From owner-chemistry@ccl.net Tue Jan 20 03:22:00 2009 From: "Markus Kaukonen markus.kaukonen ~~ iki.fi" To: CCL Subject: CCL: energy of H+ Message-Id: <-38463-090119111227-27938-DMaBY7VuaJZ0VAMhiq/Tog[a]server.ccl.net> X-Original-From: Markus Kaukonen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 19 Jan 2009 17:39:47 +0200 MIME-Version: 1.0 Sent to CCL by: Markus Kaukonen [markus.kaukonen:iki.fi] Dear Serge, You need to specify what's your solvent. In vacuum it is easy, in water difficult. Terveisin Markus On Mon, Jan 19, 2009 at 12:28 PM, Serge Dom serge.dom a gmail.com wrote: > Hello, > > I need to calculate the reaction where H connected to N of pyridine as a > reactant and in the product I have H+ and pyridine(-). > How can I calculte the energy of H+ in order to know if the reaction is > exothermic or endothermic? > > Thank you Serge -- --www=http://www.iki.fi/markus.kaukonen --Markus.Kaukonen-.-iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) --- From owner-chemistry@ccl.net Tue Jan 20 04:15:01 2009 From: "Lukasz Cwiklik cwiklik : gmail.com" To: CCL Subject: CCL: Water Molecule Simulation Message-Id: <-38464-090120040544-24809-jHTzCSFHZ8ys4bEkCZBC+g||server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 20 Jan 2009 11:01:38 +0200 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [cwiklik+*+gmail.com] On Mon, Jan 19, 2009 at 12:43 PM, Leyla Ramin l.ramin,,aeromech.usyd.edu.au wrote: > Hello, > Thanks for your reply, However I have problem with Tinker installation, Would you please send me the code of water simulation. > > Kind Regards > Leyla Ramin Hi, I do know exactly what do you mean, if you need an example input for water simulation you can find it in Tinker "test" subdirectory, eg. "test/water.*" - files for a single H2O molecule, and "test/watertiny.*" - for 81 water box. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Tue Jan 20 07:41:01 2009 From: "Ismael Ortiz Verano ieortizv() bt.unal.edu.co" To: CCL Subject: CCL: QUITEL 2009, CHITEL 2009: First call for papers Message-Id: <-38465-090120072036-13040-9PcOrK2zyLmdHhbN1FNiHA%%server.ccl.net> X-Original-From: "Ismael Ortiz Verano" Content-Type: multipart/alternative; boundary="----=_Part_29483_9903738.1232450461833" Date: Tue, 20 Jan 2009 06:21:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Ismael Ortiz Verano" [ieortizv-.-bt.unal.edu.co] ------=_Part_29483_9903738.1232450461833 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear colleagues, The organizing committee is pleased to invite you to participate in the XXX= V Congress of Theoretical Chemists of Latin Expression (QUITEL or CHITEL) to be held on the island of San Andres, Colombia, September 18-22, 2009. Following its tradition, this congress: - Will examine the state of the art of Theoretical Chemistry through plenary lectures delivered by experts in the field. - Will provide junior scientists with the opportunity to present their research results through posters and oral communications. - Will create the perfect atmosphere for scientific discussions and collaborations among participants. Please visit the congress webpage at: *www.gqt-un.unal.edu.co/quitel/ * We will send further announcements and important information (such as submission procedures, detailed program) in the near future. Do not hesitate to forward this information to your colleagues and partners or any other interested party. Please make sure you mark the dates in your agenda. Looking forward to seeing you in San Andres in 2009. Andres Reyes, on behalf of the Organizing Committee * * **To add your name to the mailing list and receive further information about QUITEL09, please send an email to quitel09|a|gmail.com with the word SUBSCRIBE as the subject.* *To remove your name from this email list, simply use the "Reply" option with "Unsubscribe" in the Subject field. Also, if you have received more than one copy of this email because of having more than one email address, you can remove the unwanted emails by using the "Reply" option and "Unsubscribe" from the address that you want removed or tell us manually which address you would like to remove.* ** * =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D * Estimados colegas: El comit=E9 organizador tiene el placer de invitarlos a participar en el XX= XV Congreso de Qu=EDmicos Te=F3ricos de Expresi=F3n Latina que se llevar=E1 a = cabo en la isla de San Andres, Colombia, entre el 18 y el 22 de septiembre del 2009= . Como es tradici=F3n en este congreso: - Se examinar=E1 el estado actual de la Qu=EDmica Te=F3rica a trav=E9s d= e conferencias plenarias dictadas por expertos en el tema. - Se dar=E1 la oportunidad a j=F3venes investigadores de dar a conocer l= os resultados de su investigaci=F3n a trav=E9s de comunicaciones orales y c= arteles. - Se permitir=E1 realizar discusiones abiertas de temas de investigaci= =F3n y a su vez establecer colaboraciones acad=E9micas entre los participantes. Por favor visite la p=E1gina: *www.gqt-un.unal.edu.co/quitel/ * Enviaremos anuncios e informaci=F3n importante (como procedimiento de inscripci=F3n, programa detallado) muy pronto. Por favor reenviar este correo a los colegas que usted crea puedan estar interesados/as. Esperamos verlos en San Andres este a=F1o. Andres Reyes, en representaci=F3n del comit=E9 organizador * * Para adicionar su nombre a la lista de correos y recibir m=E1s informaci= =F3n sobre QUITEL09, favor de enviar un email a **quitel09|a|gmail.com con la palabra SUBSCRIBE en el t=EDtulo del mensaje.* *Para quitar su nombre de esta lista, this email list, **favor de enviar u= n email a **quitel09|a|gmail.com con la palabra UNSUBSCRIBE en el t=EDtulo del mensaje. Adem=E1s**, si usted recibi=F3 mas de una copia de este email en v= arias direcciones, usted puede remover las direcciones que desea eliminar **envia= ndo un email a **quitel09|a|gmail.com con la palabra UNSUBSCRIBE en el t=EDtulo d= el mensaje desde estas direcciones.* --=20 Ismael Ortiz Verano Grupo de Qu=EDmica Te=F3rica Universidad Nacional de Colombia Tel: (57)(1) 3165000 ext 10608 ------=_Part_29483_9903738.1232450461833 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear colleagues,

