From owner-nwchem-users@emsl.pnl.gov Tue Mar 20 11:02:42 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 l2KI2fXh014262 for ; Tue, 20 Mar 2007 11:02:42 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l2KI2fXq014261 for nwchem-users-outgoing-0915; Tue, 20 Mar 2007 11:02:41 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: Throttle X-Ironport-SBRS: 1.3 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: Ao8CALO+/0VCxGT3cWdsb2JhbACPMQ4HIw X-IronPort-AV: i="4.14,305,1170662400"; d="scan'208"; a="24160245:sNHT32873568" DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; b=GIjrYs2sUpaPD1SWxA1RWFGupy7n4H3V/XsELS/8tORV7p9fuJQpSL5k1bJuDV0s8Trt8kOAIDjdhPd2YgP4jK57txmit4QEKmKj2W7WDQDdMw3lQIh/SNmfJdnsWG4HtzitiYozeivp04jBaQ1xL+k9ZQ7ObJwQZjTVW7Rqzr4=; X-YMail-OSG: F_c_AB8VM1kTTd7jis6ef74NB6axxip9cDVi_gOX8x.e9J9WGYFHEuPlXXVfv6Qj1VL8ICJ16C3L.KVsNwjs.WSFCPgqZplJTQJX5tnPdyvKX0LAvfhCfoZKp5TLiRnq Date: Tue, 20 Mar 2007 11:02:35 -0700 (PDT) From: Francesco Pietra Subject: Re: [NWCHEM] Partial atomic charges To: "Lins, Roberto D" , users nwchem In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Message-ID: <687759.85415.qm@web58912.mail.re1.yahoo.com> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Hi Roberto: Thanks. Do you have at hand a reference to breaking into fragments for MD purposes a molecule that has no repeating units? I am always brought to biopolymers or at most modified proteins. The molecules I want to study display properties that depend from the whole, with subtle chirality axes. It may well be that I did not grasp the substance of MD, though I find difficult where to break the molecule. Unless it is a formal breaking in some way, while there is behind a trait-de-union as if the molecule were intact. Apologize for such naive expressions. Thanks francesco --- "Lins, Roberto D" wrote: > Hi Francesco, > > Yes, you can use NWChem directly to compute the RESP > charges. > In the ESP module you can break up your large > molecule into > several fragments (I won't discuss the benefits of > having > smaller charge groups). For example if you'd like to > set > that atoms 1 to 15 of your molecule to have a net > charge of > 0.0 and 16 to 25 of -1.0 you could type in these > couple of > lines within the ESP deck: > > constrain 0.0 1 through 15 > constrain -1.0 16 through 25 > > From my experience, you should have at least 5-6 > atoms per > charge group when doing the RESP-fitting. Too small > charge > groups will lead to charges that will render your > molecule > with unacceptably large deviations from the > QM-calculated > dipole moment. > > Hope it helps, > > Roberto > > P.S.: The newer AMBER force fields (96 and newer) > uses > RESP-based charges instead of CHELPG. > > ---------------------------------------- > Roberto Lins, Research Scientist > Computational Biology and Bioinformatics > Pacific Northwest National Laboratory > P.O. Box 999, M/S:K7-90, ISB2/507 > Richland, WA 99352 USA > Phone: +1 (509) 375-2755 > Fax: +1 (509) 372-4720 > E-mail: roberto.lins@pnl.gov > ---------------------------------------- > > > On 3/20/07 10:00 AM, "Francesco Pietra" > wrote: > > > 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 > ____________________________________________________________________________________ Don't pick lemons. See all the new 2007 cars at Yahoo! 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