From owner-chemistry@ccl.net Mon Aug 27 01:51:01 2012 From: "Andrew Yeung andrew.yeung(!)mail.chem.tamu.edu" To: CCL Subject: CCL:G: MOPAC/MOZYME PBC calculations Message-Id: <-47472-120826211022-13028-FqCPfZB23ZySwGnzasRVgg-$-server.ccl.net> X-Original-From: "Andrew Yeung" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8; format="flowed" Date: Sun, 26 Aug 2012 20:10:13 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew Yeung" [andrew.yeung%x%mail.chem.tamu.edu] Thanks for getting back. I'll use the .arc files to generate new MOPAC input files. I suppose that MOPAC calculations are so fast that reading in force constants is not a huge advantage. I've turned to MOPAC because it is able to perform PBC calculations using semi-empirical hamiltonians, whereas Gaussian 09 is only able to use HF & DFT. Furthermore, G09 does not report enthalpies with a frequency calculation (and that must be done numerically). On Sun, 26 Aug 2012 12:12:48 -0400 "John McKelvey jmmckel::gmail.com" wrote: > > Sent to CCL by: John McKelvey [jmmckel]-[gmail.com] > Have you tried the latest version of Gaussian for all this as I >think > it also contains one of the latest MOPAC versions? > > In MOPAC itself you can use the DENOUT keyword to keep a >satisfactory > current density and then OLDENS to read YOUR_FILENAME.DEN in to >start > a subsequent job. > > You can carve out an input geometry from an archive file > (YOUR_FILENAME.ARC). To the best of my knowledge MOPAC does not > output intermediate geometries, and I am not aware that it outputs a > Hessian that can be read back in. > > Again, Gaussian included version of MOPAC can likely do all you >want. > > John McKelvey > > On Fri, Aug 24, 2012 at 6:27 PM, Andrew Yeung > andrew.yeung=-=chem.tamu.edu wrote: >> >> Sent to CCL by: Andrew Yeung [andrew.yeung^^chem.tamu.edu] >> Hi all >> >> I am doing a few PBC calculations on MOPAC, and I was hoping for >>some >> advise. >> >> Since the system is rather large (and I suppose the initial guess is >>poor), >> I cannot get SCF convergence unless I use the MOZYME keyword. The >>online >> manual (http://openmopac.net/manual/mozyme.html) gives some tips on >> multi-step jobs (MOZYME for geometry optimization, then MOPAC, then >>perhaps >> FORCE). >> >> Since my jobs have started already (MOZYME then FORCE), I want to >>let it >> run, and do the MOPAC equivalent of "geom=allcheck guess=read >>opt(readfc)" >> on the resultant output file(s). Is this possible? How else can I >>start a >> new calculation based on an old one? Should I edit the archive >>(.arc) file >> into a new MOPAC input file? >> >> Thanks for your comments. >> >> -- >> Andrew Yeung >> Donald J. Darensbourg Research Group >> Department of Chemistry, Texas A&M University >> 3255 TAMU >> College Station, TX 77843-3255 >> >> Tel: 979 845 4837 >> Fax: 979 845 >>0158http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/> >> > > > > -- > John McKelvey > 10819 Middleford Pl >Ft Wayne, IN 46818 > 260-489-2160 > jmmckel%x%gmail.com > > > > -= This is automatically added to each message by the mailing script >=- > To recover the email address of the author of the message, please >change> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Mon Aug 27 03:39:01 2012 From: "Cristian Bologa cbologa---salud.unm.edu" To: CCL Subject: CCL: prediction of peptide structures and protein-protein docking Message-Id: <-47473-120827022841-1024-649KI8GEWCAYUvEXTXWWTQ[]server.ccl.net> X-Original-From: "Cristian Bologa" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=US-ASCII Date: Mon, 27 Aug 2012 00:28:27 -0600 Mime-Version: 1.0 Sent to CCL by: "Cristian Bologa" [cbologa:+:salud.unm.edu] Hi Guiyu, Given the complexity of your problem, you should probably try to incorporate in the modeling experiment all the experimental knowledge you can get (from literature, your colleagues, etc). For example, before trying to model de novo the structure of your peptide, you can try your luck by doing a sequence similarity search on the protein data bank (PDB) to see if there are any peptides or (parts of) proteins similar to your peptide. For the docking