PM= =0ASubject: CCL:G: error in optimizing a geometry=0A =0A=0AThe following li= nk is very helpful=0Ahttp://docs.notur.no/application-support/chemistry-app= lications/gaussian-1/troubleshooting-gaussian-calculations=0A=0A=0A=0A=0APa= rtha=0A=0A=0AOn Wed, Jan 16, 2013 at 4:58 PM, iksha singh ikshasingh9:+:gma= il.com wrote:=0A=0A=0A>Sent to CCL by: "iksha = =A0singh" [ikshasingh9(-)gmail.com]=0A>I am getting the following error whi= le optimizing the fe metal with MP4 technique-=0A>=0A>=A0Error termination = via Lnk1e in /home1/raj/gaussian09//g09/l913.exe=0A>=0A>can anybody help me= out??=0A>=0A>Iksha=0A>=0A>=0A>=0A>-=3D This is automatically added to each= message by the mailing script =3D-=0A>=0A>E-mail to subscribers: CHEMISTRY= /./ccl.net or use:=0A>=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage=0A>=0A>E-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or use= =0A>=A0 =A0 =A0=0A>=0A>Subs= cribe/Unsubscribe:=0A>=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sh= tml=0A>=0A=0A>=0A>Jo= b: http://www.ccl.net/jobs=0A>Conferences: http://server.ccl.net/chemistry/= announcements/conferences/=0A>=0A>Search Messages: http://www.ccl.net/chemi= stry/searchccl/index.shtml=0A>=0A>=A0 =A0 =A0 http://www.ccl.net/spammers.t= xt=0A>=0A=0A>=0A>= =0A> --1989420431-375178358-1358358147=:1279 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Iksha;
This= is most likely about your % section ( including %CHK address, %mem, %RWF, = %nproc) or about your route section ( method of calculation, basis set, and= the property keyword).

 
 
----------------------------------------------------------------= --------------------------------------------------------------  <= /font>
`The man who makes no mistakes does not usually make anything.'
          &nb= sp;            =            Edward John Ph= elps (1822-1900)
--------------------------------------------------= ---------------------------------------------------------------------------= -
Mehdi D. Esrafili, Ph.D.
Assistant Professor of Physical Chem= istry 
Current address: Department of Chemistry,
Faculty of Basic Sciences,University of
Maragheh, Iran. <= /div>
E-mail 1: m_esrafili*|*yahoo.com
E-mail 2: esrafi= li*|*maragheh.ac.ir
----------------------------------------------------------------------= --------------------------------------------------------

From: "partha kundu partha1kundu,gmail.com" <owner-che= mistry*|*ccl.net>
To: "Esrafili, Mehdi D " &= lt;m_esrafili*|*yahoo.com>
Sent= : Wednesday, January 16, 2013 7:55 PM
Subject: CCL:G: error in optimizing a geometry

=0A
The fol= lowing link is very helpful
http://docs.notur.no/application-support/che= mistry-applications/gaussian-1/troubleshooting-gaussian-calculations
=0A= =0A=0A

Pa= rtha

On Wed, Jan 16, 2= 013 at 4:58 PM, iksha singh ikshasingh9:+:gmail.com <owner-chemistry/./ccl.net&g= t; wrote:
=0A=0A=0A
<= br>=0ASent to CCL by: "iksha  singh" [ikshasingh9(-)gmail.com]
=0AI am ge= tting the following error while optimizing the fe metal with MP4 technique-=
=0A
=0A Error termination via Lnk1e in /home1/raj/gaussian09//g= 09/l913.exe
=0A
=0Acan anybody help me out??
=0A
=0AIksha
= =0A
=0A
=0A
=0A-=3D This is automatically added to each message by= the mailing script =3D-
=0A
=0AE-mail to subscribers: CHEMISTRY/./ccl.net or use:
=0A   =  
=0A
=0AE-mail= to administrators: C= HEMISTRY-REQUEST/./ccl.net or use
=0A      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=0A
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=0A      http://www.ccl.net/chemis= try/sub_unsub.shtml
=0A
=0ABefore posting, check wait time at: http:/= /www.ccl.net
=0A
=0AJob: http://www.ccl.net/jobs
=0AConferences: h= ttp://server.ccl.net/chemistry/announcements/conferences/
=0A
=0ASear= ch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=0A
= =0A     
=0A
=0ARTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/
=0A
=0A
=0A

=0A


--1989420431-375178358-1358358147=:1279-- From owner-chemistry@ccl.net Wed Jan 16 14:48:00 2013 From: "Paulo J. Madeira pjamadeira-x-ff.ul.pt" To: CCL Subject: CCL: Avgadro does not read MOPAC2012 output file using the keyword PM7 Message-Id: <-48077-130116111415-15152-yIgmlsPbdLkoOFI1nheGcg=server.ccl.net> X-Original-From: "Paulo J. Madeira" Date: Wed, 16 Jan 2013 11:14:13 -0500 Sent to CCL by: "Paulo J. Madeira" [pjamadeira{=}ff.ul.pt] Hello I'm doing semi-empirical calculations for a while and today I came up with a unsual "error". I'm trying the new PM7 hamiltonean in MOPAC2012 and Avogadro can't read the output file (Error message: Reading molecular file failed,...) when I use the PM6 hamiltonean everything works perfectly. Does anyone knows how to circumvent this? Regards P From owner-chemistry@ccl.net Wed Jan 16 15:28:00 2013 From: "Geoffrey Hutchison geoffh(!)pitt.edu" To: CCL Subject: CCL: Avgadro does not read MOPAC2012 output file using the keyword PM7 Message-Id: <-48078-130116152531-20683-Y8WHN/81gFPd8rEtlt5FkA]^[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Wed, 16 Jan 2013 15:25:23 -0500 MIME-version: 1.0 (Mac OS X Mail 6.2 \(1499\)) Sent to CCL by: Geoffrey Hutchison [geoffh(_)pitt.edu] > I'm trying the new PM7 hamiltonean in MOPAC2012 and Avogadro can't read the output file (Error message: Reading molecular file failed,...) when I While I do have a copy of MOPAC2012, I haven't run any PM7 calculations yet. As with anything else Avogadro-related, my suggestion is to report a bug, either to the bug-tracker or the mailing list: Avogadro bug tracker: http://sourceforge.net/p/avogadro/bugs/ mailing list: avogadro-discuss.:.lists.sourceforge.net In this case, the bug tracker is probably the best, since you can easily upload an example file for us to examine. Thanks for reporting the bug! -Geoff P.S. The Avogadro paper is finally out (and open access). Please cite this if you use Avogadro: http://www.jcheminf.com/content/4/1/17 --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh.:.pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Wed Jan 16 17:14:00 2013 From: "willsd-$-appstate.edu" To: CCL Subject: CCL:G: another IR intensity units question. Message-Id: <-48079-130116154854-4613-uhQ/2i1PnZfP2RtelKC9Vw/a\server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 16 Jan 2013 20:48:36 GMT MIME-Version: 1.0 Sent to CCL by: [willsd~~appstate.edu] I have a basic question about how IR intensity is computed in Gaussian (and most other quantum chemistry codes). I know how the units (km/mol) are related to the integration over a band of the absorbance. What I am wondering is this: the absorbance can be expressed as either A=log(Pt/Pi) (decadic) or Ae=ln(Pt/Pi) (Naperian) where Pt and Pi are the transmitted and incident radiant power in a spectrometer. The two definitions (maybe the first one is a "chemist" definition and the second a "physicist" definition) are related to each other by a multiplicative factor of ln(10)=2.303. I have a wide variety of computed IR spectra (variety of DFT methods in G98, G03, and G09) and some excellent experimental spectra that I know are measured using the decadic convention. When I convert experimental band integrals into km/mol and compare with computed IR intensity for the corresponding mode(s), they differ by about a factor of 2.303, suggesting quite good prediction of absolute IR intensity, except for the conversion from base-10 to natural logs. Is it true that Gaussian (and most other codes) uses the "physicist", natural log definition of absorbance? Is there a reference that states or suggests this? I do not have a source code license so I cannot look at exactly how Gaussian does this conversion from dipole derivative to km/mol units. Thanks, Steve Williams From owner-chemistry@ccl.net Wed Jan 16 17:48:00 2013 From: "Rajarshi Guha rajarshi.guha . gmail.com" To: CCL Subject: CCL: CSA Trust CSA Trust Grant 2013 - Call for Applications Message-Id: <-48080-130116161312-22179-EPKLXtJv1QG+s2AhKEAYZQ!A!server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=f46d043894550bdfb104d36e58fa Date: Wed, 16 Jan 2013 16:13:03 -0500 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha(~)gmail.com] --f46d043894550bdfb104d36e58fa Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable On behalf of the CSA Trust. (Also see http://www.csa-trust.org/?page_id=3D9= ) *Applications Invited for CSA Trust Jacques-=C9mile Dubois Grants for 2013.= * * * The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. In support of its charter, the Trust has created a unique Grant Program, renamed in honor of Professor Jacques-=C9mile Dubois who made significant contributions to the field of cheminformatics. The Trust is currently inviting the submission of grant applications for 2013. ** *Purpose of the Grants**:* The Grant Program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds. A Grant will be awarded annually up to a maximum of ten thousand U.S. dollars ($10,000). Grants are awarded for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Grantees are also requested to recognize the support of the Trust in any paper or presentation that is given as a result of that support. *Who is Eligible**?* Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information related research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications. While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust. All requests must follow the application procedures noted below and will be weighed against the same criteria. *Which Activities are Eligible?** * Grants may be awarded to acquire the experience and education necessary to support research activities; e.g. for travel to collaborate with research groups, to attend a conference relevant to one=92s area of research, to gai= n access to special computational facilities, or to acquire unique research techniques in support of one=92s research. *Application Requirements**: * Applications must include the following documentation: 1. A letter that details the work upon which the Grant application is to be evaluated as well as details on research recently completed by the applicant; 2. The amount of Grant funds being requested and the details regarding the purpose for which the Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support of meeting attendance, etc.). The relevance of the above-stated purpose to the Trus= t=92s objectives and the clarity of this statement are essential in the evaluation of the application); 3. A brief biographical sketch, including a statement of academic qualifications; 4. Two reference letters in support of the application. Additional materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information no= t already included in items 1-4. Three copies of the complete applicatio= n document must be supplied for distribution to the Grants Committee. *Deadline for Applications**: * Applications must be received no later than March 14, 2013. Successful applicants will be notified no later than May 2, 2013. *Address for Submission of Applications**: * Three copies of the application documentation should be forwarded to: Bonnie Lawlor, CSA Trust Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA. If you wish to enter your application by e-mail, please contact Bonnie Lawlor at blawlor|a|nfais.org prior to submission so that she can contact you if the e-mail does not arrive. --=20 Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science --f46d043894550bdfb104d36e58fa Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable

On behalf of the CSA Trust. (Also see=A0http://www.csa-trust.org/?page_id=3D9)

=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0

Applications Invited for CS= A Trust Jacques-=C9mile Dubois Grants for 2013.

=A0

The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research.=A0 In support of its charter, the Trust has created a unique Grant Program, renam= ed in honor of Professor Jacques-=C9mile Dubois who made significant contribut= ions to the field of cheminformatics.=A0 The Trust is currently inviting the submission of grant applications for 2013. =

=A0

Purpose of the Grants:=A0

The Grant Program has been created to provide funding for the career development of young researchers = who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, proce= ss and retrieve information about chemical structures, reactions and compounds.=A0 A Grant will be awarded annually up to a maximum of ten thousand U.S. dollars ($10,000).=A0 Grants are award= ed for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Grantees are also requested t= o recognize the support of the Trust in any paper or presentation that is giv= en as a result of that support.

=A0

Who is Eligible?

Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information rel= ated research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications.=A0= While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust.=A0 All requests must follow the application procedures noted below and will be weighed against the same criteria.

=A0

Which Activities are Eli= gible?

Grants may be awarded to acquire the experience and education necessary to support research activiti= es; e.g. for travel to collaborate with research groups, to attend a conference relevant to one=92s area of research, to gain access to special computation= al facilities, or to acquire unique research techniques in support of one=92s research.

=A0

Application Requirements= :=A0

Applications must include the following documentation:

=A0

  1. = A letter that details the work upon which the Grant application is to be evaluated as well a= s details on research recently completed by the applicant;
  2. = The amount of Grant funds being requested and the details regarding the purpose for which = the Grant will be used (e.g. cost of equipment, travel expenses if the req= uest is for financial support of meeting attendance, etc.). The relevance o= f the above-stated purpose to the Trust=92s objectives and the clarity o= f this statement are essential in the evaluation of the application); =
  3. = A brief biographical sketch, including a statement of academic qualifications;=A0
  4. = Two reference letters in support of the application.=A0 Additional materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information not already included in items 1-4.=A0=A0 Three cop= ies of the complete application document must be supplied for distribution to the Grants Committee.

=A0

Deadline for Application= s:=A0

Applications must be received no later than March 14, 2013.=A0 Successful applicants will be notified no later than May 2, 2013.

=A0

Address for Submission o= f Applications:=A0 =

Three copies of the application documentation should be forwarded to:=A0 Bonnie Lawlor, CSA Tru= st Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA.=A0 If you wish to enter= your application by e-mail, please contact Bonnie Lawlor at blawlor|a|nfais.org prior to submission so that she can contact you if the e-mail does not arrive.


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Rajarshi Guha | http://blog.rguha.net
NIH Center for Adv= ancing Translational Science
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