From owner-chemistry@ccl.net Mon Feb 11 06:34:00 2008 From: "aa aa||chemaxon.hu" To: CCL Subject: CCL: First call for papers: ChemAxon European User Group Meeting - May 7-8, Visegrad, Hungary Message-Id: <-36260-080211060250-23631-JVLtJJ7KtV5RjlBkqkjqXA * server.ccl.net> X-Original-From: aa Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 11 Feb 2008 05:48:29 -0500 MIME-Version: 1.0 Sent to CCL by: aa [aa(a)chemaxon.hu] Excuse cross postings Good day, ChemAxon's 2008 European User Group Meeting will be held on Wednesday and Thursday, May 7-8 at the Thermal Hotel, in Visegrad, Hungary, nearby Budapest. The meeting will be preceded by a Developer Workshop day on May 6th. We are inviting those interested in presenting at the meeting to submit abstracts for review. The deadline for receipt of oral abstracts is March 17th and April 15th for poster abstracts. To submit your abstract please visit: http://www.chemaxon.com/ugm.php Presentations should address how ChemAxon toolkits have been implemented into informatics systems & products, contributed to scientific discovery through generating scientific results and enabled the process of life science discovery. To find out more, please review this 2007 meeting report by Wendy Warr (http://www.chemaxon.com/UGM/07/07_UGM_report_Warr.html) or visit the previous meeting archives which include original presentations (http://www.chemaxon.com/UGM/ugm_land.html). We hope you can participate in what has proven to be a most interesting and enjoyable cheminformatics event. See you there. Alex Alex Allardyce Dir. Marketing, ChemAxon From owner-chemistry@ccl.net Mon Feb 11 07:28:01 2008 From: "Syed T Moin tarisyed . yahoo.com" To: CCL Subject: CCL:G: Installation and Compilation of g98 Message-Id: <-36261-080211072715-20543-p9NN+L2qKbdgJjyeysvGiw]=[server.ccl.net> X-Original-From: "Syed T Moin" Date: Mon, 11 Feb 2008 07:27:11 -0500 Sent to CCL by: "Syed T Moin" [tarisyed[*]yahoo.com] Hi, I have intel xeon 32 bit cluster, i want to install gaussian 98 and do parallel compilation of it. Can any one guide me in this regard. Regards From owner-chemistry@ccl.net Mon Feb 11 10:50:00 2008 From: "Mariusz Radon mariusz.radon .. gmail.com" To: CCL Subject: CCL:G: g03 unfchk mem problem Message-Id: <-36262-080211101956-5452-We1rYj/i04ZyQm/C9uFP7g]-[server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Mon, 11 Feb 2008 15:15:46 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon*o*gmail.com] Dear Gaussian users! I am trying to create binary chk file from the formatted one (fchk) using unfchk utility. I got the following error: Read formatted file scf.fchk Write checkpoint file scf.chk Out-of-memory error in routine UFChkP (IEnd=10760694 MxCore=6291456) Use %mem=11MW to provide the minimum amount of memory required to complete this step. Error termination via Lnk1e at Mon Feb 11 14:41:39 2008. forrtl: severe (174): SIGSEGV, segmentation fault occurred OK, Gaussian tells me that I should use "%mem=11MW" to increase the available memory. But how can I do it? Where can I put the "%mem=11MW" command? The unfchk utility does not take any input file, does it? Thanks in advance! best regards, Mariusz Radon From owner-chemistry@ccl.net Mon Feb 11 12:28:01 2008 From: "Cristian V. Diaconu cvdiaconu^lanl.gov" To: CCL Subject: CCL:G: g03 unfchk mem problem Message-Id: <-36263-080211122535-12007-BN0hQIvIHpz6NO4f/akd6A!A!server.ccl.net> X-Original-From: "Cristian V. Diaconu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Mon, 11 Feb 2008 10:24:52 -0700 MIME-Version: 1.0 Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu__lanl.gov] set GAUSS_MEMDEF environment variable eg: export GAUSS_MEMDEF=134217728 for sh-like shells setenv GAUSS_MEMDEF 134217728 for [t]csh shells see http://www.gaussian.com/g_ur/m_utils.htm Mariusz Radon mariusz.radon .. gmail.com wrote: > > Sent to CCL by: Mariusz Radon [mariusz.radon*o*gmail.com] > Dear Gaussian users! > > I am trying to create binary chk file from the formatted one (fchk) > using unfchk utility. I got the following error: > > Read formatted file scf.fchk > Write checkpoint file scf.chk > Out-of-memory error in routine UFChkP (IEnd=10760694 MxCore=6291456) > Use %mem=11MW to provide the minimum amount of memory required to > complete this step. > Error termination via Lnk1e at Mon Feb 11 14:41:39 2008. > forrtl: severe (174): SIGSEGV, segmentation fault occurred > > > OK, Gaussian tells me that I should use "%mem=11MW" to increase the > available memory. But how can I do it? Where can I put the "%mem=11MW" > command? The unfchk utility does not take any input file, does it? > > Thanks in advance! > > best regards, > Mariusz Radonhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Cristian V. Diaconu Postdoctoral Research Associate Los Alamos National Laboratory Theoretical Division Theoretical Chemistry & Molecular Physics Group (T-12) Mail Stop B268 Los Alamos, NM 87545 Phone: 505-665-2635 Fax: 505-665-3909 E-mail: cvdiaconu^lanl.gov From owner-chemistry@ccl.net Mon Feb 11 13:03:01 2008 From: "David Hose anthrax_brothers ~~ hotmail.com" To: CCL Subject: CCL: Formal charges Message-Id: <-36264-080211124909-21149-Dz/DSR6zbs1p1wuH+j+Abw()server.ccl.net> X-Original-From: "David Hose" Date: Mon, 11 Feb 2008 12:49:05 -0500 Sent to CCL by: "David Hose" [anthrax_brothers===hotmail.com] If you want to display the charges on the 3D structure in Spartan, try this. From the Model menu select Labels. Depending upon your preferences, you might see the atom labels appear (default of white text on a green background, so the labels may be invisible if you have charged your background to white). Then select Configure... from the Model menu and select the appropriate radio button. If you haven't already discovered this, if you click the "P" icon in the Properties dialogue (under the Display menu), the charge of the atom selected will be added to the spreadsheet. Regards, Dave. > > Sent to CCL by: "Sina T reli" [sinatureli{:}gmail.com] > Hello, > > Is there any