part, you might want to find out if other similar peptides have been tested on that receptor, if there are any key residues important for binding to the receptor, if the peptide has been tested on any receptor mutants, etc. You could also use that information in the next iteration of peptide structure refinement. Also if the sequence of the peptide is confidential you probably do not want to upload it to any public server. Regards, Cristian Bologa, Ph.D. Research Associate Professor, Div. of Translational Informatics, Dept. of Internal Medicine, Univ. of New Mexico, School of Medicine, Innovation Discovery & Training Center, MSC10 5550, 700 Camino de Salud NE, Albuquerque, NM 87131 tel: +1-505-925-7534 fax:+1-505-925-7625 >>> "Guiyu Zhao guiyu.zhao(0)astrazeneca.com" 8/26/2012 2:30 AM >>> Sent to CCL by: "Guiyu Zhao" [guiyu.zhao{:}astrazeneca.com] Dear CCL colleagues, I'm trying to fulfill a request from my colleagues about a 17-membered peptide. They want to get a rough idea about the peptide's 3D structure and, if possible, the binding pose with a cell receptor. I feel the task is chellenging for me not only because I'm a modeler on small molecules and not familiar with protein modeling, but also because we are lack of commercial tools to do peptide structure prediction and protein-protein docking. So first of all, is there any free tool to do such calculations? RosettaDcok and BioLuminate from Schrodinger Inc. are not available to me. Then, is it reallistic to model a peptide's 3D structure without knowing anything about its secondary structure (my colleagues only provided me its sequence)? Thank you in advance for any response. Kind regards, Guiyu Zhaohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Aug 27 08:29:01 2012 From: "AMBRISH KUMAR SRIVASTAVA ambrishphysics.:.gmail.com" To: CCL Subject: CCL:G: errors in running gaussian 03 w Message-Id: <-47474-120827072516-14398-vjSbnOJMTPsHbRdnf1Sn9g . server.ccl.net> X-Original-From: "AMBRISH KUMAR SRIVASTAVA" Date: Mon, 27 Aug 2012 07:25:14 -0400 Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics(!)gmail.com] respected all, i am facing a problem during termination of job. i didnt get normal termination at the end as expected. it shows something like this: G03 W FROND END HAS STOPPED WORKING. can anybody help me in this regard?? thanks to all in advance.. AMBRISH K. SRIVASTAVA ambrishphysics]~[gmail.com From owner-chemistry@ccl.net Mon Aug 27 09:03:00 2012 From: "Ravi Kumar Venkatraman ravi.ipc.iisc * gmail.com" To: CCL Subject: CCL: Regarding NBO NLMO visualisation using gauss view Message-Id: <-47475-120827083215-18691-FD5eaQUjUmALNAryVa0QjQ*server.ccl.net> X-Original-From: Ravi Kumar Venkatraman Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 27 Aug 2012 18:02:02 +0530 MIME-Version: 1.0 Sent to CCL by: Ravi Kumar Venkatraman [ravi.ipc.iisc~~gmail.com] Dear CCL users, I would like to visualize the NBO and NLMO of a molecule. I don't know what kind of input parameters I have write for G09 and How to visualize those output using GaussView. Could anybody help me regarding this. Thank you in Advance. Yours Sincerely, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore-560012. INDIA. From owner-chemistry@ccl.net Mon Aug 27 10:40:00 2012 From: "Thomas Manz thomasamanz-*-gmail.com" To: CCL Subject: CCL: EMSL basis set exchange Message-Id: <-47476-120827103204-29337-y0D4BI40JjXGfxSJOgfOcA~~server.ccl.net> X-Original-From: Thomas Manz Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 27 Aug 2012 08:31:58 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz||gmail.com] Hi, I have been using the EMSL basis set exchange at bse.pnl.gov as a source of basis sets for quantum chemistry calculations. However, it doesn't appear to be working at this time. Has anyone heard any news about this? Are there plans to bring the EMSL basis set exchange back online? I hope this is just a temporary outage. Sincerely, Tom Manz From owner-chemistry@ccl.net Mon Aug 27 12:06:00 2012 From: "Van Dam, Hubertus J HubertusJJ.vanDam===pnnl.gov" To: CCL Subject: CCL: EMSL basis set exchange Message-Id: <-47477-120827120449-32707-6lbg8i28ZkXgpoIRDPaokw(_)server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Aug 2012 09:04:38 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam*pnnl.gov] Hi Thomas, This is indeed an unplanned temporary outage. We have run into some problems in the machine room with the cooling systems. Our guys are working as fast as they can to get this fixed but at present all machines in that room are powered off, including the basis set server. I have posted a message about this on our community forum at http://www.nwchem-sw.org/index.php/Special:AWCforum in the category "BSE: Basis Set Exchange". Apparently our technicians hope to have the system back online this afternoon, but we will post another message when that has actually happened. I apologize for the inconvenience caused, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov#ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov#ccl.net] On Behalf Of Thomas Manz thomasamanz-*-gmail.com Sent: Monday, August 27, 2012 7:32 AM To: Van Dam, Hubertus J Subject: CCL: EMSL basis set exchange Sent to CCL by: Thomas Manz [thomasamanz||gmail.com] Hi, I have been using the EMSL basis set exchange at bse.pnl.gov as a source of basis sets for quantum chemistry calculations. However, it doesn't appear to be working at this time. Has anyone heard any news about this? Are there plans to bring the EMSL basis set exchange back online? I hope this is just a temporary outage. Sincerely, Tom Manzhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Aug 27 12:41:00 2012 From: "Billy McCann bwm0005=tigermail.auburn.edu" To: CCL Subject: CCL:G: Regarding NBO NLMO visualisation using gauss view Message-Id: <-47478-120827115107-30347-7O3wSFnkpEl1TK1t9Bau2A*server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Aug 2012 15:50:40 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005]_[tigermail.auburn.edu] Hi Ravi. There has recently, past 6 months or so, been much discussion on this problem. A recent post by Wilhelm Eger should be what you're looking for. "IOP=(6/73=1) POP=NBO for NBO output and IOP=(6/73=2) POP=NBO for NLMO output. Now I get two different cube files, which can be subtracted via cubman and the resulting difference cube file can be visualized e.g. in Gaussview." To place this post in context, I'd recommend using Google's 'site' operator to search for the full discussion, e.g. "site:ccl.net Visualize NLMOs from Gaussian output/checkpoint file". I take especial notice of NBO/NLMO threads because I find them so very interesting. There's always the software (non-free) that is on http://www.chem.wisc.edu/~nbo5/. Hope that helps. Billy +++++++++++++++++++++++++ Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Reseach Auburn University, Alabama Office # = 334.844.6948 bwayne on irc.freenode.net +++++++++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu|,|ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu|,|ccl.net] On Behalf Of Ravi Kumar Venkatraman ravi.ipc.iisc * gmail.com Sent: Monday, August 27, 2012 7:32 AM To: Billy McCann Subject: CCL: Regarding NBO NLMO visualisation using gauss view Sent to CCL by: Ravi Kumar Venkatraman [ravi.ipc.iisc~~gmail.com] Dear CCL users, I would like to visualize the NBO and NLMO of a molecule. I don't know what kind of input parameters I have write for G09 and How to visualize those output using GaussView. Could anybody help me regarding this. Thank you in Advance. Yours Sincerely, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore-560012. INDIA.