From owner-chemistry@ccl.net Tue Jun 28 01:01:00 2011 From: "psavita##crlindia.com" To: CCL Subject: CCL: Br Pseudopotential Message-Id: <-44986-110628005858-502-aUjhZwSqjs+q/vte+kBStw!A!server.ccl.net> X-Original-From: psavita.:.crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 28 Jun 2011 10:34:08 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita _ crlindia.com
Hello,

I found that there exists a scheme to generate Br= pseudopotential in nwchem, that is developed by Bylaska and co-workers.You can try generating ps file from this.

Thanks and best wishes,
Savi= ta Pundlik
Computational Materials Applied Research Group
Computational Resear= ch Laboratories Ltd.,
Taco House, Damle P= ath, Off Law College Road
Pune - 411004, India.



-----owner-chemistry+psavita=3D=3Dcrlin= dia.com%%ccl.net wrote: -----

To: "Pundlik, Savita Sunil " <psavita%%crlind= ia.com>
From: "Gregorio Garc=EDa Moreno gjgarcia . ujaen.es" <= owner-chemistry%%ccl.net>
Sent by: ow= ner-chemistry+psavita=3D=3Dcrlindia.com%%ccl.net
Date: 06/27/2011 07:= 32PM
Subject: CCL: Br Pseudopotential


Sent to CCL by: =3D?ISO-8859-1?Q?Gregorio= =5FGarc=3DEDa=5FMoreno?=3D [gjgarcia]|[ujaen.es]
Hi all

I'am new = SIESTA user (program to carry out optimizations using LCAO, pseudopotential= s and DFT, but I don't know to generate Pseudopotentials.
I need a GGA/P= BE pseudopotentials for Br atom.
Could someone send me Br pseudopotentia= l file?
I will take into account this help in the aknowledgements of a p= aper,
for which such calculations is neccesary.
I always use pseudopo= tentials from SIESTA webpage, which work correctly
for me systems (organ= ic pi-conjugated molecules), but Br
pseudopotentical isn't available
=

