From chemistry-request@server.ccl.net Wed Mar 19 02:36:23 2003 Received: from [195.229.145.1] ([195.229.145.1]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2J7aKw20400 for ; Wed, 19 Mar 2003 02:36:22 -0500 Received: from no.name.available by [195.229.145.1] via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; Wed, 19 Mar 2003 11:27:35 +0400 Received: from FSD1G1D (gwd1b1h.zu.ac.ae [10.10.0.23]) by macsmtp.zu.ac.ae (8.12.5/8.12.5) with ESMTP id h2J7PXts008843 for ; Wed, 19 Mar 2003 11:25:34 +0400 Received: from EMBADOMAIN-MTA by FSD1G1D with Novell_GroupWise; Wed, 19 Mar 2003 11:34:25 +0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0 Date: Wed, 19 Mar 2003 11:33:45 +0400 From: "Iman Boukhobza" To: "<" Subject: File conversion Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h2J7aNw20401 Hello every body I am using Mopac to do conversion from atomic coordinates to a z-matrix format My question is: Are the bond length obtained after conversion accurate? I have the bond length from crystallographic data and what I really need are the angles and in specific dihedral angles. Thus, does anybody use these conversions before? Your help is very much appreciated Iman From chemistry-request@server.ccl.net Tue Mar 18 20:39:33 2003 Received: from smtp.unc.edu ([152.2.1.242]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2J1dXw12108 for ; Tue, 18 Mar 2003 20:39:33 -0500 Received: from m38909 (m38909.pha.unc.edu [152.2.147.236]) by smtp.unc.edu (8.12.2/8.12.2) with SMTP id h2J1dUxw015034 for ; Tue, 18 Mar 2003 20:39:30 -0500 (EST) Message-ID: <003801c2edb8$6962e750$ec930298@m38909> From: "Jun Feng" To: Subject: Born Energy and Delphi Date: Tue, 18 Mar 2003 20:39:41 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0035_01C2ED8E.80454F00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0035_01C2ED8E.80454F00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Collegues: I tried to use Delphi to reproduce the Born energy (~162kT) for an atom = with 1.7 A radii and +1 formal charge, but I found=20 that the difference of the two grid energies cannot match the Born = energy while the reaction field energy=20 matched the Born energy quite well. The boudary condition I used is full = coulombic. What's the problem? Any idea? Jun Feng ------=_NextPart_000_0035_01C2ED8E.80454F00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Collegues:
 
I tried to use Delphi to reproduce the = Born energy=20 (~162kT) for an atom with 1.7 A radii and +1 formal charge, but I = found=20
that the difference of the two grid = energies cannot=20 match the Born energy while the reaction field energy
matched the Born energy quite well. The = boudary=20 condition I used is full coulombic. What's the problem?
Any idea?
 
