From owner-nwchem-users@emsl.pnl.gov Tue Mar 20 10:33:19 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l2KHXIfV012187 for ; Tue, 20 Mar 2007 10:33:19 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l2KHXI2W012186 for nwchem-users-outgoing-0915; Tue, 20 Mar 2007 10:33:18 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Possible-Spoof: True X-IronPort-AV: i="4.14,305,1170662400"; d="scan'208"; a="15758698:sNHT42541989" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: RE: [NWCHEM] Partial atomic charges Date: Tue, 20 Mar 2007 10:33:11 -0700 Message-ID: In-Reply-To: <326510.24826.qm@web58913.mail.re1.yahoo.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] Partial atomic charges thread-index: AcdrEsVgIGhsLCBgRuK8QVUJYGUPaAAArGBA References: <326510.24826.qm@web58913.mail.re1.yahoo.com> From: "Straatsma, T P" To: "Francesco Pietra" , "users nwchem" X-OriginalArrivalTime: 20 Mar 2007 17:33:16.0364 (UTC) FILETIME=[D7E060C0:01C76B15] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id l2KHXHDR012183 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk For AMBER the procedure to get partial atomic charges if HF/6-31g* followed by RESP fitting. Two-stage RESP is available in NWChem and avoids the CHELPG limitation you mention. For effective MD you should break your molecule into segments. Dr. T.P.Straatsma, Associate Division Director Computational Biology and Bioinformatics Pacific Northwest National Laboratory P.O.Box 999, MSIN K7-90 Richland, WA 99352 Tel. (509) 375-2802 Adm. (509) 372-4623 Fax (509) 372-4720 -----Original Message----- From: owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Francesco Pietra Sent: Tuesday, March 20, 2007 10:01 To: users nwchem Subject: [NWCHEM] Partial atomic charges I am setting up classical (Amber FF) simulations on natural products, where the "fragment" is the final "sequence" approaching the limit of 99 atoms. Difficult, if possible at all, to cut the molecule into fragments. In learning about the method used to define the partial charges, I came across a discouraging (for my type of job) description: "One of the weak points of CHELPG (and other approaches based on fitting the MEP) is the treatment of larger systems, in which some of the innermost atoms are located far away from the points at which the MEP is evaluated. In such a situation, variations of the innermost atomic charges will not lead to significant changes of the MEP potential outside of the molecule and fitting of these atomic charges will therefore not result in meaningful results. It should also be remembered that atomic charges can depend strongly on the conformation of the molecule. Representative atomic charges for flexible molecules should therefore be derived as average values over several conformers. Using ethanol as an example, the charge parameters derived for the Cs symmetric conformer A and the C1 symmetric conformer B vary, in part, by almost 30%. The variation is, however, rather different for different parts of the system(http://www.cup.uni-muenchen.de/oc/zipse/compchem/pop/chelpg.html) " At any event, for a given novel fragment (geometry optimized with MM global space search), should the RHF-ESP calculation be preceded by a RHF-Geometry calculation? I rely on Ecce for the ESP calculation, though it seems to me that the question I posed is valid also for using NWChem directly. Thanks francesco pietra ________________________________________________________________________ ____________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097