From qibvigap@lg.ehu.es Fri Feb 14 07:23:06 1997 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id GAA13378; Fri, 14 Feb 1997 06:56:47 -0500 (EST) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA04150; Fri, 14 Feb 97 12:55:28 GMT Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA12626; Fri, 14 Feb 1997 13:02:35 GMT Date: Fri, 14 Feb 1997 13:02:34 +0000 (WET) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: MK, CHELP, and CHELPG in G94: RMS, RRMS Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I think several days ago there was a message in this list dealing with the meaning of the RMS when fitting charges to electrostatic potentials. I didn't see answers. That's the reason I post another question related to it. I understand that RMS and RRMS measure the agreement of the fitting procedure. But, are they internal to each method (MK, CHELP or CHELPG) or can they be compared? I mean, if I calculate ESP fitted charges with the three methods mentioned, can I assume that the best fit is the one with the lowest RMS? I would also welcome some expalnation about what the difference is among these three procedures, since I don't have access to the original papers in J. Comp. Chem. Thanks a lot for your help Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From schiffer@h1tw0036.hoechst.com Fri Feb 14 09:23:13 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id IAA13862; Fri, 14 Feb 1997 08:40:46 -0500 (EST) Received: by backup.hoechst.com (SMI-8.6/SMI-SVR4) id OAA16520; Fri, 14 Feb 1997 14:38:46 +0100 Received: from unknown(134.81.79.248) by backup via smap (V1.3) id sma016503; Fri Feb 14 14:38:08 1997 Received: from 134.81.76.36 by fra28.hiserv.de with SMTP (Microsoft Exchange Internet Mail Connector Version 4.0.994.63) id DVQXMAXF; Fri, 14 Feb 1997 14:43:08 +0100 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA24867; Fri, 14 Feb 1997 14:38:16 +0100 Message-ID: <33046AC8.41C6@h1tw0036.hoechst.com> Date: Fri, 14 Feb 1997 14:38:16 +0100 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List Subject: Singlet Oxygen with UHF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, can anybody please tell me how to compute the lowest singlet state of the oxygen molecule (singlet-Delta_gerade, 0.984 eV above the triplet-Sigma_gerade ground state) with the UHF method ? I would greatly appreciate any help. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com From underhil@me2.rmc.ca Fri Feb 14 09:27:06 1997 Received: from sv2.rmc.ca for underhil@me2.rmc.ca by www.ccl.net (8.8.3/950822.1) id JAA13959; Fri, 14 Feb 1997 09:03:35 -0500 (EST) Message-Id: <199702141403.JAA13959@www.ccl.net> Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP (1.37.109.15/16.2) id AA175499113; Fri, 14 Feb 1997 09:05:13 -0500 Date: Fri, 14 Feb 1997 09:05:13 -0500 X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: underhil@me2.rmc.ca (Ross Underhill) Subject: Simulating the effect of liquids and gases on films I'm interested in examining the structure and self-assembly of multilayer films using molecular mechanics. Unfortunately, the structure of these films - often their existance - depends on the presence of a liquid or gas medium which helps to hold the film onto the substrate even if it is not incorporated into the film. A trivial example would be Langmuir-Blodget films of stearic acid on aluminum. In air a multilayer film is stable for months. When the sample is introduced to vacuum, all but the layer directly attached to the aluminum rapidly sublimate from the surface. To study the self assembly of a monolayer film at the solid-liquid interface one properly needs to incorporate the liquid itself. However, the inclusion of the liquid molecules rapidly drives the computational effort through the roof. It seems to me that it ought to be possible to simulate the effect of the liquid by a viscous damping term, possibly only applied to atoms on the solvent accessible surface of a molecule. Has anyone looked at handling this problem in this kind of way or have any comments to make on whether they think this kind of approach would be feasible? Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario K7K 5L0 (613) 541-6000 X6175 From qibvigap@lg.ehu.es Fri Feb 14 11:23:15 1997 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id KAA15100; Fri, 14 Feb 1997 10:52:01 -0500 (EST) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA09329; Fri, 14 Feb 97 16:50:30 GMT Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA23259; Fri, 14 Feb 1997 16:30:04 GMT Date: Fri, 14 Feb 1997 16:30:03 +0000 (WET) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: MK, CHELP, and CHELPG in G94 (2): Dipole Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Another question related to the previous one. Does it make any sense to constrain the ESP calculated charges to fit the dipole moment for CHARGED molecules? I am not sure about it, since the dipole moment value depends on the choice of origin for non-neutral molecules. Thanks a lot for your help Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From hinsen@lmspc2.ibs.fr Fri Feb 14 11:47:41 1997 Received: from ibs.ibs.fr for hinsen@lmspc2.ibs.fr by www.ccl.net (8.8.3/950822.1) id KAA15143; Fri, 14 Feb 1997 10:58:21 -0500 (EST) Received: from lmspc2.ibs.fr (hinsen@lmspc2.ibs.fr [192.134.36.142]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id QAA25138; Fri, 14 Feb 1997 16:59:27 +0100 Received: (from hinsen@localhost) by lmspc2.ibs.fr (8.8.5/8.8.5) id QAA12893; Fri, 14 Feb 1997 16:58:21 +0100 Date: Fri, 14 Feb 1997 16:58:21 +0100 Message-Id: <199702141558.QAA12893@lmspc2.ibs.fr> From: Konrad Hinsen To: chemistry@www.ccl.net Subject: Improper dihedrals in the Amber potential I am using the Amber94 potential (http://www.amber.ucsf.edu/amber/ff94.html) in my own code, and I noticed one problem to which I could not find a solution in the description of the force field file or in the original publication on this force field: the correct interpretation of the improper dihedral parameters. An improper dihedral is defined by four atoms, a central one and three other atoms bound to it. Each of the three bonds can be used to define the intersection line of the two planes, and in the absence of special symmetry the three angles will be different. So which one should I take? The description file doesn't say anything on the interpretation of the four atom types in an improper dihedral entry, but from looking at the examples it is clear that the third atom must be the central one. By analogy with proper dihedrals one may further assume that the bond between the second and third atom defines the intersection line. That settles the question except for two cases: when the first two atom types are equal (as in CA-CA-C -OH) or undefined (as in X -X -C -O), there are two possible interpretations, leading to different potential energies. I'd be interested to know whether there is an "official" interpretation, or if not, what other people have decided to do about it. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From qiang@euch4e.chem.emory.edu Fri Feb 14 13:23:10 1997 Received: from euch4e.chem.emory.edu for qiang@euch4e.chem.emory.edu by www.ccl.net (8.8.3/950822.1) id NAA16247; Fri, 14 Feb 1997 13:03:16 -0500 (EST) From: Received: from localhost by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA21056; Fri, 14 Feb 1997 13:03:11 -0500 Date: Fri, 14 Feb 1997 13:03:10 -0500 (EST) To: "Dr. Heinz Schiffer" Cc: Computational Chemistry List Subject: Re: CCL:Singlet Oxygen with UHF In-Reply-To: <33046AC8.41C6@h1tw0036.hoechst.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 14 Feb 1997, Dr. Heinz Schiffer wrote: > Hi, > can anybody please tell me how to compute the lowest singlet state > of the oxygen molecule (singlet-Delta_gerade, 0.984 eV above the > triplet-Sigma_gerade ground state) with the UHF method ? Since it's multi-configuration in nature (2-degenerate determinants), u cann't do it with UHF if u use real orbitals. U have to use CASSCF instead. However, if u write down the wave function in terms of complex orbitals, u can do it. Try that option with Gaussian (I've never done it myself though) Good luck. > I would greatly appreciate any help. > Ciao, > Heinz > -- > Dr. Heinz Schiffer Phone ++49-69-305-2330 > Hoechst CR&T Fax ++49-69-305-81162 > Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com > 65926 Frankfurt am Main schiffer@msmwia.hoechst.com > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: schiffer@h1tw0036.hoechst.com > -- Original Sender From: Address: schiffer@h1tw0036.hoechst.