From chemistry-request@server.ccl.net Tue Mar 19 03:53:55 2002 Received: from relay3.softcomca.com ([168.144.1.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2J8rtp32348 for ; Tue, 19 Mar 2002 03:53:55 -0500 Received: from m2w085.softcomca.com ([168.144.108.85]) by relay3.softcomca.com with Microsoft SMTPSVC(5.0.2195.4905); Tue, 19 Mar 2002 03:53:56 -0500 X-Originating-IP: 202.185.72.119 X-URL: http://www.mail2web.com/ Subject: histidine state Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Tue, 19 Mar 2002 03:53:49 -0500 To: "chemistry@ccl.net" Reply-To: nepenthes@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-ID: X-OriginalArrivalTime: 19 Mar 2002 08:53:56.0954 (UTC) FILETIME=[9AB67BA0:01C1CF23] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id g2J8rtp32349 Dear CCLers, I have some questions regarding the state of histidine in proteins. I know that histidine can exist as with a weak positive charge in pH7, but also it might depend on the surrounding environment and neighbours. Is there a way that I can find out how the neighbouring residues can affect histidine? If I take my protein to be at pH7, can I assume that histidine will have a positive charge? Both NE1 and ND1 will have hydrogens then. From what I've read, either one can be protonated or both will be. Also, from the structures that I've found, the double bonds exist in the side chain between CG=CD2 and ND1=CE1. Would the double bond exist for NE1=CE1 instead ? I would like to get more information about this as I'm not sure how to treat the histidine residues in my protein. Thank you for your time. Regards, Rowyna -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Tue Mar 19 04:11:15 2002 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2J9BEp00460 for ; Tue, 19 Mar 2002 04:11:14 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se; Tue, 19 Mar 2002 10:09:21 +0100 Received: from werkman.bmc.uu.se (werkman.bmc.uu.se [130.238.37.169]) by XRAY.bmc.uu.se (8.11.6/8.8.7) with ESMTP id g2J9DE131445; Tue, 19 Mar 2002 10:13:14 +0100 Date: Tue, 19 Mar 2002 14:02:01 +0100 (CET) From: David van der Spoel X-X-Sender: To: "nepenthes@vplaces.net" cc: "chemistry@ccl.net" Subject: Re: CCL:histidine state In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Mar 2002, nepenthes@vplaces.net wrote: >Dear CCLers, > >I have some questions regarding the state of histidine in proteins. I >know that histidine can exist as with a weak positive charge in pH7, but >also it might depend on the surrounding environment and neighbours. Is >there a way that I can find out how the neighbouring residues can affect >histidine? If I take my protein to be at pH7, can I assume that histidine >will have a positive charge? Both NE1 and ND1 will have hydrogens then. >From what I've read, either one can be protonated or both will be. In a protein you can check the hydrogen bonding network. In solution 90% is NE1 and 10% ND1 (at pH7) Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Tue Mar 19 07:03:13 2002 Received: from mhub2.bbsrc.ac.uk ([149.155.202.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JC3Cp03024 for ; Tue, 19 Mar 2002 07:03:13 -0500 Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.31 #1) id 16nIFf-0003l1-04 for chemistry@ccl.net; Tue, 19 Mar 2002 11:58:03 +0000 Received: from bits-exch1.bits.bbsrc.ac.uk ([149.155.108.13]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id G7TL0N3S; Tue, 19 Mar 2002 11:58:31 -0000 Received: by bits-exch1.bits.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id ; Tue, 19 Mar 2002 11:58:31 -0000 Message-ID: <41773CEF2B8FD411920200508BDCDC12BE13B6@bits-exch1.bits.bbsrc.ac.uk> From: "michael hanlon (BITS)" To: "'chemistry@ccl.net'" Subject: GRAMM - opinions? Date: Tue, 19 Mar 2002 11:58:30 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-ECS-MailScanner-BBSRC: Found to be clean Dear List I'd be grateful for opinions on the docking program GRAMM Mike Dr. Mike Hanlon Molecular Biology Computing Support BBSRC Bioscience IT Services West Common Harpenden Herts AL5 2JE Phone: 01582 714904 Email: molbio.support@bbsrc.ac.uk Web: http://www.molbiol.bbsrc.ac.uk From chemistry-request@server.ccl.net Tue Mar 19 07:56:18 2002 Received: from igcar.ernet.in ([202.141.82.