The organiz= ing committee is pleased to invite you to participate in the XXXV Congress of Theoretical Chemists of Latin Expression (QUITEL or CHITEL= ) to be held on the island of San Andres, Colombia, September 18-22, 2009.

Following its tradition, this congress:
  • Will examine the state of the art of Theoretical Chemistry through plenary lectures delivered by experts in the field.
    • <= li>Will provide junior scientists with the opportunity to present their research results through posters and oral communications.
  • Will create the perfect atmosphere for scientific discussions and collaborations among participants.
Please visit th= e congress webpage at:


We will send further announcements and important infor= mation (such as submission procedures, detailed program) in the near future= .

Do not hesitate to forward this information to your colleagues and partners or any other interested party. Please make sure you mark the dates in your agenda.


Looking forward to seeing you in San Andr= es in 2009.

Andres Reyes, on behalf of the Organiz= ing Committee


* To add your name to the mailing list and receive further informati= on about QUITEL09, please send an email to quitel09|a|gmail.com with the word SUBSCRIBE as t= he subject.

To remove your name from this email list, simply use the "Reply&= quot; option with "Unsubscribe" in the Subject field. Also, if you have received more than one copy of this email because of having more than one email address, you can remove the unwanted emails by using the "Reply" option and "Unsubscribe" from the address that = you want removed or tell us manually which address you would like to remove.


<= i>

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D


Estimados colegas:

El comit=E9 organizador tiene el placer de invitarlos a participar en el XXXV Congreso de Qu=EDmicos Te=F3ricos de Expresi=F3n Latina que se llevar=E1 a cabo en la isla de San Andres, Colombia, entre el 18 y el 22 de septiembre del 2009.

Como es tradici=F3n en este congreso:

  • Se examinar=E1 el estado actual de la Qu=EDmica Te=F3rica a trav=E9s de conferencias plenarias dictadas por expertos en el tema. 
  • Se dar=E1 la oportunidad a j=F3venes investigadores de dar a conocer los resultados de su investigaci=F3n a trav=E9s de comunicaciones orales y carteles.
  • Se permitir=E1 realizar discusiones abiertas de temas de investigaci=F3n y a su vez establecer colaboraciones acad=E9micas entre los participantes.
Por favor visite la p=E1gina= :


Enviaremos anuncios e informaci=F3n importante (como procedimiento de in= scripci=F3n, programa detallado) muy pronto.

Por favor reenviar este correo a los colegas que usted crea puedan estar= interesados/as.

Esperamos verlos en San Andres este a=F1o.

Andres Reyes, en representaci=F3n del comit=E9 organizador


* Para adicionar su nombre a la lista de correos y recibir m=E1s informaci= =F3n sobre QUITEL09, favor de enviar un email a quitel09|a|gmail.com con la palabra S= UBSCRIBE en el t=EDtulo del mensaje.

Para quitar su nombre de esta lista,  this email list, fa= vor de enviar un email a quitel09|a|gmail.com con la palabra UNSUBSCRIBE en el t=EDtu= lo del mensaje. Adem=E1s, si usted recibi=F3 mas de una copia= de este email en varias direcciones, usted puede remover las direcciones q= ue desea eliminar enviando un email a quitel09|a|gmail.com con la palabra UNSU= BSCRIBE en el t=EDtulo del mensaje desde estas direcciones.





