From owner-chemistry@ccl.net Thu Dec 27 01:11:01 2007 From: "Guanna Li gnli-$-dicp.ac.cn" To: CCL Subject: CCL: how to using gaussian03 COSMO solvent model best? Message-Id: <-35932-071227010908-19524-vT9UqPQ0dFwthJqJeFZvaw],[server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Thu, 27 Dec 2007 14:09:56 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli()dicp.ac.cn] Dear all, I using cosmo model to calculate system in water, but the opt step energy always oscillate, could anyone give me some advice? Thank you very much! -------------- 2007-12-27 Best wishes Guanna Li Email: gnli-#-dicp.ac.cn From owner-chemistry@ccl.net Thu Dec 27 05:32:00 2007 From: "Bala Subramanian bala()igib.res.in" To: CCL Subject: CCL: protein-rna docking Message-Id: <-35933-071227052605-10205-7q4kQbJAoDVmMy33BG3Rng:-:server.ccl.net> X-Original-From: "Bala Subramanian" Date: Thu, 27 Dec 2007 05:26:01 -0500 Sent to CCL by: "Bala Subramanian" [bala.:.igib.res.in] Dear CCLers, Someone please suggest me a software especially a freeware highly suited for protein-RNA docking. Thanks in advance, Bala From owner-chemistry@ccl.net Thu Dec 27 06:02:00 2007 From: "Ridha Khalfa khalfaridha * hotmail.com" To: CCL Subject: CCL:G: Error message in an ONIOM calculation Message-Id: <-35934-071227053135-10812-/MWbWL/AsRsw0laBZtNizA(a)server.ccl.net> X-Original-From: "Ridha Khalfa" Date: Thu, 27 Dec 2007 05:31:31 -0500 Sent to CCL by: "Ridha Khalfa" [khalfaridha|-|hotmail.com] Dear all, I am trying to carry out an ONIOM calculation using the following keywords: #N ONIOM(B3LYP/6-31g(d,p):UFF) opt=z-matrix geom=modify guess=read energy minimisation in AKR1C1 ONIOM with aa's -2 3 0 1 0 1 however, the calculation fails after sometime with the following error message: Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 440 basis functions, 763 primitive gaussians, 440 cartesian basis functions 78 alpha electrons 78 beta electrons nuclear repulsion energy Inf Hartrees. NAtoms= 301 NActive= 46 NUniq= 46 SFac= 1.00D+00 NAtFMM= 60 Big=F One-electron integrals computed using PRISM. NBasis= 440 RedAO= T NBF= 440 NBsUse= 37 1.00D-06 NBFU= 37 Initial guess read from the read-write file: Unable to project occupied orbitals ! Error termination via Lnk1e in /bb/che/wilkiej/g03/l401.exe at Mon Dec 24 17:12:19 2007. Job cpu time: 2 days 23 hours 3 minutes 0.4 seconds. File lengths (MBytes): RWF= 90 Int= 0 D2E= 0 Chk= 69 Scr= 159 ( Can anyone tel me what is wrong and how I can solve the problem? From owner-chemistry@ccl.net Thu Dec 27 06:50:00 2007 From: "Greg Warren greg++eyesopen.com" To: CCL Subject: CCL: Setting up new (academic) research lab; software purchase questions Message-Id: <-35935-071227064758-26722-qqY0Umpk3TcOlkChLG/bwg:_:server.ccl.net> X-Original-From: Greg Warren Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 Dec 2007 03:50:08 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg#,#eyesopen.com] Dear Dave, There is little point in a vendor extolling the virtues of their software, since you will be making a decision based on science, cost and possibly familiarity. However, I would like to point out that all of the software from OpenEye Scientific Software, Inc. is available for academic research at no cost. The links are http://www.eyesopen.com/ For an on-line application please see http://www.eyesopen.com/forms/academic_license_app.php Sincerely, Greg -- ======================================== Gregory Warren, PhD Senior Applications Scientist OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg[]eyesopen.com ======================================== Dave . ccl_list~~giantscience.com wrote: > Sent to CCL by: "Dave ." [ccl_list,,giantscience.com] > I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening. > > The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite. > > The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable? > > I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly. > > Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger. > > I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily.> > > From owner-chemistry@ccl.net Thu Dec 27 07:24:00 2007 From: "Arthur computationalboy.:.gmail.com" To: CCL Subject: CCL: protein-rna docking Message-Id: <-35936-071227064109-23820-pt7kvjzBHPM8Vocc6i1qPw||server.ccl.net> X-Original-From: "Arthur" Content-Type: multipart/alternative; boundary="----=_NextPart_07122719375570348301713_002" Date: Thu, 27 Dec 2007 19:37:59 +0800 MIME-Version: 1.0 Sent to CCL by: "Arthur"[computationalboy^gmail.com] ------=_NextPart_07122719375570348301713_002 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 SGksQmFsYToNCkp1c3QgdHJ5IDNELURPQ0ssWkRPQ0ssSEFERE9DSyxFU0NIRVIsSEVYLFJPU0VU VEEgRE9DSyxHUkFNTSxET1QuDQpUaGV5IGFyZSBhbGwgZnJlZSBvciBmcmVlIGZvciBhY2FkZW1p YyByZXNlYXJjaGVycywgYW5kIHNvbWUgY2FuIGJlIHVzZWQgcGFyYWxsZWx5LiANCkhvd2V2ZXIs IGl0IG1heSBiZSBkaWZmaWN1bHQgZm9yIHlvdSB0byBtb2RlbCB0aGUgM0Qgc3RydWN0dXJlIG9m 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CCL:G: how to using gaussian03 COSMO solvent model best? Message-Id: <-35937-071227052452-10088-GCUcejhP4Bz0gSj/ofO6Tw^_^server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 27 Dec 2007 11:24:28 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas%%chem.elte.hu] Hi Guanna, My advise is using Opt=GDIIS with solvent model optimizations. If it still fails try increasing the "ALPHA" scaling factor for the definition of the cavity ( http://www.gaussian.com/g_ur/k_scrf.htm ). Then a single point energy calculation can be used with the original settings. Keep in mind that you should calculate the energies for all structures on the study the same way. Good luck! Ödön On Thu, 2007-12-27 at 14:09 +0800, Guanna Li gnli-$-dicp.ac.cn wrote: > Sent to CCL by: "Guanna Li" [gnli()dicp.ac.cn] > Dear all, > I using cosmo model to calculate system in water, but the opt step energy always oscillate, could anyone give me some advice? > Thank you very much! > > -------------- > 2007-12-27 > Best wishes > > Guanna Li > Email: gnli%a%dicp.ac.cn> > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Thu Dec 27 09:26:01 2007 From: "immanuel feng feng.immanuel,,gmail.com" To: CCL Subject: CCL:G: =?GB2312?B?UmU6IENDTDpHOiBDQ0yjukdhdXNzaWFuIHNvbHZlbnQgbW9kZWw=?= Message-Id: <-35938-071227033916-1971-uxeua0kMYjpkk31niygfAQ*|*server.ccl.net> X-Original-From: "immanuel feng" Content-Type: multipart/alternative; boundary="----=_Part_11871_19350285.1198741140035" Date: Thu, 27 Dec 2007 15:39:00 +0800 MIME-Version: 1.0 Sent to CCL by: "immanuel feng" [feng.immanuel]^[gmail.com] ------=_Part_11871_19350285.1198741140035 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline There is a keyword" solvent" for different solvent, like solvent=h2o or solvent =ch3ch2oh, refer to page 157 of 03 manual Best, Immanuel 2007/12/25, Guanna Li gnli##dicp.ac.cn : > > > Sent to CCL by: "Guanna Li" [gnli-$-dicp.ac.cn] > Dear all, > Now I want to simulate solvent system by Gaussian03, but the solvent > is alcohol not water, which parameter I have to set in the input file ? > could anyone can give me an example ? > Thank you very much! > > -------------- > 2007-12-25 > Best wishes > > Guanna Li > > State Key Laboratory of Catalysis > Dalian Institute of Chemical Physics > Chinese Academy of Sciences > > 457 Zhongshan Road, Dalian 116023, China > > Tel: +86-411-8437 9302 > Email: gnli~!~dicp.ac.cn> > > ------=_Part_11871_19350285.1198741140035 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
There is a keyword" solvent" for different solvent, like solvent=h2o or solvent =ch3ch2oh, refer to page 157 of 03 manual
 