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JCu9p04087 for ; Tue, 19 Mar 2002 07:56:17 -0500 Received: from igcar.ernet.in (localhost.localdomain [127.0.0.1]) by igcar.ernet.in (8.9.3/8.9.3) with ESMTP id SAA01840 for ; Tue, 19 Mar 2002 18:31:21 +0530 Received: from [203.199.205.25] ([203.199.205.25]) by igcar.ernet.in (8.9.3/8.9.3) with SMTP id SAA01832 for ; Tue, 19 Mar 2002 18:31:16 +0530 Received: from [10.1.1.100] by [203.199.205.25] via smtpd (for igcar.ernet.in [202.141.82.2]) with SMTP; 19 Mar 2002 12:56:48 UT Received: (from Urcl@localhost) by igcmail.igcar.ernet.in (8.9.3+Sun/8.9.1) id SAA19246 for chemistry@ccl.net; Tue, 19 Mar 2002 18:27:41 -0500 (GMT) X-Authentication-Warning: igcmail.igcar.ernet.in: Urcl set sender to vvenkat@igcar.ernet.in using -f >Received: from localhost by rcl.igcar.ernet.in (8.9.1b+Sun/SMI-SVR4) id SAA05837; Tue, 19 Mar 2002 18:26:01 -0500 (GMT) Date: Tue, 19 Mar 2002 18:26:01 -0500 (GMT) From: "V.Venkatesan" X-Sender: vvenkat@rcl To: chemistry@ccl.net Subject: BOND ORDER VS GAUSSIAN 94W In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HELLO WHAT IS THE FORMAT OF INPUT I HAVE TO GIVE TO CALCULATE BOND ORDER OF MOLECULE THROUGH NBO IN GAUSSIAN 94W? ANYBODY HELP FOR THESE PURPOSE ******************************************************************************* NAME:V.VENKATESAN ADDRESS:MATERIALS CHEMISTRY DIVISION RADIOCHEMICAL LABORATORY INDIRA GANDHI CENTRE FOR ATOMIC RESEACH KALPAKKAM-603102 TAMILNADU INDIA E-MAIL ID:vvenkat@igcar.ernet.in ******************************************************************************* From chemistry-request@server.ccl.net Tue Mar 19 06:46:12 2002 Received: from garoe.ccti.ull.es ([193.145.120.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JBkBp02807 for ; Tue, 19 Mar 2002 06:46:11 -0500 Received: from miguel ([193.145.116.85]) by garoe.ccti.ull.es (8.11.2/8.11.1) with SMTP id g2JBk4J10902 for ; Tue, 19 Mar 2002 11:46:04 GMT Message-ID: <009501c1cf3d$8b9a8980$557491c1@biologia.ull.es> From: "=?iso-8859-1?Q?Miguel_A._Ram=EDrez?=" To: Subject: Summary:Pseudopotential+AIM Date: Tue, 19 Mar 2002 11:59:38 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0092_01C1CF3D.8B6FD000" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0092_01C1CF3D.8B6FD000 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, Some times ago, I posted this question: Please, I'm working with structures containing Co-Co bonds. I'm using = LANL2DZ as pseudopotential for the core electrons of the cobalt, In = thats conditions, could I use AIM methodology to analyse the molecule?. = Thank you Thanks for the useful replies: =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Hi Miguel, I think you could, but... As far as I know AIM needs the total electron density to be able to produce sensible results. So if you are using a pseudopotential you will need to add the density of the core electrons back in before you feed your density to the AIM package. Huub -- =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Hola Miguel, Lo que ocurre cuando se usan pseudopotenciales, es que el m=E1ximo = (punto cr=EDtico 3,-3) en el n=FAcleo se transforma en un m=EDnimo (3,+3), y = eso puede hacer que el PC de enlace (3,-1) no aparezca, y que aparezcan m=E1ximos = (3,-3) en la capa de valencia del metal. En todo caso, todo depende de la = mol=E9cula, y en concreto del tipo de enlace entre los =E1tomos que usan pseudopotenciales, as=ED que lo mejor es realizar pruebas. Te = recomendar=EDa el art=EDculo Journal of Computational Chemistry, Vol. 18, No. 3, 416-429 = (te lo puedo enviar por correo, si no tienes acceso a =E9l). Yo he hecho bastantes c=E1lculos con LANL2DZ (aunque ninguno con enlace metal-metal) y en general los PC de enlace los localizo sin problemas, y adem=E1s presentan valores de densidad, laplaciana,... correctos. Eso = s=ED, al no existir m=E1ximo en el n=FAcleo, el "bond path" no conecta el PC de = enlace con el PC (3,-3) en el n=FAcleo. Tambi=E9n puedo realizar las integrales = sobre los =E1tomos sin problemas. Un grupo que ha trabajado con LANL2DZ y enlace metal-metal es el del = difunto J. M. Molina, de Granada. Te puedo recomendar esta referencia Journal of Molecular Structure (Theochem) 493 (1999) 249-257, pero estoy seguro que tienen m=E1s art=EDculos sobre el tema. Espero que la anterior te sirva de ayuda. SI tienes alguna duda, no = dudes en preguntarme, aunque yo no soy ni mucho menos un experto en el tema. Un saludo Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qu=EDmica Inorg=E1nica, Facultad de Ciencias Universidad del Pa=EDs Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6012579 Fax. 94 4648500 ______________________________________ I am not sure in your specific case but I do know that pseudo potentials = can give incorrect numbers of critical points in the electron density = (i.e. 1 Bond Critical Point) in a water molecule compared to the usual = two. As such I would also expect other features of the density to be = different too. Personally I would not trust pseudopotential = calculations.