Jun Feng
 
------=_NextPart_000_0035_01C2ED8E.80454F00-- From chemistry-request@server.ccl.net Tue Mar 18 11:43:51 2003 Received: from antivirus1.its.rochester.edu ([128.151.57.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2IGhpw27518 for ; Tue, 18 Mar 2003 11:43:51 -0500 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.8/8.12.4) with ESMTP id h2IGhoQt028061 for ; Tue, 18 Mar 2003 11:43:51 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.8/8.12.4) with SMTP id h2IGhlDC028042 for ; Tue, 18 Mar 2003 11:43:47 -0500 (EST) Received: from localhost (weiz@localhost) by mail.rochester.edu (8.12.8/8.12.1) with ESMTP id h2IGhkiY020622 for ; Tue, 18 Mar 2003 11:43:46 -0500 (EST) X-Authentication-Warning: mail1.ats.rochester.edu: weiz owned process doing -bs Date: Tue, 18 Mar 2003 11:43:46 -0500 (EST) From: Wei Zhuang X-Sender: weiz@mail1.ats.rochester.edu To: chemistry@ccl.net Subject: one question about comparing structures in CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi,all: I want to compare two structures in charmm, the command I use is: ******************* coor orie rms ******************8 and charmm gives out ******************** TOTAL SQUARE DIFF IS 5.3526 DENOMINATOR IS 18.0000 THUS RMS DIFF IS 0.545311 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. *********************** my question is: 1)what is the criteria of judging how close these two structures are from the output above, wei zhuang e-mail:weiz@mail.rochester.edu office phone:716-2750387 From chemistry-request@server.ccl.net Tue Mar 18 10:21:12 2003 Received: from pscuxc.psc.edu ([128.182.66.177]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2IFLCw23970 for ; Tue, 18 Mar 2003 10:21:12 -0500 Received: from pscuxc.psc.edu (localhost.psc.edu [127.0.0.1]) by pscuxc.psc.edu (8.12.8/8.12.5) with ESMTP id h2IFLCg2025677 for ; Tue, 18 Mar 2003 10:21:12 -0500 (EST) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.12.8/8.12.8/Submit) with ESMTP id h2IFLBG2025854 for ; Tue, 18 Mar 2003 10:21:12 -0500 (EST) Date: Tue, 18 Mar 2003 10:21:11 -0500 (EST) From: Troy Wymore To: Subject: NAMD: Looping through input file Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I would like to be able to run a 500 ps simulation using NAMD but have the ouput files divided up into 20 ps sections and numbered consecutively. I'm not sure how to setup my input file to accomplish this easy task (sorry, new to tcl scripts) with just one config file. So basically I need some help with how to loop through an input file with NAMD. Any help is much appreciated. Best regards, Troy Wymore From chemistry-request@server.ccl.net Tue Mar 18 21:08:20 2003 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2J28Kw12939 for ; Tue, 18 Mar 2003 21:08:20 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout4.cac.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2J289Lv010860; Tue, 18 Mar 2003 18:08:09 -0800 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2J289wa022108 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Tue, 18 Mar 2003 18:08:09 -0800 Message-ID: <3E77D10C.1040301@u.washington.edu> Date: Tue, 18 Mar 2003 18:08:12 -0800 From: Carsten Detering User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net, autodock@scripps.edu Subject: autodock Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi all, I am trying to (Auto)dock a sample database of 50 compounds, and the ligands include the atom types CANHOSFIcn (c being Cl and n being an N that carries a proton). My problem is, although I changed MAX_MAPS in the autocomm.h file to 16, I still get an error message with an unsuccessful completion of autogrid (I also tried to use the autocomm.h-extra-maps): >/usr/local/AutoDock/bin/linux.RedHat8/autogrid3: ERROR: Too many "map" >keywords (10); this program can only calculate 10 maps. >Remove a "map" keyword from the GPF, or change the definition of >"MAX_MAPS" in "autocomm.h". > > > >/usr/local/AutoDock/bin/linux.RedHat8/autogrid3: Unsuccessful >completion. My question now is: is AutoDock in general capable of only dealing with a maximum of 9 atom types for the ligand (the tenth being the electrostatic map) or is there something I have overseen?? This is the part of my autocomm.h file: __________________________________________________________________________ #define MAX_MAPS 16 /* Maximum number of energy maps */ #define ATOM_MAPS 14 /* Number of