Best,
 
Immanuel

 
2007/12/25, Guanna Li gnli##dicp.ac.cn <owner-chemistry*o*ccl.net>:

Sent to CCL by: "Guanna Li" [gnli-$-dicp.ac.cn]
  Dear all,
    Now I want to simulate solvent system by Gaussian03, but the solvent is alcohol not water, which parameter I have to set in the input file ?
    could anyone can give me an example ?
    Thank you very much!

--------------
2007-12-25
Best wishes

Guanna Li

State Key Laboratory of Catalysis
Dalian Institute of Chemical Physics
Chinese Academy of Sciences

457 Zhongshan Road, Dalian 116023, China

Tel: +86-411-8437 9302
Email: gnli~!~dicp.ac.cn



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------=_Part_11871_19350285.1198741140035-- From owner-chemistry@ccl.net Thu Dec 27 16:56:01 2007 From: "spitaleri.andrea---hsr.it" To: CCL Subject: CCL: protein-rna docking Message-Id: <-35939-071227102112-32091-er21KhxPt4ByONE83aa9bw(~)server.ccl.net> X-Original-From: Content-Language: en Content-Type: multipart/mixed; boundary="--7739748115742c09" Date: Thu, 27 Dec 2007 15:14:14 +0100 MIME-Version: 1.0 Sent to CCL by: [spitaleri.andrea|a|hsr.it] This is a multi-part message in MIME format. ----7739748115742c09 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi there, have look to HADDOCK program: www.nmr.chem.uu.nl/haddock/ Regards, andrea Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) Tel: 0039-0226433497/4922 Fax: 0039-0226434153 ----- Original Message ----- > From: "Bala Subramanian bala()igib.res.in" Date: Thursday, December 27, 2007 11:26 am Subject: CCL: protein-rna docking > > Sent to CCL by: "Bala Subramanian" [bala.:.igib.res.in] > Dear CCLers, > > Someone please suggest me a software especially a freeware highly > suited for protein-RNA docking. > > Thanks in advance, > Bala > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the (a) sign. You > can also> Conferences: http://server.ccl.net/chemistr > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > RTFI: http://www.ccl.net/chemistr > > > ----7739748115742c09 Content-Type: text/x-vcard; name="spitaleri.andrea.vcf"; charset="iso-8859-1" Content-Disposition: attachment; filename="spitaleri.andrea.vcf" Content-Description: Card for Content-Transfer-Encoding: quoted-printable begin=3Avcard n=3ASpitaleri=3BAndrea fn=3AAndrea Spitaleri tel=3Bfax=3A+390226434153 org=3ADibit Scientific Insititute=3BBioMolecular Structure adr=3A=3B=3Bvia Olgettina 58=3BMilan=3B=3B24132=3BItaly version=3A2=2E1 email=3Binternet=3Aspitaleri=2Eandrea=40hsr=2Eit title=3ADr end=3Avcard ----7739748115742c09--