From owner-chemistry@ccl.net Fri Jan 1 09:06:01 2010 From: "John Simmie john.simmie(!)nuigalway.ie" To: CCL Subject: CCL:G: RegRaf memory problem Message-Id: <-40982-100101090448-29884-n+xf6Lev23prQXSOGi/Z2A * server.ccl.net> X-Original-From: "John Simmie" Date: Fri, 1 Jan 2010 09:04:44 -0500 Sent to CCL by: "John Simmie" [john.simmie_._nuigalway.ie] In a single-point calculation of a nine-heavy atoms species (Gaussian-09) #N Geom=AllCheck Guess=TCheck SCRF=Check QCISD(T)/6-311++G(2df,p) I am told that Not enough memory in RegRaf. Error termination via Lnk1e in /ichec/packages/gaussian/09a02/l508.exe at Thu Dec 31 18:53:17 2009. Job cpu time: 0 days 0 hours 2 minutes 15.5 seconds. File lengths (MBytes): RWF= 20073 Int= 0 D2E= 0 Chk= 7 Scr= 1 but I am using the maximum amount already %mem=48GB %nproc=8 Suggestions please? John Simmie::NUI Galway::Ireland john.simmie%nuigalway.ie From owner-chemistry@ccl.net Fri Jan 1 09:41:01 2010 From: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes jafernandes^_^ua.pt" To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40983-091231090323-32571-NjblqZL+k7zjQU36+ZF/sA[]server.ccl.net> X-Original-From: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1;format="flowed" Date: Thu, 31 Dec 2009 12:03:03 +0000 MIME-Version: 1.0 Sent to CCL by: "=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes" [jafernandes/./ua.pt] Hello Sanghwa I think most cristalline structures have planar NHCO groups too. I can't be completely sure, because I can't access the cambridge database where I am now (at home). I've already optimized amide groups and it resulted in a planar structure. I don't remember at which level, but I didn't use constraints. So, for having a realistic structure the NHCO group must be planar. Try to use HF/6-31G** or RB3LYP/6-31G**. Happy new year Jose Em Wed, 30 Dec 2009 22:11:42 -0500 "Sanghwa Han hansh,kangwon.ac.kr" escreveu: > > Sent to CCL by: "Sanghwa Han" [hansh~~kangwon.ac.kr] > Dear colleagues, > > In Biochemistry textbooks, an amide bond (NH-CO) in a >peptide is explained to be planar. > But when I optimize a capped amino acid (e.g. ACE-Amino >Acid-NME) using HF/6-31G* for RESP charge derivation, the >dihedral HN-CO often deviates from planarity by as much >as 20 degrees. > Do I need to constrain the HN-CO to 0 degrees to obtain >an optimized structure that is used in a RESP charge >derivation? > Does anybody know if the amide group can be non-planar >in experimentally determined structures? > > Thanks. > > Sanghwa Han > > > > -= This is automatically added to each message by the >mailing script =- > To recover the email address of the author of the >message, please change > the strange characters on the top line to the !A! sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > José Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 From owner-chemistry@ccl.net Fri Jan 1 15:25:01 2010 From: "Frank Neese neese_._thch.uni-bonn.de" To: CCL Subject: CCL:G: RegRaf memory problem Message-Id: <-40984-100101152344-11210-tcVvgveEkyQWMrPBBYS+vQ||server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Fri, 01 Jan 2010 20:26:16 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese .. thch.uni-bonn.de] Dear John Simmie, i assume that this calculation could be well done with ORCA (available for free at: http://www.thch.uni-bonn.de/tc/orca/). best regards, Frank Neese > Sent to CCL by: "John Simmie" [john.simmie_._nuigalway.ie] > In a single-point calculation of a nine-heavy atoms species (Gaussian-09) > #N Geom=AllCheck Guess=TCheck SCRF=Check QCISD(T)/6-311++G(2df,p) > I am told that > > Not enough memory in RegRaf. > Error termination via Lnk1e in /ichec/packages/gaussian/09a02/l508.exe at Thu Dec 31 18:53:17 2009. > Job cpu time: 0 days 0 hours 2 minutes 15.5 seconds. > File lengths (MBytes): RWF= 20073 Int= 0 D2E= 0 Chk= 7 Scr= 1 > > but I am using the maximum amount already > %mem=48GB > %nproc=8 > > Suggestions please? > -- ----------------------------------------------------------------- Prof. Dr. Frank Neese Chair of Theoretical Chemistry Department of Chemistry University of Bonn Wegelerstr. 12 D-53115 Bonn Germany E-Mail: neese[*]thch.uni-bonn.de URL: http://www.thch.uni-bonn.de/tc/ Telephone: +49-228-732351 -----------------------------------------------------------------