atomic affinity grids */ /* 0,1,2,... are for atomic interactions */ /* last is for electrostatics */ #define VECLENMAX 16 /* For AVS fld files... */ #define ATOMTYPE "CNOSHXMPIF" /* 0123456789 */ #define COVALENTTYPE 'Z' #define COVALENTTYPE2 'Y' #define CARBON 0 #define NITROGEN 1 #define OXYGEN 2 #define SULPHUR 3 #define HYDROGEN 4 #define UNKNOWN 5 #define METAL 6 #define PHOSPHOROUS 7 #define IODINE 8 #define FLOURINE 9 #define NATOMTYPES 15 /* Number of atom types for atomic interactions */ #define MAX_TYPES MAX_MAPS /* Maximum number of atom types used. */ _______________________________________________________________________ Thanks again for any helpful comments! Carsten -- Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665 From chemistry-request@server.ccl.net Tue Mar 18 05:39:21 2003 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2IAdKw16111 for ; Tue, 18 Mar 2003 05:39:20 -0500 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] helo=apollo) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 18vMuJ-0006CD-00 for chemistry@ccl.net; Tue, 18 Mar 2003 11:37:59 -0800 From: "Daniele Bellocchi" To: Subject: Summary of TS optimization Date: Tue, 18 Mar 2003 11:34:58 +0100 Message-ID: <000001c2ed3a$099d3920$480dfa8d@apollo> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C2ED42.6B7E50E0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C2ED42.6B7E50E0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Everyone, I would like to thank who get me the following usefull answer to my question. I started an eigenvalue-following transition state optimization in g98 but the run failed giving the following error message: ------------------------------------------------------------------------ -------------------- dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 66048 FType=2 FMxFil=10000 Number 0 Base 20480 End 66048 End1 66048 Wr Pntr 20480 Rd Pntr 20480 Error termination in NtrErr: NtrErr Called from FileIO. ------------------------------------------------------------------------ --------------------- I used the following route for TS search: # PM3 test opt=(EF,TS,calcfc,ModRed) scf=direct freq Can anybody tell me how to solve this problem?Thanks a lot! ------------------------------------------------------------------------ ------------------------------------------------- Hey, you ask for 2 jobs. the first one is the TS optimization, the 2nd the FREQ calculation. Are you sure that the first job doesn't terminated correctly? It could be only the 2nd job that can not start. Hope this helps. Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 Universite Henri Poincare (F) 33 3 83 68 43 71 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr ------------------------------------------------------------------------ ----- Hello Daniele, maybe (I'm not sure) you have an old chk-File in your directory and your g98 jobs tries to use this, because its given in the input: %chk=... As you don't need this file to restart (your command line has no such option), you should remove it. (If you are not sure, please show me the upper part of your input, containing the %chk line) Hope that helps. Bye Elmar Elmar Gerwalin , University of Kaiserslautern,Germany Dept. of Theoretical Chemistry and IT Service Team elg@chemie.uni-kl.de 0631-205-2749 ------------------------------------------------------------------------ ------------- Dr. Bellocchi, The EF options are not consistent with redundant internal coordinates. If you want to use EF you will need to define a Z-matrix and use Z-matrix constraints. Alternatively you can leave out EF and use Modredundant. Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com ------------------------------------------------------------------------ -------------- Hi, can you forward the answers to me too, cause I have problems with eigenvalue following.Thank you in advance. Best regards. Nurcan Senyurt [senyurtn@boun.edu.tr] ------------------------------------------------------------------------ ------------------------------------------------------------------------ ----------------------------------------------------------------------- Best Regards Daniele Bellocchi, PhD Student Molecular Modeling Section Istituto di Chimica e Tecnologia del Farmaco University of Perugia Italy ------=_NextPart_000_0001_01C2ED42.6B7E50E0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Everyone,