=20 regards,=20 Sean O'Brien=20 *************************************************************************= ******** Dr. Sean E. O'Brien Cancer Research Laboratories School Of Pharmaceutical Sciences University of Nottingham University Park Nottingham NG7 2RD 0115 951 3423 *************************************************************************= ******** =20 miguel, it is possible to use AIM with pseudo potentials, there is a paper by=20 ron gillespie and richard bader among others from a few years back that examined the changes in topolgy seen when usin such bases, and the effect of the size of the valence functions, i think that the conclusion was that you should NOT use a minimal basis for TM compounds. noj --=20 Dr. N.O.J. Malcolm n.malcolm@umist.ac.uk Chemistry Department =20 UMIST, Sackville Street Manchester, England. M60 1QD ____________________________________________________________ Hola, Yes, you can use AIM to analyze your electronic density. The difference between a pseudopotential calculation and a full electron treatment is = the core density, which does not exists when using pseudos. But that not affects the form of the valence density, which is what you want to = analyze. Hope it helps ________________________________________________________________ Carles Bo Dept. de Quimica Fisica i Inorganica Universitat Rovira i Virgili Voice +34 977 55 9569 Pl. Imperial Tarraco, 1 FAX +34 977 55 9563 43005 - Tarragona =20 SPAIN http://www.quimica.urv.es/~w3qfi http://www.quimica.urv.es/cgi-bin/card?bo+qfi ________________________________________________________________ You'll have to drill back through articles around 1994 from Gernot Frenking, but the basic answer is, "Not Really". Because of the missing core electrons, there are problems determining the bond paths near the atoms using the ecps. You could also check my paper in Organometallics, 1999, 18, p4800 on Ruthenium Silylenes, where I compared the bond critical point values and energy densities determined by AIM with the LANL2DZ ECP on Ruthenium. The critical point values are low when compared with the all electron case. Frenking's article (which I can't find this morning quickly) discusses = ECP vs. All Electron, plus a couple of schemes to try to replace the core density. None are consistently successful. You should also look in Inorganic Chemistry around 1994/1995 when Gillespy and Bytheway discuss polarization of formally core electrons by strong ligands in early TM oxo-fluorides, and effect that would be lost if ECPs were used. -Fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold@northwestern.edu __________________________________________________________ In principle you can but you have to add back in the "missing" electrons before proceeding with the analysis. =20 --David Shobe S=FCd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com __________________________________________________________________ In fact, it's impossible to use pseudopotential with AIM. I suggest you to make a simple point energy calculation at a higher = level with a full basis set like DZVP You can find it and other basis sets at the address http://www.emsl.pnl.gov:2080/forms/basisform.html Sincerely yours Etienne Derat --=20 Etienne Derat Doctorant Groupe Mod=E9lisation et R=E9activit=E9 Chimique=20 UMR 6519 "R=E9actions s=E9lectives et Applications" Universit=E9 de Reims Champagne-Ardenne T=E9l : +33 3 26 91 32 45 Fax : +33 3 26 91 31 66 ________________________________________________ Dr. Mu=3DF1oz, The problem with using AIM and molecules using described with ECP's is that the integration of the density requires the full density. I know of no implementation of AIM that can either work without that core density or can "replace" it by analyzing the core potential. So in short, no there is no option for using AIM with ECP's. Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com _________________________________________________ =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Miguel A. Ram=EDrez Mu=F1oz Instituto Universitario de Bio-Org=E1nica "Antonio Gonz=E1lez" Universidad de La Laguna Astrof=EDsico Francisco S=E1nchez, n=BA 2 38206, La Laguna, Tenerife, Spain Tfno: (22)318594 mramirez@ull.es http://webpages.ull.es/users/mramirez.htm ------=_NextPart_000_0092_01C1CF3D.8B6FD000 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
Some times ago, I posted this=20 question:
 