--
Ismael Ortiz Verano
Grupo de Qu= =EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (57)(1) 31650= 00 ext 10608
------=_Part_29483_9903738.1232450461833-- From owner-chemistry@ccl.net Tue Jan 20 08:15:00 2009 From: "Serge Dom serge.dom[a]gmail.com" To: CCL Subject: CCL: energy of H+ Message-Id: <-38466-090120071059-12188-/e5e4SZzl+iOtqjkKKcycA-$-server.ccl.net> X-Original-From: Serge Dom Content-Type: multipart/alternative; boundary=0015174c16ea6d21c00460e811f1 Date: Tue, 20 Jan 2009 13:09:07 +0200 MIME-Version: 1.0 Sent to CCL by: Serge Dom [serge.dom~~gmail.com] --0015174c16ea6d21c00460e811f1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thank you for your answer. If energy of H+ is zero I need only calculate pyridine-h and pyridine (-) in order to calculate difference in energy between product and reactant. Pyridine-h (0,2) has total energy -248.8282688 au at PW91/cc-pVTZ level and pyridine (-) (-1,2) has energy -248.2369938. So elimination of the proton from pyridine-h molecule is not thermodynamically favorable. Is it correct? Serge --0015174c16ea6d21c00460e811f1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Thank you for your answer.
If energy of H+ is zero I need only calculate pyridine-h and pyridine (-) in order to calculate difference in energy between
product and reactant. Pyridine-h (0,2) has total energy -248.8282688 au at PW91/cc-pVTZ level and pyridine (-) (-1,2) has energy
-248.2369938. So elimination of the proton from pyridine-h molecule is not thermodynamically favorable. Is it correct?
 