I would like to thank who get me the following usefull answer to my = question.

 

 

I started an eigenvalue-following transition state optimization in g98 but the run failed giving the = following error message:

 

 

-------------------------------------------= -----------------------------

--------------------

dumping /fiocom/, unit =3D 3 = NFiles =3D     1 SizExt = =3D    524288 WInBlk = =3D

512

       &nbs= p;           defal =3D T LstWrd =3D       = 66048 FType=3D2 FMxFil=3D10000

 

 Number       &nbs= p;   0

 Base       &nbs= p; 20480

 End       &nbs= p;  66048

 End1       &nbs= p; 66048

 Wr Pntr      = 20480

 Rd Pntr      = 20480

 Error termination in = NtrErr:

 NtrErr Called from = FileIO.

 

-------------------------------------------= -----------------------------

---------------------

 

I used the following route for TS search:

 

# PM3 test = opt=3D(EF,TS,calcfc,ModRed) scf=3Ddirect freq

 

Can anybody tell me how to solve = this problem?Thanks a lot!

 

-------------------------------------------= -------------------------------------------------------------------------= -----

 

Hey,

 

you ask for 2 jobs. the first one = is the TS optimization, the 2nd the FREQ calculation. Are you sure that the = first job doesn't terminated correctly? It could be only the 2nd job that can not = start. Hope this helps.

 

 

Ast. Pr. Xavier Assfeld       &nbs= p;     Xavier.Assfeld@lctn.uhp-nancy.fr

Laboratoire de Chimie theorique     (T) 33 3 83 = 68 43 74

Universite Henri Poincare       &nbs= p;   (F) 33 3 83 68 43 71

F-54506 Nancy BP 239       &nbs= p;        http://www.lctn.uhp-nancy.fr

 

-------------------------------------------------------------------= ----------

Hello = Daniele,

 

maybe (I'm not sure) you have an = old chk-File in your directory and your g98

jobs tries to use this, because = its given in the input: %chk=3D...

 

As you don't need this file to = restart (your command line has no such option),

you should remove = it.

 

(If you are not sure, please show = me the upper part of your input, containing

the %chk = line)

 

Hope that = helps.

Bye

Elmar

 

Elmar Gerwalin ,   University of Kaiserslautern,Germany

       &nbs= p;           Dept. of Theoretical Chemistry

       &nbs= p;           and  IT Service = Team

       &nbs= p;           elg@chemie.uni-kl.de    0631-205-2749

-------------------------------------------= ------------------------------------------

 

Dr. = Bellocchi,

 

   The EF options are not = consistent with redundant internal coordinates. If you want to use EF you will need = to define a Z-matrix and use Z-matrix constraints.  Alternatively you can leave out = EF and use Modredundant.

 

 

Douglas J. = Fox

  Technical Support

  Gaussian, Inc.

  help@gaussian.com=

 

-------------------------------------------= -------------------------------------------

 

Hi, can you forward the answers = to me too, cause I have problems with eigenvalue following.Thank you in = advance.  Best regards.

 

Nurcan Senyurt [senyurtn@boun.edu.tr]

 

-----------------------= -------------------------------------------------------------------------= -------------------------------------------------------------------------= ----------------------------------------------

 

 

Best= Regards

 

Daniele Bellocchi, PhD Student

Molecular Modeling Section

Istituto di Chimica = e Tecnologia del Farmaco

University of Perugia

Italy

 

 