Please, I'm = working with=20 structures containing Co-Co bonds. I'm using LANL2DZ as pseudopotential = for the=20 core electrons of the cobalt, In thats conditions, could I use AIM = methodology=20 to analyse the molecule?. Thank you
 
Thanks for the useful = replies:
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
Hi Miguel,

I think you could, = but... As far=20 as I know AIM needs the total electron
density to be able to produce = sensible=20 results. So if you are using a
pseudopotential you will need to add = the=20 density of the core electrons
back in before you feed your density to = the AIM=20 package.

Huub


--

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Huub=20 van=20 Dam           &nbs= p;            = ;      =20 E-mail: h.j.j.vandam@dl.ac.uk
CCLRC = Daresbury=20 Laboratory          &nb= sp;      =20 phone: +44-1925-603362
Daresbury,=20 Warrington          &nb= sp;           &nbs= p; =20 fax: +44-1925-603634
Cheshire, UK
WA4=20 4AD

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D
Hola=20 Miguel,

Lo que ocurre cuando se usan pseudopotenciales, es que el = m=E1ximo=20 (punto
cr=EDtico 3,-3) en el n=FAcleo se transforma en un m=EDnimo = (3,+3), y eso=20 puede
hacer que el PC de enlace (3,-1) no aparezca, y que aparezcan = m=E1ximos=20 (3,-3)
en la capa de valencia del metal. En todo caso, todo depende = de la=20 mol=E9cula,
y en concreto del tipo de enlace entre los =E1tomos que=20 usan
pseudopotenciales, as=ED que lo mejor es realizar pruebas. Te = recomendar=EDa=20 el
art=EDculo  Journal of Computational Chemistry, Vol. 18, No. = 3, 416-429=20 (te lo
puedo enviar por correo, si no tienes acceso a = =E9l).

Yo he hecho=20 bastantes c=E1lculos con LANL2DZ (aunque ninguno con = enlace
metal-metal) y en=20 general los PC de enlace los localizo sin problemas, y
adem=E1s = presentan=20 valores de densidad, laplaciana,... correctos. Eso s=ED, al
no = existir m=E1ximo=20 en el n=FAcleo, el "bond path" no conecta el PC de enlace
con el PC = (3,-3) en=20 el n=FAcleo. Tambi=E9n puedo realizar las integrales sobre
los = =E1tomos sin=20 problemas.
Un grupo que ha trabajado con LANL2DZ y enlace metal-metal = es el=20 del difunto
J. M. Molina, de Granada. Te puedo recomendar esta = referencia=20 Journal of
Molecular Structure (Theochem) 493 (1999) 249-257, pero = estoy=20 seguro que
tienen m=E1s art=EDculos sobre el tema.

Espero que = la anterior=20 te sirva de ayuda. SI tienes alguna duda, no dudes en
preguntarme, = aunque yo=20 no soy ni mucho menos un experto en el tema.

Un=20 saludo

Pablo

----------------------------------------------= ----------
Pablo=20 Vitoria Garcia
Dpto. Qu=EDmica Inorg=E1nica, Facultad de = Ciencias
Universidad=20 del Pa=EDs Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao = (Bizkaia)

Tfno. 94=20 6012579
Fax. 94=20 4648500
______________________________________
I am not sure in your specific = case but=20 I do know that pseudo potentials can give incorrect numbers of = critical=20 points in the electron density (i.e. 1 Bond Critical Point) in a water = molecule=20 compared to the usual two. As such I would also expect other features of = the=20 density to be different too. Personally I would not trust = pseudopotential=20 calculations.=20

regards,=20

Sean=20 O'Brien 
********************************************************= *************************
Dr.=20 Sean E. O'Brien
Cancer Research Laboratories
School Of = Pharmaceutical=20 Sciences
University of Nottingham
University = Park
Nottingham
NG7=20 2RD
0115 951=20 3423
*****************************************************************= ****************  
 =20 miguel,

it is possible to use AIM with pseudo potentials, there = is a=20 paper by
ron gillespie and richard bader among others from a few = years back=20 that
examined the changes in topolgy seen when usin such bases, and=20 the
effect of the size of the valence functions, i think that the=20 conclusion
was that you should NOT use a minimal basis for TM=20 compounds.

noj
--
  Dr. N.O.J.=20 Malcolm           =            =20 n.malcolm@umist.ac.uk
 = =20 Chemistry=20 Department          &nb= sp;       =20
  UMIST, Sackville Street
  Manchester, England. M60 = 1QD

____________________________________________________________


Hola,

Yes, you can use AIM to analyze your electronic = density. The=20 difference
between a pseudopotential calculation and a full electron=20 treatment is the
core density, which does not exists when using = pseudos. But=20 that not
affects the form of the valence density, which is what you = want to=20 analyze.

Hope it=20 helps
 __________________________________________________________= ______

 =20 Carles Bo
  Dept. de Quimica Fisica i Inorganica
  = Universitat=20 Rovira i Virgili          = Voice +34=20 977 55 9569
  Pl. Imperial Tarraco,=20 1            =  =20 FAX   +34 977 55 9563
  43005 -=20 Tarragona          &nbs= p;     =20
 =20 SPAIN           &n= bsp;           &nb= sp;=20 http://www.quimica.urv.es/~w3qf= i
          &nbs= p;       =20 http://www.quimica= .urv.es/cgi-bin/card?bo+qfi
______________________________________= __________________________


You'll have to drill back through articles around 1994 from=20 Gernot
Frenking, but the basic answer is, "Not Really".  Because = of the=20 missing
core electrons, there are problems determining the bond paths = near=20 the
atoms using the ecps.

You could also check my paper in=20 Organometallics, 1999, 18, p4800 on
Ruthenium Silylenes, where I = compared the=20 bond critical point values and
energy densities determined by AIM = with the=20 LANL2DZ ECP on Ruthenium.
The critical point values are low when = compared=20 with the all electron
case.