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Aug 27 13:16:00 2012 From: "John Keller jwkeller..alaska.edu" To: CCL Subject: CCL: IQmol (Win 7) crashes opening a QChem 4.0 output.out file Message-Id: <-47479-120827130436-2117-sA5rEy3tm3NHcv2v4dP91g(0)server.ccl.net> X-Original-From: John Keller Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 27 Aug 2012 09:04:29 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller|,|alaska.edu] Hi - (I'll answer my own question...) Andrew Gilbert the IQmol developer says this is bug for some Win7 users, which has to do with Win7 not properly loading the Babel plugin. Anyway, the workaround is to first draw a small molecule like ethylene, Select Force Field, and Minimize Structure. This forces loading of the Babel plugin. Then try to open the output.out file. I works for my Win7 systems. John Keller On Fri, Aug 24, 2012 at 8:11 PM, John Keller jwkeller]_[alaska.edu wrote: > > Sent to CCL by: "John Keller" [jwkeller..alaska.edu] > My IQmol 2.0.1 application for Win 7 can open Q-Chem 4.0 Test.Fchk files and display MO surfaces, etc., however it crashes whenever I try to open an output.out file from any type of Q-Chem opt, freq, or SP job. These jobs run successfully according to the output.out text, and they are processed correctly by WebMO, so why can't IQmol handle them? Has anyone else had this problem, or know a work-around? > (I posted this question at www.iqmol.org too, but have not heard back yet.) > John Keller > jwkeller_-_alaska.edu > Dept of Chemistry & Biochemistry > University of Alaska Fairbanks> > From owner-chemistry@ccl.net Mon Aug 27 13:51:00 2012 From: "AYORINDE HASSAN ayo_hassan_+_yahoo.com" To: CCL Subject: CCL: EMSL basis set exchange Message-Id: <-47480-120827125938-30052-E/2kdxRdWHyZwKi/UaeVRg\a/server.ccl.net> X-Original-From: AYORINDE HASSAN Content-Type: multipart/alternative; boundary="1234169369-1014739862-1346086771=:64752" Date: Mon, 27 Aug 2012 09:59:31 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: AYORINDE HASSAN [ayo_hassan(~)yahoo.com] --1234169369-1014739862-1346086771=:64752 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hey Thomas,=0AIt is temporarily down. See this thread to follow the develop= ment concerning its reinstatement:=0A=0A=0Ahttp://www.nwchem-sw.org/index.p= hp/Special:AWCforum/st/id549/=0A=0AThe thread also discusses how you can al= ternatively get your desired basis sets during the outage.=0A=0A=0A=0A=0A__= ______________________________=0A From: Thomas Manz thomasamanz-*-gmail.com= =0ATo: "Hassan, Ayorinde " =0ASent: Monday, August 27, 2012 9:31 AM=0ASubject: CCL: EMSL basi= s set exchange=0A =0A=0ASent to CCL by: Thomas Manz [thomasamanz||gmail.com= ]=0AHi,=0A=0AI have been using the EMSL basis set exchange at bse.pnl.gov a= s a=0Asource of basis sets for quantum chemistry calculations.=0AHowever, i= t doesn't appear to be working at this time.=0AHas anyone heard any news ab= out this?=0AAre there plans to bring the EMSL basis set exchange back onlin= e?=0AI hope this is just a temporary outage.=0A=0ASincerely,=0A=0ATom Manz= =0A=0A=0A=0A-=3D This is automatically added to each message by the mailing= script =3D-=0ATo recover the email address of the author of the message, p= lease change=0Athe strange characters on the top line to the *o* sign. You ca= n also=0A=0A=0AE-mail = to subscribers: CHEMISTRY*o*ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/= cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUE= ST*o*ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sage=0A=0A=0A=A0 =A0 =A0 http://www.ccl.net/chemistr= y/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://www.ccl.n= et=0A=0A=0AConferences: http://server.ccl.net/= chemistry/announcements/conferences/=0A=0ASearch Messages: http://www.ccl.n= et/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL with = 5.7.1 error, check:=0A=A0 =A0 =A0=0A=0ARTFI= : http://www.ccl.net/chemistry/aboutccl/instructions/ --1234169369-1014739862-1346086771=:64752 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hey Thomas= ,
It is temporarily down. See this thread to follow = the development concerning its reinstatement:
http://www.nwchem-sw.org/index.php/Special:AWCfor= um/st/id549/

The th= read also discusses how you can alternatively get your desired basis sets d= uring the outage.

=
=
From: Thom= as Manz thomasamanz-*-gmail.com <owner-chemistry*o*ccl.net>
To: "Hassan, Ayorinde " <ayo_hassan*o*yahoo.com>
Se= nt: Monday, August 27, 2012 9:31 AM
Subject: CCL: EMSL basis set exchange
 =

=0A
Sent to CCL by: Thomas Manz [thomasamanz||gmail.com]
H= i,

I have been using the EMSL basis set exchange at bse.pnl.gov as a
source of basis s= ets for quantum chemistry calculations.