tool that will calculate formal charges on a molecular system and display it? I have tried spartan but couldnt figure how it displays formal charges though there is an option for it in the display menu... > > Thanks From owner-chemistry@ccl.net Mon Feb 11 13:50:01 2008 From: "Pablo Vitoria pablo.vitoria]*[ehu.es" To: CCL Subject: CCL:G: g03 unfchk mem problem Message-Id: <-36265-080211122336-11832-hnR6G9kgjLoPyytDwVW8Og++server.ccl.net> X-Original-From: Pablo Vitoria Content-Type: multipart/mixed; boundary="------------040209090200020905040509" Date: Mon, 11 Feb 2008 17:49:34 +0100 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria [pablo.vitoria[a]ehu.es] This is a multi-part message in MIME format. --------------040209090200020905040509 Content-Type: text/plain; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: 8bit Mariusz Radon mariusz.radon .. gmail.com escribió: > > Sent to CCL by: Mariusz Radon [mariusz.radon*o*gmail.com] > Dear Gaussian users! > > I am trying to create binary chk file from the formatted one (fchk) > using unfchk utility. I got the following error: > OK, Gaussian tells me that I should use "%mem=11MW" to increase the > available memory. But how can I do it? Where can I put the "%mem=11MW" > command? The unfchk utility does not take any input file, does it? > > Thanks in advance! > > best regards, > Mariusz Radon Hi Mariusz, From the manual: "The /GAUSS_MEMDEF/ environment variable may be used to increase the memory available to utilities which do not offer such an option themselves. Its value should be set to the desired amount of memory in words." So you should define the GAUSS_MEMDEF variable. Pablo -- ******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del País Vasco (UPV/EHU) Fac. Ciencia y Tecnología, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax +34 946013500 ******************************** --------------040209090200020905040509 Content-Type: text/x-vcard; charset=utf-8; name="pablo_vitoria.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="pablo_vitoria.vcf" begin:vcard fn;quoted-printable:Pablo Vitoria Garc=C3=ADa n;quoted-printable:Vitoria Garc=C3=ADa;Pablo org;quoted-printable:Universidad del Pa=C3=ADs Vasco (UPV/EHU);Servicios Generales de Rayos X adr;quoted-printable;quoted-printable:Barrio Sarriena s/n;;Facultad de Ciencia y Tecnolog=C3=ADa, edificio CD3;Leioa;Bizkaia;E-48940;Espa=C3=B1a email;internet:pablo.vitoria . ehu.es title;quoted-printable:T=C3=A9cnico tel;work:946015334 version:2.1 end:vcard --------------040209090200020905040509-- From owner-chemistry@ccl.net Mon Feb 11 14:33:01 2008 From: "DIEGOI GOMEZ darkego21~~yahoo.com" To: CCL Subject: CCL:G: NMR caculation Message-Id: <-36266-080209212042-16389-71ka0UC3iFOIbTJDpLj1Zw^-^server.ccl.net> X-Original-From: DIEGOI GOMEZ Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1662192387-1202606429=:56631" Date: Sat, 9 Feb 2008 17:20:29 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: DIEGOI GOMEZ [darkego21:_:yahoo.com] --0-1662192387-1202606429=:56631 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Javad I am not an expert but some time ago I was trying with a big sistem too, and got a similar problem; so I added cycles in the process and the qc keyword, for example, the command line that I added was : # B3LYP/LanL2dz SCF=(maxcycle=90000, qc) the adittion of this last keywords could help you... "javad beheshtian computational.center],[gmail.com" wrote: Sent to CCL by: "javad beheshtian" [computational.center .. gmail.com] Dear CCL Subscribers, I run a set of similar Gaussian jobs (NMR calculations for system consisting of 61 atoms). All this calculations have been finished with the "Normal Termination". However, I am not able to get "Normal Termination" if I slightly change the system. I just remove some atoms and add new ones (so that the totals size of the system increases to 64 atoms). In the "problematic" case I have no error message. Gaussian just stops. In the and of the output file I find the following: **** Warning!!: The largest alpha MO coefficient is 0.12682133D+03 Differentiating once with respect to magnetic field using GIAOs. Electric field/nuclear overlap derivatives assumed to be zero. Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 8193 NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T. Symmetry not used in FoFCou. FMM levels: 10 Number of levels for PrismC: 9 PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. There are 3 degrees of freedom in the 1st order CPHF. 3 vectors were produced by pass 0. AX will form 3 AO Fock derivatives at one time. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. 3 vectors were produced by pass 1. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. 3 vectors were produced by pass 2. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4 . . . 1 vectors were produced by pass142. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. 1 vectors were produced by pass143. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. also input file is : %mem=1800Mb %nproc=4 %chk=/root/work/w1b/50-1wBnmr.chk %rwf=/home/student/tmp/s1,245mw,/home/student/tmp/s2,245mw,/home/student/tmp/s3,245mw,/home/student/tmp/s4,245mw,/home/student/tmp/s5,245mw # b3lyp/6-31+g* prop=efg nmr pop=nbo maxdisk=50GB 0 1 N -0.820146 5.162667 0.594445 H -1.378215 5.976629 0.351741 N -0.815997 2.952748 1.757583 B -1.532634 4.157957 1.383629 N -2.992371 4.146667 1.486120 H -3.436900 5.014950 1.200732 N -2.873310 1.681326 1.102722 B -3.468464 2.962562 0.770443 N -4.218302 3.065244 -0.481126 . . . Does any body know what Gaussian try to do here and why it cannot finish that? Thank you in advance, Javad Beheshtian computational.center_+_gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtDiego Armando Gómez Hernández Licenciado en Química Universidad Distrital Francisco José de Caldas Bogotá-Colombia --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-1662192387-1202606429=:56631 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Javad