------=_NextPart_000_0001_01C2ED42.6B7E50E0-- From chemistry-request@server.ccl.net Tue Mar 18 06:17:21 2003 Received: from mail.chemie.fu-berlin.de ([160.45.24.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2IBHLw16674 for ; Tue, 18 Mar 2003 06:17:21 -0500 Received: from koala.chemie.fu-berlin.de ([160.45.20.25]) (3043 bytes) by mail.chemie.fu-berlin.de via sendmail with P:esmtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Tue, 18 Mar 2003 12:17:15 +0100 (CET) (Smail-3.2.0.111) Date: Tue, 18 Mar 2003 12:17:10 +0100 (CET) From: Leticia Gonzalez To: CHEMISTRY@ccl.net Subject: MQRD, 2003: Multidimensional Quantum Reaction Dynamics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT ******************************************************* * Multidimensional Quantum Reaction Dynamics 2003 * * MQRD 2003 * ******************************************************* http://www.bcp.fu-berlin.de/MQRD2003/index.html July 17-18, 2003 -Berlin, Germany Chair: J. Manz, Freie Universität Berlin CALL FOR PARTICIPANTS: This conference meeting will bring together, for the first time, leading experts in the field for presentations and discussions of various complementary state-of-the-art techniques, as well as forthcoming applications. This should catalyze extensions and combinations of the different approaches and stimulate advanced simulations of more complex reaction systems and in new domains of reaction dynamics e.g. biomolecules or catalysis. It will also serve as meeting place for young scientists who are planning to enter the field. Recent developments of new methods allow quantum simulations of reaction dynamics in high dimensionality- an area which was accessible solely for classical molecular dynamics in the past. These methods- ranging from the Multi-Configuration Time Dependent Hartree approach to various semiclassical techniques- describe the nuclear motions of molecules with important quantum effects such as zero point energies, tunnelling, interferences and branching of wavepackets toward competing products. The quantum simulations open the possibility for new applications from small polyatomic molecules in the gas phase to reaction dynamics in the condensed phase. The time of the conference, July 17 -July 18, 2003 has been chosen such that the participants can attend complementary conferences in Europe, in particular the International Congress on Quantum Chemistry ICQC 2003 (Bonn, July 20-25, chair: S.D. Peyerimhoff, http://www.icqc.uni-bonn.de). INVITED SPEAKERS: -Ben-Nun, Michal (Fremont, USA) -Coker, David (Boston, USA) -Gerber, Benny (Jerusalem, Israel) -Hammes-Schiffer, Sharon (University Park, USA) -Köppel, Horst (Heidelberg, Germany) -Kühn, Oliver (Berlin, Germany) -Luckhaus, David (Göttingen, Germany) -Mahahpatra, Susanta (Hyderabad, India) -Makri, Nancy (Urbana, USA) -Manthe, Uwe (Garching, Germany) -Martens, Craig (Irvine, USA) -Martinez, Todd (Urbana, USA) -Meyer, Hans-Dieter (Heidelberg, Germany) -Nakamura, Hiroki (Okazaki, Japan) -Miller, William H. (Berkeley, USA) -Takatsuka, Kazuo (Tokyo, Japan) -Thoss, Michael (Garching, Germany) -Worth, Graham (London, England) -Zhang, John Z. H. (New York, USA) From chemistry-request@server.ccl.net Tue Mar 18 09:27:41 2003 Received: from evans.univer.kharkov.ua ([80.92.225.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2IERaw22261 for ; Tue, 18 Mar 2003 09:27:39 -0500 Received: from spin.univer.kharkov.ua (spin.univer.kharkov.ua [192.168.213.252]) by evans.univer.kharkov.ua (8.12.6/8.12.5) with SMTP id h2IERUfS003098 for ; Tue, 18 Mar 2003 16:27:31 +0200 Received: by spin.univer.kharkov.ua with Microsoft Mail id <01C2ED6A.AC4CDD30@spin.univer.kharkov.ua>; Tue, 18 Mar 2003 16:23:13 +0200 Message-ID: <01C2ED6A.AC4CDD30@spin.univer.kharkov.ua> From: "sergey i. kotelevskii" To: "'CCL community'" Subject: Correlation Consistency for Li, Be Date: Tue, 18 Mar 2003 16:23:11 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h2IERfw22265 Dear All, Could anyone help me with a sort of Correlation Consistent Basis Sets for light metal atoms, Li and/or Be? As far as I know, there were no cc-pVNz for these atoms until recently. And, if they are still absent, what sort of basis is best suited to perform optimizations of (Li,H,C,N,O) molecules at MP4, QCISD, or CCSD level? Any suggestions are welcome. Thank you. Serghey ************************************************************************************************* Serghey I. Kotelevskii, Department of Theoretical Chemistry and Astrochemistry, Research Institute for Chemistry, Kharkiv VNKarazin National University, Svobody Square 4, UA-61077 Kharkiv, UKRAINE E-mail: kotelevskiy@univer.kharkov.ua From owner-chemisstry@ccl.net Wed Mar 19 12:56:00 2003 -0500 Return-Path: Message-ID: <1048096423.3e78aea75c3f0@webmail.portugalmail.pt> Date: Wed, 19 Mar 2003 17:53:43 +0000 From: nelson_fonseca@portugalmail.pt To: CCL Subject: Force Field for Macrocycle Ligands Dear all I would like to know if there are any Force Field specialy optimized for modelling Macrocycle Ligands, and where can I get it. Best regards __________________________________________________________ O email preferido dos portugueses agora com 100Mb de espaço e acesso gratuito à Internet http://www.portugalmail.com/gold/