Frenking's article (which I can't = find=20 this morning quickly) discusses ECP
vs. All Electron, plus a couple = of=20 schemes to try to replace the core
density.  None are = consistently=20 successful.  You should also look in
Inorganic Chemistry around=20 1994/1995 when Gillespy and Bytheway discuss
polarization of formally = core=20 electrons by strong ligands in early TM
oxo-fluorides, and effect = that would=20 be lost if ECPs were used.

-Fred

Frederick P. Arnold, = Jr.
NUIT,=20 Northwestern U.
f-arnold@northwestern.edu

__________________________________________________________
In = principle=20 you can but you have to add back in the "missing" electrons
before = proceeding=20 with the analysis.
 
--David Shobe
S=FCd-Chemie = Inc.
phone (502)=20 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com
=
__________________________________________________________________

In fact, it’s impossible to use = pseudopotential=20 with AIM.
I suggest  you to make a simple point energy = calculation at a=20 higher level with a full basis set like DZVP
You can find it and = other basis=20 sets at the=20 address
http://www.emsl.pnl.gov:2080/forms/basisform.html

Since= rely=20 yours

Etienne Derat
--

Etienne = Derat
Doctorant
Groupe=20 Mod=E9lisation et R=E9activit=E9 Chimique
UMR 6519 "R=E9actions = s=E9lectives et=20 Applications"
Universit=E9 de Reims Champagne-Ardenne

T=E9l : = +33 3 26 91=20 32 45
Fax : +33 3 26 91 31=20 66
________________________________________________
Dr. Mu=3DF1oz,

   The = problem with=20 using AIM and molecules using described with ECP's
is that the = integration of=20 the density requires the full density.
I know of no implementation of = AIM=20 that can either work without that
core density or can "replace" it by = analyzing the core potential.

   So in short, no there = is no=20 option for using AIM with ECP's.

Douglas J. Fox
  Technical=20 Support
  Gaussian, Inc.
  help@gaussian.com
_________________________________________________
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
 