I am not an expert but some time ago I was trying with a big sistem too, and got a similar problem; so I added cycles in the process and the qc keyword, for example, the command line that I added was :

# B3LYP/LanL2dz SCF=(maxcycle=90000, qc)

the adittion of this last  keywords could help you...

"javad beheshtian computational.center],[gmail.com" <owner-chemistry|-|ccl.net> wrote:

Sent to CCL by: "javad beheshtian" [computational.center .. gmail.com]

Dear CCL Subscribers,

I run a set of similar Gaussian jobs (NMR calculations for system consisting of 61 atoms). All this calculations have been finished with the "Normal Termination".
However, I am not able to get "Normal Termination" if I slightly
change the system. I just remove some atoms and add new ones (so that the totals
size of the system increases to 64 atoms).
In the "problematic" case I have no error message. Gaussian just
stops. In the and of the output file I find the following:

**** Warning!!: The largest alpha MO coefficient is 0.12682133D+03

Differentiating once with respect to magnetic field using GIAOs.
Electric field/nuclear overlap derivatives assumed to be zero.
Symmetry not used in FoFDir.
MinBra= 0 MaxBra= 2 Meth= 1.
IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0.
FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 8193
NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T.
Symmetry not used in FoFCou.
FMM levels: 10 Number of levels for PrismC: 9
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
There are 3 degrees of freedom in the 1st order CPHF.
3 vectors were produced by pass 0.
AX will form 3 AO Fock derivatives at one time.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
3 vectors were produced by pass 1.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
3 vectors were produced by pass 2.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4

.
.
.