Thanks in advance



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= From owner-chemistry@ccl.net Tue Jun 28 07:27:00 2011 From: "Nichodemus Maria Arockiam mnichodemus() yahoo.com" To: CCL Subject: CCL:G: Dihedral scan Message-Id: <-44987-110628072528-16099-MTxAZt+X4LwM6c4pQFPJpA() server.ccl.net> X-Original-From: "Nichodemus Maria Arockiam" Date: Tue, 28 Jun 2011 07:25:26 -0400 Sent to CCL by: "Nichodemus Maria Arockiam" [mnichodemus{=}yahoo.com] How to do dihedral scan in Gaussian 03. Thanks in advance Nichodemus M From owner-chemistry@ccl.net Tue Jun 28 08:01:00 2011 From: "zhixin zhang zzx0640717..126.com" To: CCL Subject: CCL: remote homology modeling Message-Id: <-44988-110628035122-2161-5+IuoX2ol6nRDODmqTUQvg,,server.ccl.net> X-Original-From: "zhixin zhang" Date: Tue, 28 Jun 2011 03:51:20 -0400 Sent to CCL by: "zhixin zhang" [zzx0640717[A]126.com] Dear CCL Subscribers, I met a problem about homology modeling of a protein ,and honestly I am a little lost. Because of no appropriate templates ,I have divided the protein into two parts, N and C-terminal domains. But there is still no appropriate template for N-terminal domains,for sequence identities <25%,I tooke remote homology modeling into consideration. I have used CPHmodels-3.0 for the N-terminal domains model construction,but the result was incompletesome important residues were lost.Therefore,I request you to help me giving your suggestion/advice how to solve this problem,or is there any software for remote homology modeling. Thank you in advance. With best regards, zhixin,zhang zhixin, zhang zzx0640717]=[126.com From owner-chemistry@ccl.net Tue Jun 28 08:36:01 2011 From: "Nichodemus Maria Arockiam mnichodemus**gmail.com" To: CCL Subject: CCL:G: Gaussian dihesdral scan Message-Id: <-44989-110628072034-6357-wB81pc24DuBRxegz3oKD+Q .. server.ccl.net> X-Original-From: "Nichodemus Maria Arockiam" Date: Tue, 28 Jun 2011 07:20:31 -0400 Sent to CCL by: "Nichodemus Maria Arockiam" [mnichodemus,,gmail.com] How to do gaussian dihedral scan in Gaussian 03. Thanks in advance Nichodemus From owner-chemistry@ccl.net Tue Jun 28 09:11:00 2011 From: "Marcel Brautzsch marcel.brautzsch+/-student.uni-halle.de" To: CCL Subject: CCL:G: Theoritical emision spectroscopy using gaussian09 Message-Id: <-44990-110628071442-31056-1SMmjSR6vkaPLadYLEu52Q-#-server.ccl.net> X-Original-From: "Marcel Brautzsch" Date: Tue, 28 Jun 2011 07:14:40 -0400 Sent to CCL by: "Marcel Brautzsch" [marcel.brautzsch[-]student.uni-halle.de] Hello Debasish Mandal, check the example section on http://www.gaussian.com/g_tech/g_ur/k_scrf.htm with the title Fluoresence example: Emission (Fluorescence) from First Excited State (n*) of Acetaldehyde. For a wider range of the spectra, you should try to use not only the first excited state but also some strong (high oscillator strenth) transitions with higher energy. You maybe need to investigate in more then just the first 6 states in STEP 2 to get a good spectra. Best regards, Marcel Brautzsch > "Debasish Mandal spdm]*[iacs.res.in" wrote: > > Sent to CCL by: "Debasish Mandal" [spdm() iacs.res.in] > Actually I have an experimental fluorescence spectra for a organic pi-conjugated molecule (plotted as fluorescence intensity vs wavelength) in > different solvent e.g. in water,methanol etc. Is it possible to reproduce the above type of spectra theoretically using g09 and gaussview 5.0.9? Please anyone give me an idea about this.any help is greately appreaciated. > > Thanks & Regards > Debasish > > From owner-chemistry@ccl.net Tue Jun 28 09:46:00 2011 From: "Serdar Bado?lu sbadoglu a gazi.edu.tr" To: CCL Subject: CCL: band deconvolution analysis Message-Id: <-44991-110628081754-18501-8HnALMx1b9pubuSC/3FIbw[#]server.ccl.net> X-Original-From: "Serdar Bado?lu" Content-Type: text/plain; charset="iso-8859-9" Date: Tue, 28 Jun 2011 12:15:48 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu[a]gazi.edu.tr] Actually I need to identify individiual bands covered under broad bands in a complex experimental spectrum. The sample I have recorded most probably exhibits dimerization in solid state (because I have several medium and strong intensity peaks which were not predicted by DFT calculations). Plus, the compound itself has several conformers. And I have thick IR peaks although the Raman spectrum shows only narrow bands. That's why I'm asking for band deconvolution analysis. Any help will be great. Regards. -- Serdar BADOGLU Gazi University Department of Physics From owner-chemistry@ccl.net Tue Jun 28 15:07:00 2011 From: "Antonio Arapiraca arapiraca]-[gmail.com" To: CCL Subject: CCL: Dalton Software installation Message-Id: <-44992-110628094031-17713-TgiT94VD3CdeBrarOhPGYw---server.ccl.net> X-Original-From: Antonio Arapiraca Content-Type: multipart/alternative; boundary=0016364c7bc93cf2b404a6c5cf78 Date: Tue, 28 Jun 2011 10:40:22 -0300 MIME-Version: 1.0 Sent to CCL by: Antonio Arapiraca [arapiraca^-^gmail.com] --0016364c7bc93cf2b404a6c5cf78 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Henry, The main problem in the Dalton 2.0 installation is to build properly a Makefile.config. There are a version to MAC OSX in the link: http://wiki.ctcc.no/doku.php?id=3Dpublic:howto:dalton_mac This works in our G5 machine, but I did a serial installation. In this case you need to perform some changes. 1 - To erase the -DVAR_MPI flags and linuxparallel.x mention; 2 - Set the correct path to your FORTRAN and C compilers; 3 - Set the correct path to your installation and basis set directory. Is very instructive a search for "Makefile" word in the Dalton users mailin= g list. Let me know if any of that is not clear Regards Arapiraca 2011/6/27 Henry Martinez hmartine||gmail.com > > Sent to CCL by: "Henry Martinez" [hmartine*o*gmail.com] > Hello everyone, > I have been reading from the Dalton User manual how to install the Dalton > software, and honestly I am a little lost. I was wondering if anybody kno= ws > a more step by step manual that I could follow. This could be for linux, = or > even better MAC OSX. > Thanks a lot for the help > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Ant=F4nio F. C. Arapiraca Prof. do Ensino B=E1sico T=E9cnico e Tecnol=F3gico CEFET-MG Campus X Curvelo =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 You can be free!!!Use Free software http://www.softwarelivre.org http://www.gnu.org --0016364c7bc93cf2b404a6c5cf78 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Henry,
=A0
The main problem in the Dalton 2.0 installation is to build properly a=
Makefile.config. There are a version to MAC OSX in the link:
This works in our G5 machine, but I did a serial installation. In this= case you need to perform some changes.
=A0
1 - To erase the -DVAR_MPI flags and linuxparallel.x mention;
2 - Set the correct path to your FORTRAN and C compilers;
3 - Set the correct path to your installation and basis set directory.=
=A0
Is very instructive a search for "Makefile" word in the Dalt= on users mailing list.
=A0
Let me know if any of that is not clear
=A0
Regards
=A0
Arapiraca

2011/6/27 Henry Martinez hmartine||gmail.com <owner-chemistry-x-ccl.net>

Sent to CCL by: "Henry = =A0Martinez" [hmartine*o*gmail.com]
Hello everyone,
I have been reading from the Dalton User manual how to i= nstall the Dalton software, and honestly I am a little lost. I was wonderin= g if anybody knows a more step by step manual that I could follow. This cou= ld be for linux, or even better MAC OSX.
Thanks a lot for the help



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--
Ant=F4nio F. C. Arapiraca
Prof. do Ensino B=E1sico T=E9cnico e Tecn= ol=F3gico
CEFET-MG=A0Campus X Curvelo
=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=3DYou can be free!!!Use Free software
http://www.softwarelivre.org
http://www.gnu.org

--0016364c7bc93cf2b404a6c5cf78-- From owner-chemistry@ccl.net Tue Jun 28 20:30:00 2011 From: "kails dand kails.dand ~ yahoo.com" To: CCL Subject: CCL: keeping variables constant in gamess Message-Id: <-44993-110628195756-30649-9vYtzCEF0CDgFjgyTXpMHg^^^server.ccl.net> X-Original-From: "kails dand" Date: Tue, 28 Jun 2011 19:57:53 -0400 Sent to CCL by: "kails dand" [kails.dand]^[yahoo.com] Dear all, I am trying to fix some geometric parameters while optimizing using zmatrix in gamess. I have no idea how to do this. Could you please help me out. Your help is greatly appreciated. Thanks Kails