Dr. Miguel A. Ram=EDrez = Mu=F1oz
Instituto=20 Universitario de Bio-Org=E1nica "Antonio Gonz=E1lez"
Universidad de = La=20 Laguna
Astrof=EDsico Francisco S=E1nchez, n=BA 2
38206, La Laguna, = Tenerife,=20 Spain
     Tfno:=20 (22)318594
      mramirez@ull.es
   =   =20 http://webpages.ull.es= /users/mramirez.htm
------=_NextPart_000_0092_01C1CF3D.8B6FD000-- From chemistry-request@server.ccl.net Tue Mar 19 03:36:28 2002 Received: from tungsten.chem.vu.nl ([130.37.144.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2J8aRp32027 for ; Tue, 19 Mar 2002 03:36:27 -0500 Received: from tungsten.chem.vu.nl (LOCALHOST [127.0.0.1]) by tungsten.chem.vu.nl (8.10.0/8.10.0) with ESMTP id g2J8biO15061 for ; Tue, 19 Mar 2002 09:37:45 +0100 (MET) Message-Id: <200203190837.g2J8biO15061@tungsten.chem.vu.nl> X-Mailer: exmh version 2.0.2 2/24/98 To: chemistry@ccl.net From: Stan van Gisbergen Subject: New release ADF density functional package Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Tue, 19 Mar 2002 09:37:44 +0100 Sender: vgisberg@tungsten.chem.vu.nl Dear CCL-list, SCM proudly announces the 2002 release of ADF, the complete density functional program for chemists, with the following new features: - additional and improved Slater type basis sets - improved xc potentials (SAOP and GRAC) for property calculations - modern GGA and meta-GGA energy functionals - NMR spin-spin coupling constants, including relativistic effects - new EPR/NMR program for high-spin states and analysis - analytic second derivatives - combination of linear scaling and parallelization techniques - improved efficiency for QM/MM calculations with many thousands of atoms For further information, visit our website (http://www.scm.com), contact us by E-mail (info@scm.com), or visit booth 936 at the upcoming ACS meeting in Orlando. A review paper and a brochure are available on request. Best regards, Stan van Gisbergen, CEO of Scientific Computing & Modelling NV (SCM) From chemistry-request@server.ccl.net Tue Mar 19 07:45:31 2002 Received: from mail.laposte.net ([160.92.113.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JCjUp03730 for ; Tue, 19 Mar 2002 07:45:30 -0500 Received: from nouveaupc (80.14.187.207) by mail.laposte.net (5.5.044) id 3C9102D70004A2E4 for CHEMISTRY@ccl.net; Tue, 19 Mar 2002 13:45:12 +0100 Message-ID: <008501c1cf43$f9ba9e40$0b00000a@nouveaupc> From: "Alexandre Hocquet" To: Subject: Tjalling Koopmans Date: Tue, 19 Mar 2002 13:45:39 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 I guess it it is well known that the Koopmans that won the 1975 nobel prize in economics is also the same person that is quoted in our famous Koopmans "theorem". I was surprised the other day to learn that his past in theoretical chemistry is unknowned to the economists. As a matter of fact, here is how he presented this period of his life in his nobel prize autobiography (http://www.nobel.se/economics/laureates/1975/koopmans-autobio.html) : "in 1930, I switched [from mathematics] my emphasis to theoretical physics - a timid compromise between my desire for a subject matter closer to real life and the obvious argument in favor of a field in which my mathematical training could be put to use. [...] Below, I cite my one publication in quantum mechanics so that I can add here that Kramers's generosity and my inexperience combined to prevent his being listed as co-author of that paper. He should have been, because, although the main proposition was my own idea, Kramers, besides guiding the writing, also supplied the proof" This means that his paper ("Ueber die Zuordaung von Wellenfunktionen und Eigenwerten zu den einzelnen Elektronen eines Atoms, "Physica 1, no. 2, 1934, pp. 104-113) was the only one he ever wrote in the field. I know it was not uncommon at the time that people publishing in theoretical physics/chemistry were in fact mathematicians, but i am surprised that his work seemed so secondary in his career. Could it be that he was even unaware of how much he is quoted in theoretical chemistry ? Any hints ? ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomoléculaire et Cellulaire ESA CNRS 7033 hocquet@lpbc.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Mar 19 03:25:13 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2J8PCp31838 for ; Tue, 19 Mar 2002 03:25:13 -0500 Received: from ccc.uni-erlangen.de (temeraire.chemie.uni-erlangen.de [131.188.128.73]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id JAA04466 for ; Tue, 19 Mar 2002 09:25:07 +0100 (MET) Sender: Anselm.Horn@Organik.Uni-Erlangen.DE Message-ID: <3C96F0A9.53703435@ccc.uni-erlangen.de> Date: Tue, 19 Mar 2002 09:02:49 +0100 From: Anselm Horn Organization: CCC X-Mailer: Mozilla 4.78 [en] (X11; U; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Summary - free molecule editor under Linux Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, last week I posted a question about a free molecule editor under Linux. Many thanks to all who answered !! (summary below) Best regards, Anselm ====================================================================== Original question: ------------------------- I am looking for a free 3D-molecule editor/builder (not just viewer) under Linux/Unix. Input should be mouse-and-click-orientated (not just visualized Z-matrix-input), and ideally it should run without any additional installation effords (i.e. statically linked; C/C++/[Java]). At the moment, I am only aware of Pymol and GDIS. Are there any established alternatives ? My motivation is to offer our Windows-trained students some familiar input facility and visualization tool... ====================================================================== Here are the summarized answers: ------------------------- I'm rather biased towards the Ghemical package under the GNOME environment. Excellent editor and improving fairly quickly. The package uses the new Open Babel project (included) for file translation to many file formats. There are now RPMs and Debian .debs available too. -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry ------------------------- Hello, perhaps take a look at WebMO: http://www.webmo.net Kind regards, Wibke Sudholt University of California, San Diego USA ------------------------- Dear Anselm, the Marvin Java applets are not totally free but maybe worth a look: http://www.chemaxon.com/marvin/ Cheers Thomas Wein ------------------------- Please look at http://chemviz.ncsa.uiuc.edu/ under nanocad editor or http://chemviz.ncsa.uiuc.edu/cgi-bin/nanocad/nanocad.cgi You can register and get an account free. This applet will be included in a java based portal application to be distributed in the next few months. Sudhakar. ------------------------- Dear Anselm, My response may be way off the mark, Linux-wise, but if you are ever in need of a very inexpensive Windows molecule builder, please consider looking at ArgusLab (www.arguslab.com). Sincerely, Mark Thompson ------------------------- Anselm, I'm curious about what your experience has been with PyMOL so far, in terms of being a builder. The project is still in 'early days' and the documentation on building is nonexistent, but have you been able to use it for this purpose at all? If you have, are the critical missing components you would add first in order to help address your basic needs? Obviously PyMOL won't change greatly overnight, but over the next 6-12 months, I'd like it to evolve into a better and better tool for this kind of thing, particularly when it comes to students... Cheers, Warren -- mailto:warren@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 ------------------------- -- _______________________________________________________________________ Anselm Horn, Dipl. Chem. Univ. Anselm.Horn@ccc.uni-erlangen.de ___ / __| ___ Computer Chemie Centrum | / ___ / __| | | / __|| / Naegelsbachstrasse 25 \ \__ | / | | D-91025 Erlangen \___|| | \ \__ Deutschland / Germany \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 \___| http://www.ccc.uni-erlangen.de/clark/horn/index.html _______________________________________________________________________ From chemistry-request@server.ccl.net Tue Mar 19 11:01:24 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JG1Np07588 for ; Tue, 19 Mar 2002 11:01:24 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 7AE0A1CBD87; Tue, 19 Mar 2002 17:01:17 +0100 (CET) Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by smtp2.ruc.dk (Postfix) with ESMTP id B87851CBD84; Tue, 19 Mar 2002 17:01:16 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id QAA27180; Tue, 19 Mar 2002 16:31:06 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 19 Mar 02 17:01:14 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 19 Mar 02 17:01:04 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Alexandre Hocquet" Date: Tue, 19 Mar 2002 17:01:01 +0100 Subject: CCL: T. Koopmans --> O. Burrau Reply-To: spanget@ruc.dk Cc: CHEMISTRY@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <8E78D4226A7@virgil.ruc.dk> Alexandre Hocquet: > I guess it it is well known that the Koopmans that won the 1975 > nobel prize in economics is also the same person that is quoted in > our famous Koopmans "theorem". > > I was surprised the other day to learn that his past in theoretical > chemistry is unknowned to the economists. .... Dear Alexandre, your story reminds me of another, albeit less famous one, namely that of Oeyvind Burrau. He was born in Copenhagen, Denmark, in 1896 and was educated as a practical mathematician in the life insurance field, but in 1926-1927 he was associated with Niels Bohr's Institute of Theoretical Physics in Copenhagen. In 1926 he performed what would seem to be the first ab initio quantum mechanical calculation of a molecular species with a covalent bond: By numerical integration in spheroidical coordinates, he solved the Schroedinger equation for the hydrogen molecule cation (within the approximation later to be associated with the names of Born and Oppenheimer): Oe. Burrau: "Berechnung des Energiewertes des Wasserstoff Molekel-Ions (H2+) im Normalzustand", Die Naturwissenschaften, 16-17 (1927). ["Zuschrift", submitted 22. November 1926] Oe. Burrau: "Berechnung des Energiewertes des Wasserstoff Molekel-Ions (H2+) im Normalzustand", Det Kgl. Danske Videnskabernes Selskab, Mathematisk-fysiske Meddelelser VII,14 (1927). The latter, full paper shows potential energy curves and plots of the electron density distribution. However, Burrau did not continue in this field, but switched to that of geodesy where he had a brillant career, leading to the post of "State Geodesian of Denmark" during 1952-63. - In the Danish "Who's Who" (Kraks Blaa Bog 1973), Burrau's brief association with Bohr's Institute and his contribution to the birth of computational quantum chemistry and is not mentioned at all. Yours, Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Tue Mar 19 08:28:14 2002 Received: from mail1.chula.com ([202.183.214.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JDSDp04677 for ; Tue, 19 Mar 2002 08:28:13 -0500 Received: from mail1.chula.com (mail1.chula.com [127.0.0.1]) by mail1.chula.com (8.11.2/8.11.2) with ESMTP id g2JDNnM10866; Tue, 19 Mar 2002 20:23:49 +0700 Received: from [161.200.255.163] by mail1.chula.com with HTTP; Tue, 19 Mar 2002 20:23:49 +0700 (ICT) Message-ID: <7247017.1016544229369.JavaMail.root@mail1.chula.com> Date: Tue, 19 Mar 2002 20:23:49 +0700 (ICT) From: Somsak Tonmunphean To: chemistry@ccl.net Subject: Dock calculation with real solvents Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would like to do the docking calculation which includes the real solvents molecules. The AutoDock includes solvent effect by using the dielectric constant but I want the real solvents. Does anybody know method or software for this purpose ? Thank you in advance. Your sincerely, Somsak. From chemistry-request@server.ccl.net Tue Mar 19 13:20:33 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JIKXp10944 for ; Tue, 19 Mar 2002 13:20:33 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA02978; Tue, 19 Mar 2002 13:20:23 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3C977758.2A38A7CC@cornell.edu> Date: Tue, 19 Mar 2002 12:37:29 -0500 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: trajectory file conversion Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Is there a way to convert a CHARMm dcd file that was written on a unix machine to one that can be read by a Linux version of CHARMm? I tried DYNA FORM on the unix box and then DYNA UNFORM on the Linux machine, but this didn't work because DYNA UNFORM couldn't read the NTITLE value or version number. Alternatively, how can one write the correct info to the dhx file? Thanks, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Tue Mar 19 13:19:05 2002 Received: from c001.snv.cp.net ([209.228.32.114]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2JIJ5p10889 for ; Tue, 19 Mar 2002 13:19:05 -0500 Received: (cpmta 557 invoked from network); 19 Mar 2002 10:18:52 -0800 Received: from 209.228.32.129 (HELO mail.roberttopper.com.criticalpath.net) by smtp.register-admin.com (209.228.32.114) with SMTP; 19 Mar 2002 10:18:52 -0800 X-Sent: 19 Mar 2002 18:18:52 GMT Received: from [199.98.21.13] by mail.roberttopper.com with HTTP; Tue, 19 Mar 2002 10:18:50 -0800 (PST) Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 To: CHEMISTRY@ccl.net Cc: topper@cooper.edu From: topper@cooper.edu Subject: Please Join the ECCC8 Discussion Online X-Sent-From: roberttopper@roberttopper.com Date: Tue, 19 Mar 2002 10:18:50 -0800 (PST) X-Mailer: Web Mail 5.0.7-2 Sender: roberttopper@roberttopper.com Message-Id: <20020319101852.515.c001-h015.c001.wm@mail.roberttopper.com.criticalpath.net> Dear colleagues, Please consider joining us online at the 8th Electronic Computational Chemistry conference: http://eccc8.cooper.edu This week is the "interactive session;" presenters will attempt to answer all posted questions within 24 hours. We have an excellent group of presentations and the discussions have been animated and interesting. Please join us! As always, ECCC8 is free and open to all. Best wishes, Robert Topper ECCC8 Principal Organizer Department of Chemistry School of Engineering The Cooper Union 51 Astor Place New York, NY 10003 http://www.cooper.edu/engineering/chemechem ELECTRONIC COMPUTATIONAL CHEMISTRY CONFERENCE APRIL 2001 http://eccc7.cooper.edu ********************* Robert Q. Topper, Ph.D. Associate Professor of Chemistry School of Engineering The Cooper Union for the Advancement of Science and Art 51 Astor Place New York, NY 10003 ********************* http://www.cooper.edu/engineering/chemechem/ ********************* From chemistry-request@server.ccl.net Tue Mar 19 15:13:58 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JKDwp13068 for ; Tue, 19 Mar 2002 15:13:58 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g2JKDr717010; Tue, 19 Mar 2002 14:13:53 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g2JKDqv04265; Tue, 19 Mar 2002 14:13:52 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Tue, 19 Mar 2002 14:13:52 -0600 (CST) From: Jim Phillips To: "Dr. Richard L. Wood" cc: "chemistry@ccl.net" Subject: Re: CCL:trajectory file conversion In-Reply-To: <3C977758.2A38A7CC@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Try FlipDCD. http://www.ks.uiuc.edu/Development/MDTools/flipdcd/ -Jim On Tue, 19 Mar 2002, Dr. Richard L. Wood wrote: > Hi all > > Is there a way to convert a CHARMm dcd file that was written on a > unix machine to one that can be read by a Linux version of CHARMm? > > I tried DYNA FORM on the unix box and then DYNA UNFORM on the > Linux machine, but this didn't work because DYNA UNFORM couldn't > read the NTITLE value or version number. > > Alternatively, how can one write the correct info to the dhx file? > > Thanks, > Richard > > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Department of Food Science > 120 Stocking Hall > Cornell University, Ithaca, NY 14853 > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Mar 19 16:25:09 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JLP8p14374 for ; Tue, 19 Mar 2002 16:25:08 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA12648; Tue, 19 Mar 2002 16:19:30 -0500 (EST) Date: Tue, 19 Mar 2002 16:19:30 -0500 From: Rick Venable To: Jim Phillips cc: "Dr. Richard L. Wood" , "chemistry@ccl.net" Subject: Re: CCL:trajectory file conversion In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Mar 2002, Jim Phillips wrote: > Try FlipDCD. http://www.ks.uiuc.edu/Development/MDTools/flipdcd/ > > -Jim I found this to be a problem for CHARMM (vs. CHARMm); flipdcd seemed to be written for REAL*4 trajectories such as the commercial CHARMm creates, while the academic CHARMM switched to REAL*8 several years ago. I never got flipdcd to work on CHARMM REAL*8 trajectories. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Tue Mar 19 17:52:20 2002 Received: from imo-m04.mx.aol.com ([64.12.136.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2JMqKp16646 for ; Tue, 19 Mar 2002 17:52:20 -0500 Received: from Jalbout5551@aol.com by imo-m04.mx.aol.com (mail_out_v32.5.) id g.135.b3760ba (25916) for ; Tue, 19 Mar 2002 17:52:01 -0500 (EST) From: Jalbout5551@aol.com Message-ID: <135.b3760ba.29c91b11@aol.com> Date: Tue, 19 Mar 2002 17:52:01 EST Subject: Fractional Charges To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="part1_135.b3760ba.29c91b11_boundary" X-Mailer: AOL 6.0 for Windows US sub 10564 --part1_135.b3760ba.29c91b11_boundary Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Dear Colleagues: Is it possible in GAUSSIAN to calculate atoms nuclear charges? For example: F(-1/3), where the the monatomic system is X and the charge is Z so the ground state is F(0) (in the above case)? If it cannot can you recommend a pacakge that will? Best Wishes; Abraham F. Jalbout Department of Chemistry University of New Orleans --part1_135.b3760ba.29c91b11_boundary Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: 7bit Dear Colleagues:

Is it possible in GAUSSIAN to calculate atoms nuclear charges? For example:

F(-1/3),

where the the monatomic system is X and the charge is Z so the ground state is F(0) (in the above case)?

If it cannot can you recommend a pacakge that will?




Best Wishes;

Abraham F. Jalbout
Department of Chemistry
University of New Orleans

--part1_135.b3760ba.29c91b11_boundary--