However, it doesn't appear to be= working at this time.
Has anyone heard any news about this?
Are ther= e plans to bring the EMSL basis set exchange back online?
I hope this is= just a temporary outage.

Sincerely,

Tom Manz



= -=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 chang= e=

E-mail to subs= cribers: CHEMISTRY*o*ccl.net or use:
     

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


--1234169369-1014739862-1346086771=:64752-- From owner-chemistry@ccl.net Mon Aug 27 14:26:00 2012 From: "Sergio Galembeck segalemb{}usp.br" To: CCL Subject: CCL: Regarding NBO NLMO visualisation using gauss view Message-Id: <-47481-120827132321-25293-yYkV2SNAfK89jSw11g4Tog*server.ccl.net> X-Original-From: Sergio Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 27 Aug 2012 14:23:06 -0300 Mime-Version: 1.0 (Apple Message framework v1278) Sent to CCL by: Sergio Galembeck [segalemb-.-usp.br] Dear Ravi, The best way to visualize NBOs ot NLMOs by using GaussView is to use the keyword pop=(full,savenbos) or pop=(full,savenlmos), repectively. Hope this help you, Sergio On 27/08/2012, at 09:32, Ravi Kumar Venkatraman ravi.ipc.iisc * gmail.com wrote: > > Sent to CCL by: Ravi Kumar Venkatraman [ravi.ipc.iisc~~gmail.com] > Dear CCL users, > I would like to visualize the NBO and NLMO of > a molecule. I don't know what kind of input parameters I have write > for G09 and How to visualize those output using GaussView. Could > anybody help me regarding this. > > Thank you in Advance. > > Yours Sincerely, > Ravi Kumar Venkatraman, > IPC Dept., IISc, > Bangalore-560012. > INDIA.> > > From owner-chemistry@ccl.net Mon Aug 27 15:00:00 2012 From: "Jim Kress ccl_nospam__kressworks.com" To: CCL Subject: CCL: EMSL basis set exchange Message-Id: <-47482-120827133706-11967-aK4FZLVdz8QrFu5qltcq7A__server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 27 Aug 2012 13:36:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam/a\kressworks.com] Isn't there a mirror for this information in Europe or another country/ location? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com()ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com()ccl.net] On Behalf > Of Van Dam, Hubertus J HubertusJJ.vanDam===pnnl.gov > Sent: Monday, August 27, 2012 12:05 PM > To: Kress, Jim > Subject: CCL: EMSL basis set exchange > > > Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam*pnnl.gov] Hi > Thomas, > > This is indeed an unplanned temporary outage. We have run into some > problems in the machine room with the cooling systems. Our guys are > working as fast as they can to get this fixed but at present all machines in that > room are powered off, including the basis set server. I have posted a > message about this on our community forum at http://www.nwchem- > sw.org/index.php/Special:AWCforum in the category "BSE: Basis Set > Exchange". Apparently our technicians hope to have the system back online > this afternoon, but we will post another message when that has actually > happened. > > I apologize for the inconvenience caused, > > Huub > > -----Original Message----- > > From: owner-chemistry+hubertus.vandam==pnnl.gov~!~ccl.net > > [mailto:owner-chemistry+hubertus.vandam==pnnl.gov~!~ccl.net] On > Behalf > > Of Thomas Manz thomasamanz-*-gmail.com > Sent: Monday, August 27, 2012 7:32 AM > To: Van Dam, Hubertus J > Subject: CCL: EMSL basis set exchange > > > Sent to CCL by: Thomas Manz [thomasamanz||gmail.com] Hi, > > I have been using the EMSL basis set exchange at bse.pnl.gov as a source of > basis sets for quantum chemistry calculations. > However, it doesn't appear to be working at this time. > Has anyone heard any news about this? > Are there plans to bring the EMSL basis set exchange back online? > I hope this is just a temporary outage. > > Sincerely, > > Tom Manzhttp://www.ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlh > ttp://www.ccl.net/spammers.txtTo > recover the email address of the author of the message, please change the > strange characters on the top line to the () sign. You can also look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Mon Aug 27 16:17:00 2012 From: "Joseph Katigbak jkatigba^^^stevens.edu" To: CCL Subject: CCL:G: Wachters basis set for Mn Message-Id: <-47483-120827161551-4832-I9iYQtJMiZjBcH1fEo4lFQ**server.ccl.net> X-Original-From: "Joseph Katigbak" Date: Mon, 27 Aug 2012 16:15:49 -0400 Sent to CCL by: "Joseph Katigbak" [jkatigba++stevens.edu] Hi there everyone, I'm starting a new project on Manganese complexes with H2O2 and want to do some initial B3LYP calculations first. I had previously used The Wachters basis set for Fe and someone suggested it would be good for Mn as well. If you guys have the Wachters basis set for Mn in the Gaussian09 format I would be soooooo thankful. Thank you sooo much for any help. -Joseph From owner-chemistry@ccl.net Mon Aug 27 16:51:00 2012 From: "DeJong, Wibe A Wibe.DeJong:-:pnnl.gov" To: CCL Subject: CCL: EMSL basis set exchange Message-Id: <-47484-120827163312-11914-aWrnx/gsYWYGuGjGFRmmFQ^_^server.ccl.net> X-Original-From: "DeJong, Wibe A" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Aug 2012 13:33:02 -0700 MIME-Version: 1.0 Sent to CCL by: "DeJong, Wibe A" [Wibe.DeJong_-_pnnl.gov] Just FYI, the EMSL basis set exchange at bse.pnl.gov is available again. We will be investigating the possibility to put a mirror in place. Thanks, Bert de Jong EMSL -----Original Message----- > From: owner-chemistry+bert.dejong==pnl.gov(~)ccl.net [mailto:owner-chemistry+bert.dejong==pnl.gov(~)ccl.net] On Behalf Of Jim Kress ccl_nospam__kressworks.com Sent: Monday, August 27, 2012 10:37 AM To: DeJong, Wibe A Subject: CCL: EMSL basis set exchange Sent to CCL by: "Jim Kress" [ccl_nospam/a\kressworks.com] Isn't there a mirror for this information in Europe or another country/ location? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com=-=ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com=-=ccl.net] On > Behalf Of Van Dam, Hubertus J HubertusJJ.vanDam===pnnl.gov > Sent: Monday, August 27, 2012 12:05 PM > To: Kress, Jim > Subject: CCL: EMSL basis set exchange > > > Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam*pnnl.gov] Hi > Thomas, > > This is indeed an unplanned temporary outage. We have run into some > problems in the machine room with the cooling systems. Our guys are > working as fast as they can to get this fixed but at present all > machines in that > room are powered off, including the basis set server. I have posted a > message about this on our community forum at http://www.nwchem- > sw.org/index.php/Special:AWCforum in the category "BSE: Basis Set > Exchange". Apparently our technicians hope to have the system back > online this afternoon, but we will post another message when that has > actually happened. > > I apologize for the inconvenience caused, > > Huub > > -----Original Message----- > > From: owner-chemistry+hubertus.vandam==pnnl.gov~!~ccl.net > > [mailto:owner-chemistry+hubertus.vandam==pnnl.gov~!~ccl.net] On > Behalf > > Of Thomas Manz thomasamanz-*-gmail.com > Sent: Monday, August 27, 2012 7:32 AM > To: Van Dam, Hubertus J > Subject: CCL: EMSL basis set exchange > > > Sent to CCL by: Thomas Manz [thomasamanz||gmail.com] Hi, > > I have been using the EMSL basis set exchange at bse.pnl.gov as a > source of > basis sets for quantum chemistry calculations. > However, it doesn't appear to be working at this time. > Has anyone heard any news about this? > Are there plans to bring the EMSL basis set exchange back online? > I hope this is just a temporary outage. > > Sincerely, > > Tom Manzhttp://www.ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlh > ttp://www.ccl.net/spammers.txtTo > recover the email address of the author of the message, please change > the strange characters on the top line to the =-= sign. You can also > look up the X- > Original-From: line in the mail header.