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > ______________________________________________________________ Qiang Cui Dept. of Chem. Emory Univ. 508 Webster Dr. Apt.#2 Atlanta, GA 30322. Decatur, GA 30033. (404)-727-2381 (404)-636-6149 http://tswww.cc.emory.edu/~qcui ______________________________________________________________ From JeffAyres@worldnet.att.net Fri Feb 14 13:29:07 1997 Received: from mtigwc02.worldnet.att.net for JeffAyres@worldnet.att.net by www.ccl.net (8.8.3/950822.1) id NAA16268; Fri, 14 Feb 1997 13:06:32 -0500 (EST) Received: from LOCALNAME ([207.147.168.112]) by mtigwc02.worldnet.att.net (post.office MTA v2.0 0613 ) with SMTP id AAA29788; Fri, 14 Feb 1997 18:06:01 +0000 Message-ID: <3304B866.2216@worldnet.att.net> Date: Fri, 14 Feb 1997 11:09:26 -0800 From: "Jeffrey J. Ayres" Organization: independent X-Mailer: Mozilla 3.01Gold (Win16; I) MIME-Version: 1.0 To: bruce@nmr.utmb.edu CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:Helical Axes References: <9702131424.ZM11527@cosy.utmb.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Bruce A. Luxon wrote: > > Fellow Netters & Nettees, > > Does anyone have a routine, a reference or a thought on how to > construct the central axis of a DNA or RNA double helix - > especially for A-DNA (B is reasonably well-behaved)? I've > searched quite a bit and tried several approaches but so far > nothing I've dug up is satisfactory for the relatively short > segments I'm looking at (e.g. 10-mers or less). Long segments can > be done several ways but the short ones are difficult. Hmmm... > > All info gratefully received. > > Bruce Luxon > > -- > > *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* > * Bruce A. Luxon, Ph.D * > * Assistant Professor * > * Sealy Center for Structural Biology U > * Dept. of Human Biological Chemistry & Genetics T > * University of Texas Medical Branch M > * Galveston, TX 77555-1157 B > * * > * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * > * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * > *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: bruce@cosy.utmb.edu > -- Original Sender From: Address: bruce@cosy.utmb.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html Subject: Re: CCL:Helical Axes Date: Fri, 14 Feb 1997 11:00:41 -0800 From: "Jeffrey J. Ayres" Organization: independent To: bruce@nmr.utmb.edu References: 1 Bruce A. Luxon wrote: > > Fellow Netters & Nettees, > > Does anyone have a routine, a reference or a thought on how to > construct the central axis of a DNA or RNA double helix - > especially for A-DNA (B is reasonably well-behaved)? I've > searched quite a bit and tried several approaches but so far > nothing I've dug up is satisfactory for the relatively short > segments I'm looking at (e.g. 10-mers or less). Long segments can > be done several ways but the short ones are difficult. Hmmm... > > All info gratefully received. > > Bruce Luxon > > -- > > *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* > * Bruce A. Luxon, Ph.D * > * Assistant Professor * > * Sealy Center for Structural Biology U > * Dept. of Human Biological Chemistry & Genetics T > * University of Texas Medical Branch M > * Galveston, TX 77555-1157 B > * * > * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * > * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * > *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: bruce@cosy.utmb.edu > -- Original Sender From: Address: bruce@cosy.utmb.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html Attn: B Luxon, Your question is the same as one faced during my thesis at Cal. State University in Hayward. A program developed by Richard E. Dickerson at UCLA called NEWHELIX93.TEX may provide some answers. Unforntunately I do not have first hand experience with the program, for two reasons. First after acquiring the program from UCLA I was unable to get the program to run. Second communications with Dr. Dickerson were impossible even after calls placed by the chair of the department. I have a copy of the program on account at LLNL, since I'm not familiar with the copyright laws concerning the program it is probably safer if you acquired the program from the Protein Data Base http://www.pdb.bnl.nih.gov. The program is stored in the archives. I do not know the exact address of the archive file, as a freind helped me to access the file at PDB. The program is supposedly available by contacting Dr. Dickerson at UCLA (RED@UCLAUE), however he never answered requests via email I was unable to locate the program. Dr. Dickerson's programs do various calculations from alpha to zeta plus tilt, roll, twist... on short segments. Since several of these depend on the position the helical axis his program most likely includes a method for calculating the helical axis for 10 mers. An article which maybe of some help is DiGabriele A. D., Sanderson M. R., and Steitz, T.A. "Crystal Lattice Packing is Important in Determining the Bend of a DNA Dodecamer Containing an Adenine Tract" Proc. Natl. Acad. Sci. Vol 86 pp 1816-1820 Another article which may be of some use McCall, M., Brown, T., and Kennard, O. "The Crystal Structure of d(GGGGCCCC) a model for Poly(dG)-poly(dC)." J. Mol. Biol. 1985 183, 385-396. Both of the above articles cite Dr. Dickerson's programs however they do not describe Dr. Dickerson's method of calculating the helix axis. From ross@cgl.ucsf.EDU Fri Feb 14 15:23:19 1997 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.8.3/950822.1) id OAA16948; Fri, 14 Feb 1997 14:47:45 -0500 (EST) From: Received: (from ross@localhost) by socrates.ucsf.EDU (8.8.5/GSC4.26) id LAA11194; Fri, 14 Feb 1997 11:47:43 -0800 (PST) Date: Fri, 14 Feb 1997 11:47:43 -0800 (PST) Message-Id: <199702141947.LAA11194@socrates.ucsf.EDU> To: chemistry@www.ccl.net Subject: Improper dihedrals in the Amber potential Cc: hinsen@ibs.ibs.fr I am using the Amber94 potential (http://www.amber.ucsf.edu/amber/ff94.html) ... An improper dihedral is defined by four atoms, a central one and three other atoms bound to it. Each of the three bonds can be used to define the intersection line of the two planes, and in the absence of special symmetry the three angles will be different. So which one should I take? This info is in the documentation describing the format of the file involved, (http://www.amber.ucsf.edu/amber/doc/prep.doc): > where the central atom (K) is the third atom in the improper > and the order of the other three is determined alphabetically > by atom type and if types are the same by atom number. It also bears repetition in the page on deriving new parameters, http://www.amber.ucsf.edu/amber/newparams.html, which perhaps is the most detailed explanation of the force field terms. Note that the rule given is arbitrary and is mainly intended to provide uniformity; no general 'right answer' exists in the physical sense. I'd be interested to know whether there is an "official" interpretation, This is it.. Bill Ross, UCSF From korkin@qtp.ufl.edu Fri Feb 14 17:23:13 1997 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id RAA17567; Fri, 14 Feb 1997 17:05:28 -0500 (EST) Received: from red by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id RAA00982; Fri, 14 Feb 1997 17:01:05 -0500 Date: Fri, 14 Feb 1997 17:01:05 -0500 (EST) From: Anatoli Korkin Reply-To: Anatoli Korkin Subject: Re: CCL:G:Singlet Oxygen with UHF To: chemistry@www.ccl.net Cc: qiang@euch4e.chem.emory.edu, bartlett@qtp.ufl.edu, balkova@nadn.navy.mil, perera@qtp.ufl.edu, BOYD@AC.DAL.CA, pvrs@organik.uni-erlangen.de Message-ID: MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: bCB5A9Bg8IkGDXvJaHeR4w== X-Mailer: dtmail 1.2.0 CDE Version 1.2_14 SunOS 5.6 sun4d sparc > > > Hi, > > can anybody please tell me how to compute the lowest singlet state > > of the oxygen molecule (singlet-Delta_gerade, 0.984 eV above the > > triplet-Sigma_gerade ground state) with the UHF method ? > The ACES II program has two-determinat coupled-cluster method. You will get in a consistent way both right energies and wave functions for the lowest triplet and both singlet states. The type of the reference function is not important if you do not care about a spin contamination. Technically you can use the orbitals from ROHF or UHF solution for the triplet oxygen. For theory look: A. Balkova, R.J. Bartlett, J. Chem.Phys. Lett., 1992, 193, 364, and references therein. For some recent examples: A.A. Korkin, A. Balkova, R.J. Bartlett, R.J. Boyd, P.v.R. Schleyer, J. Phys. Chem. 1996, 100, 5702. To get the ACES program contact Prof. Rodney J. Bartlett (bartlett@qtp.ufl.edu) or Dr. Ajith Perera (perera@qtp. ufl.edu). Anatoli Korkin ------------- End Forwarded Message -------------