1 vectors were produced by pass142.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
1 vectors were produced by pass143.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.
PrismC: NFx= 2048 NFxT= 4 NFxU= 4.


also input file is :

%mem=1800Mb
%nproc=4
%chk=/root/work/w1b/50-1wBnmr.chk
%rwf=/home/student/tmp/s1,245mw,/home/student/tmp/s2,245mw,/home/student/tmp/s3,245mw,/home/student/tmp/s4,245mw,/home/student/tmp/s5,245mw
# b3lyp/6-31+g* prop=efg nmr pop=nbo maxdisk=50GB



0 1
N -0.820146 5.162667 0.594445
H -1.378215 5.976629 0.351741
N -0.815997 2.952748 1.757583
B -1.532634 4.157957 1.383629
N -2.992371 4.146667 1.486120
H -3.436900 5.014950 1.200732
N -2.873310 1.681326 1.102722
B -3.468464 2.962562 0.770443
N -4.218302 3.065244 -0.481126

.
.
.


Does any body know what Gaussian try to do here and why it cannot finish that?

Thank you in advance,

Javad Beheshtian


computational.center_+_gmail.com







Diego Armando Gómez Hernández
Licenciado en Química
Universidad Distrital Francisco José de Caldas
Bogotá-Colombia

Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-1662192387-1202606429=:56631-- From owner-chemistry@ccl.net Mon Feb 11 19:27:00 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli_-_gmail.com" To: CCL Subject: CCL: Formal charges Message-Id: <-36267-080211173058-9561-OAQXR8xtvmLjG3w+oUwkng..server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_20791_28192064.1202765730323" Date: Mon, 11 Feb 2008 23:35:30 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli:+:gmail.com] ------=_Part_20791_28192064.1202765730323 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline But when I select labels and then formal charges nothing is displayed on the screen even after I run the calculations. Other charges show though (like mulliken etc). Also there is no option for formal charges in the display menu... On Feb 11, 2008 7:49 PM, David Hose anthrax_brothers ~~ hotmail.com < owner-chemistry]*[ccl.net> wrote: > > Sent to CCL by: "David Hose" [anthrax_brothers===hotmail.com] > If you want to display the charges on the 3D structure in Spartan, try > this. From the Model menu > select Labels. Depending upon your preferences, you might see the atom > labels appear (default of > white text on a green background, so the labels may be invisible if you > have charged your background > to white). Then select Configure... from the Model menu and select the > appropriate radio button. > > If you haven't already discovered this, if you click the "P" icon in the > Properties dialogue (under the > Display menu), the charge of the atom selected will be added to the > spreadsheet. > > Regards, > > Dave. > > > > > Sent to CCL by: "Sina T reli" [sinatureli{:}gmail.com] > > Hello, > > > > Is there any tool that will calculate formal charges on a molecular > system and display it? I have tried > spartan but couldnt figure how it displays formal charges though there is > an option for it in the > display menu... > > > > Thanks> > > ------=_Part_20791_28192064.1202765730323 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline But when I select labels and then formal charges nothing is displayed on the screen even after I run the calculations. Other charges show though (like mulliken etc). Also there is no option for formal charges in the display menu...

On Feb 11, 2008 7:49 PM, David Hose anthrax_brothers ~~ hotmail.com <owner-chemistry]*[ccl.net> wrote:

Sent to CCL by: "David  Hose" [anthrax_brothers===hotmail.com]
If you want to display the charges on the 3D structure in Spartan, try this.  From the Model menu
select Labels.  Depending upon your preferences, you might see the atom labels appear (default of
white text on a green background, so the labels may be invisible if you have charged your background
to white).  Then select Configure... from the Model menu and select the appropriate radio button.

If you haven't already discovered this, if you click the "P" icon in the Properties dialogue (under the
Display menu), the charge of the atom selected will be added to the spreadsheet.

Regards,

Dave.

>
> Sent to CCL by: "Sina  T  reli" [sinatureli{:}gmail.com]
> Hello,
>
> Is there any tool that will calculate formal charges on a molecular system and display it? I have tried
spartan but couldnt figure how it displays formal charges though there is an option for it in the
display menu...
>
> Thanks



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