Serge
--0015174c16ea6d21c00460e811f1-- From owner-chemistry@ccl.net Tue Jan 20 09:16:00 2009 From: "atul agarwal aagarwal|achillion.com" To: CCL Subject: CCL: descriptors for peptides Message-Id: <-38467-090120091414-3444-ocJHkatGDOQhb0/7z2zEGA^server.ccl.net> X-Original-From: "atul agarwal" Date: Tue, 20 Jan 2009 09:14:10 -0500 Sent to CCL by: "atul agarwal" [aagarwal .. achillion.com] Hi, Are there any 2D and 3D descriptors available for peptides? References of their application and availability for pharma will be highly appreciated. thanks! Atul From owner-chemistry@ccl.net Tue Jan 20 18:54:01 2009 From: "Alex Rudn rudikk99[a]yahoo.com" To: CCL Subject: CCL:G: convert command line gamess into gaussian Message-Id: <-38468-090120172311-7521-zR8JNX55YSzZ/Ct6xuCJMg*|*server.ccl.net> X-Original-From: "Alex Rudn" Date: Tue, 20 Jan 2009 17:23:07 -0500 Sent to CCL by: "Alex Rudn" [rudikk99]![yahoo.com] Hi everyone, could you please convert gamess command line into gaussian? $CONTRL RUNTYP=ENERGY $END $SYSTEM MEMORY=70000000 MEMDDI=2000000 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $ELPOT IEPOT=1 WHERE=PDC OUTPUT=BOTH $END $PDC PTSEL=CONNOLLY CONSTR=NONE PTDENS=1.6801711224 $END $CONTRL SCFTYP=RHF EXETYP=RUN MOLPLT=.TRUE. $END $STATPT NSTEP=100 $END $GUESS GUESS=HUCKEL $END $CONTRL COORD=ZMT NZVAR=1452 ICHARG=0 MULT=2 $END $DATA remark line goes here thanks in advance Alex From owner-chemistry@ccl.net Tue Jan 20 19:51:01 2009 From: "Alan Shusterman alan+*+reed.edu" To: CCL Subject: CCL: Re-submitting a previously 'killed' job in spartan Message-Id: <-38469-090120130955-28878-OJSpghFBbmnSkXBjUNEsyQ]*[server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 20 Jan 2009 10:09:39 -0800 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan=-=reed.edu] Richard, Spartan writes scratch files that can (sometimes) be used to restart a job. The nature of the scratch files depends on which platform you are using. For example, on a Windows computer, I think there will be a file with the name 'WFxxxxx' (where 'xxxxx' are some numerical digits) in your Temp folder (this information is only approximately true; I don't have a Windows computer handy to get the precise file names or locations). If you drag this file to another folder and open it with Spartan (you might have to rename it first?), you may be able to restart your calculation. Restarts seem to be more successful with jobs that involve geometry optimization and less successful with other kinds of calculations. I strongly encourage you to email Wavefunction for the most complete/accurate answer to a great question. Sincerely, Alan Richard Tia richtiagh(_)gmail.com wrote: > Sent to CCL by: "Richard Tia" [richtiagh(-)gmail.com] > Hi everybody, > Please forgive me if my question sounds trivial but I'm new to spartan. > If I had to kill a job on spartan '06 for some reason, can I get it to start from where it left off when I re-submit later or it will have to start all over again(from scratch). > > Thanks in advance for your assistance. > > Richard Tia > KNUST, Kumasi > Ghana > richtiagh,,gmail.com> > > > From owner-chemistry@ccl.net Tue Jan 20 23:59:01 2009 From: "Ismael Ortiz Verano ieortizv%a%bt.unal.edu.co" To: CCL Subject: CCL:G: convert command line gamess into gaussian Message-Id: <-38470-090120235530-19970-peijPlaOKHMmUHtwjNbSiw##server.ccl.net> X-Original-From: Ismael Ortiz Verano Content-Type: multipart/alternative; boundary=0016e65bc1ce230f5a0460f6f6dc Date: Tue, 20 Jan 2009 23:55:14 -0500 MIME-Version: 1.0 Sent to CCL by: Ismael Ortiz Verano [ieortizv:bt.unal.edu.co] --0016e65bc1ce230f5a0460f6f6dc Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Alex, You should try using babel in linux, and with the single line: babel -igamin file.inp -ogau file.com you should convert your gamess input file into gaussian input file. --=20 Ismael Ortiz Verano Grupo de Qu=EDmica Te=F3rica Universidad Nacional de Colombia Tel: (57)(1) 3165000 ext 10608 2009/1/20 Alex Rudn rudikk99[a]yahoo.com > > Sent to CCL by: "Alex Rudn" [rudikk99]![yahoo.com] > Hi everyone, > > could you please convert gamess command line into gaussian? > > $CONTRL RUNTYP=3DENERGY $END > $SYSTEM MEMORY=3D70000000 MEMDDI=3D2000000 $END > $BASIS GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $END > $ELPOT IEPOT=3D1 WHERE=3DPDC OUTPUT=3DBOTH $END > $PDC PTSEL=3DCONNOLLY CONSTR=3DNONE PTDENS=3D1.6801711224 $END > $CONTRL SCFTYP=3DRHF EXETYP=3DRUN MOLPLT=3D.TRUE. $END > $STATPT NSTEP=3D100 $END > $GUESS GUESS=3DHUCKEL $END > $CONTRL COORD=3DZMT NZVAR=3D1452 ICHARG=3D0 MULT=3D2 $END > $DATA > remark line goes here > > thanks in advance > > Alex > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Ismael Ortiz Verano Grupo de Qu=EDmica Te=F3rica Universidad Nacional de Colombia Tel: (57)(1) 3165000 ext 10608 --0016e65bc1ce230f5a0460f6f6dc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Alex,

You should try using babel in linux, and with the single li= ne:

babel -igamin file.inp -ogau file.c= om

you should convert your gamess input file into gaussian input= file.


--
Ismael Ortiz Verano
Grupo de Qu=EDmica Te=F3rica
Unive= rsidad Nacional de Colombia
Tel: (57)(1) 3165000 ext 10608


2009/1/20 Alex Rudn rudikk99[a]yahoo.com <owner-chemistry|,|ccl.net>

Sent to CCL by: "Alex  Rudn" [rudikk99]![yahoo.com]
Hi everyone,

could you please convert gamess command line into gaussian?

 $CONTRL RUNTYP=3DENERGY $END
 $SYSTEM MEMORY=3D70000000 MEMDDI=3D2000000 $END
 $BASIS GBASIS=3DN31 NGAUSS=3D6 NDFUNC=3D1 $END
 $ELPOT IEPOT=3D1 WHERE=3DPDC OUTPUT=3DBOTH $END
 $PDC PTSEL=3DCONNOLLY CONSTR=3DNONE PTDENS=3D1.6801711224 $END
 $CONTRL SCFTYP=3DRHF EXETYP=3DRUN MOLPLT=3D.TRUE. $END
 $STATPT NSTEP=3D100 $END
 $GUESS GUESS=3DHUCKEL $END
 $CONTRL COORD=3DZMT NZVAR=3D1452 ICHARG=3D0 MULT=3D2 $END
 $DATA
remark line goes here

thanks in advance

Alex



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--
Ismael Ortiz Verano
= Grupo de Qu=EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (5= 7)(1) 3165000 ext 10608
--0016e65bc1ce230f5a0460f6f6dc--