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Aug 27 17:27:00 2012 From: "Van Dam, Hubertus J HubertusJJ.vanDam%%pnnl.gov" To: CCL Subject: CCL: EMSL basis set exchange: service restored Message-Id: <-47485-120827170000-26292-s4VanK6GbQQAs3dUB5tbsQ!A!server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Aug 2012 13:59:48 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam{}pnnl.gov] Hi Jim, Just two comments from my end. First of all good news: the service is back. Second, yes there used to be a mirror that was hosted at Daresbury Laboratory in the UK. However, with the internet improving in speed and quality it was concluded some years back that in practice there was no real justification for having a mirror anymore. In particular as there was some manual effort involved in synchronizing the data sets. So that mirror service has been terminated. On our end we have noticed a considerable response to this incident and we realize that it is at the very least desirable to have a more robust infrastructure. So we are looking into the options on this topic. Any comments on that may be posted on the forum (http://www.nwchem-sw.org/index.php/Special:AWCforum) or you can send them to me. Again we apologize for this service interruption. Best wishes, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov ~~ ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov ~~ ccl.net] On Behalf Of Jim Kress ccl_nospam__kressworks.com Sent: Monday, August 27, 2012 10:37 AM To: Van Dam, Hubertus J Subject: CCL: EMSL basis set exchange Sent to CCL by: "Jim Kress" [ccl_nospam/a\kressworks.com] Isn't there a mirror for this information in Europe or another country/ location? Jim From owner-chemistry@ccl.net Mon Aug 27 18:01:00 2012 From: "Joop van Lenthe j.h.vanlenthe.|-|.uu.nl" To: CCL Subject: CCL:G: Wachters basis set for Mn Message-Id: <-47486-120827171926-8875-3XweqWmwTNJJOR08UQeRyw|-|server.ccl.net> X-Original-From: Joop van Lenthe Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 27 Aug 2012 23:19:10 +0200 Mime-Version: 1.0 (Apple Message framework v1278) Sent to CCL by: Joop van Lenthe [j.h.vanlenthe-*-uu.nl] try the basis set changen https://bse.pnl.gov/bse/portal Joop =============================== Joop van Lenthe Theoretical Chemistry Group Utrecht Condensed matter and Interfaces Ornstein Laboratory, k108 tel. -31-30-2532733 http://tc5.chem.uu.nl/joop joop#chem.uu.nl =============================== On 27/08/2012, at 10:15 PM, Joseph Katigbak jkatigba^^^stevens.edu wrote: > > Sent to CCL by: "Joseph Katigbak" [jkatigba++stevens.edu] > Hi there everyone, I'm starting a new project on Manganese complexes with H2O2 > and want to do some initial B3LYP calculations first. I had previously used The > Wachters basis set for Fe and someone suggested it would be good for Mn as > well. If you guys have the Wachters basis set for Mn in the Gaussian09 format I > would be soooooo thankful. Thank you sooo much for any help. > > -Joseph> > From owner-chemistry@ccl.net Mon Aug 27 18:36:00 2012 From: "Van Dam, Hubertus J HubertusJJ.vanDam---pnnl.gov" To: CCL Subject: CCL:G: Wachters basis set for Mn Message-Id: <-47487-120827174847-32096-w9w9wAyG2ckNsbf69kEQBQ++server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 Aug 2012 14:48:05 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam!A!pnnl.gov] Hi Joseph, How about visiting the Basis Set Exchange (now we are up and running again, see http://bse.pnl.gov). It has the Wachters basis set for Mn. It can also generate the basis set in the Gaussian94 format, but I would be very much surprised if that format would be different from the Gaussian09 format. So I guess you should be able to use that data right away. Best wishes, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov!A!ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov!A!ccl.net] On Behalf Of Joseph Katigbak jkatigba^^^stevens.edu Sent: Monday, August 27, 2012 1:16 PM To: Van Dam, Hubertus J Subject: CCL:G: Wachters basis set for Mn Sent to CCL by: "Joseph Katigbak" [jkatigba++stevens.edu] Hi there everyone, I'm starting a new project on Manganese complexes with H2O2 and want to do some initial B3LYP calculations first. I had previously used The Wachters basis set for Fe and someone suggested it would be good for Mn as well. If you guys have the Wachters basis set for Mn in the Gaussian09 format I would be soooooo thankful. Thank you sooo much for any help. -Josephhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt