From chemistry-request@server.ccl.net Thu Oct 19 16:08:37 2000 Received: from dns2.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05309 for ; Thu, 19 Oct 2000 16:08:36 -0400 Received: from biggeek (dialup-63.214.10.154.Seattle1.Level3.net [63.214.10.154]) by dns2.seanet.com (8.9.3/8.9.0) with SMTP id NAA27944 for ; Thu, 19 Oct 2000 13:08:35 -0700 (PDT) Message-ID: <00b801c03a07$b8dcbcf0$01808080@biggeek> From: "Mark A. Thompson" To: Subject: ArgusLab 2.0: now includes a Molecule Builder Date: Thu, 19 Oct 2000 13:03:59 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00B5_01C039CD.0B8AAB50" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_00B5_01C039CD.0B8AAB50 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable ArgusLab 2.0 beta1 is available for download. http://www.seanet.com/~mthompson/ArgusLab ArgusLab is a molecular modeling program for Microsoft Windows operating = systems. Overview of 2.0 features: ----------------------------- 1. Interactive 3D Molecule Builder with: Interactive 3D manipulator Fragment Library Beautify Geometry Automatically Add/Hide/Delete Hydrogens Cut & Paste Supports Multiple-Level Undo/Redo. Multiple Rendering Styles for Atoms and Bonds Geometry Monitors 2. Calculation Types Single-Point Energies Optimize Geometries Electronic Excitation Spectra Self Consistent Reaction Field (SCRF) Solvent Model for = Electronic Spectra 3. Molecular Mechanics=20 Universal Force Field (UFF) for the entire periodic table 4. Quantum Mechanics Extended Huckel for entire periodic table MNDO, AM1, and PM3 semi-empirical Hamiltonians INDO1/s semi-empirical Hamiltonian Restricted and Unrestricted Hartree-Fock SCF 5. File Types: supports XYZ, PDB, and ArgusLab XML file formats. 6. HTML Help 7. No size limitations for molecules or calculations other than = available system resources 8. Multi-threaded architecture allows multiple molecules opened = simultaneously and running calculations 9. Runs on Windows 95/98, Windows NT 4.0, Windows 2000 ------=_NextPart_000_00B5_01C039CD.0B8AAB50 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

ArgusLab 2.0 beta1 is = available for=20 download.

http://www.seanet.com/= ~mthompson/ArgusLab

ArgusLab is a molecular = modeling program=20 for Microsoft Windows operating systems.

Overview of 2.0 = features:

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

1. Interactive 3D Molecule = Builder=20 with:
        Interactive 3D=20 manipulator
        Fragment=20 Library
        Beautify=20 Geometry
        Automatically = Add/Hide/Delete=20 Hydrogens
        Cut &=20 Paste
        Supports Multiple-Level=20 Undo/Redo.
        Multiple Rendering = Styles=20 for Atoms and Bonds
        Geometry=20 Monitors

2. Calculation=20 Types
        Single-Point=20 Energies
        Optimize=20 Geometries
        Electronic = Excitation=20 Spectra
        Self Consistent = Reaction Field=20 (SCRF) Solvent Model for Electronic Spectra

3. Molecular=20 Mechanics
Universal Force = Field=20 (UFF) for the entire periodic table

4. Quantum=20 Mechanics
        Extended Huckel for = entire=20 periodic table
        MNDO, AM1, and = PM3=20 semi-empirical Hamiltonians
        = INDO1/s=20 semi-empirical Hamiltonian
        = Restricted=20 and Unrestricted Hartree-Fock SCF

5. File Types: supports XYZ, = PDB, and=20 ArgusLab XML file formats.

6. HTML Help

7. No size limitations for = molecules or=20 calculations other than available system resources

8. Multi-threaded = architecture allows=20 multiple molecules opened simultaneously and running=20 calculations

9. Runs on Windows 95/98, = Windows NT 4.0,=20 Windows 2000

------=_NextPart_000_00B5_01C039CD.0B8AAB50-- From chemistry-request@server.ccl.net Thu Oct 19 16:22:09 2000 Received: from dagger.nd.edu (dagger.nd.edu [129.74.250.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05368 for ; Thu, 19 Oct 2000 16:22:09 -0400 Received: from nd.edu (ruthenium.helios.nd.edu [129.74.220.44]) by dagger.nd.edu (8.10.2/8.10.2) with ESMTP id e9JKM8113781 for ; Thu, 19 Oct 2000 15:22:08 -0500 (EST) Sender: ptran@nd.edu Message-ID: <39EF57F1.673117E8@nd.edu> Date: Thu, 19 Oct 2000 15:22:09 -0500 From: Pierre Tran X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: format problem Content-Type: multipart/alternative; boundary="------------11D753D5C6D6CFF85D2807BF" --------------11D753D5C6D6CFF85D2807BF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, Is there a way to "map the atoms" of a pdb file of a crystal structure taken from Brookhaven data bank and use it in InsightII and perform minimization on it. The program complained and did not recognise the structure, here is the error message, when I tried to attribute the potentials : error: CRO:U8:C5' has open or undefined valences error: CRO:U8:C4' has open or undefined valences error: CRO:U8:C3' has open or undefined valences error: CRO:U8:O3' has open or undefined valences error: CRO:U8:C2' has open or undefined valences error: CRO:U8:C1' has open or undefined valences error: CRO:U8:N4 has open or undefined valences I need a program which allows the protonation of the structure and make it recognised by insightII and use it to perform minimization. Thank you. -- Pierre TRAN --------------11D753D5C6D6CFF85D2807BF Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all,

Is there a way to "map the atoms" of a pdb file of a crystal structure taken from Brookhaven data bank and use it in InsightII and perform minimization on it.
The program complained and did not recognise the structure, here is the error message, when I tried to attribute the potentials :

error: CRO:U8:C5' has open or undefined valences
error: CRO:U8:C4' has open or undefined valences
error: CRO:U8:C3' has open or undefined valences
error: CRO:U8:O3' has open or undefined valences
error: CRO:U8:C2' has open or undefined valences
error: CRO:U8:C1' has open or undefined valences
error: CRO:U8:N4 has open or undefined valences

I need a program which allows the protonation of the structure and make it recognised by insightII and use it to perform minimization.

Thank you.

-- 
Pierre TRAN

--------------11D753D5C6D6CFF85D2807BF-- From chemistry-request@server.ccl.net Fri Oct 20 15:27:27 2000 Received: from post2.inre.asu.edu (post2.inre.asu.edu [129.219.110.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA11357 for ; Fri, 20 Oct 2000 15:27:27 -0400 Received: from conversion.post2.inre.asu.edu by asu.edu (PMDF V6.0-24 #47347) id <0G2Q00E01TQ1JX@asu.edu> for CHEMISTRY@ccl.net; Fri, 20 Oct 2000 12:20:25 -0700 (MST) Received: from smtp.asu.edu (smtp.asu.edu [129.219.13.92]) by asu.edu (PMDF V6.0-24 #47347) with ESMTP id <0G2Q00E2LTQ1F3@asu.edu> for CHEMISTRY@ccl.net; Fri, 20 Oct 2000 12:20:25 -0700 (MST) Received: from samwise.asu.edu (samwise.eas.asu.edu [149.169.26.89]) by smtp.asu.edu (8.9.3/8.9.3) with ESMTP id MAA18547 for ; Fri, 20 Oct 2000 12:20:25 -0700 (MST) Date: Fri, 20 Oct 2000 12:23:00 -0700 From: "Benjamin J. Moritz" Subject: Z-Matrix Software X-Sender: bmoritz@imap4.asu.edu To: CHEMISTRY@ccl.net Message-id: <5.0.0.25.0.20001020122140.00a5b940@imap4.asu.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.0 Content-type: multipart/alternative; boundary="Boundary_(ID_k3QA1vImrxJN/EHH6ZRCuQ)" --Boundary_(ID_k3QA1vImrxJN/EHH6ZRCuQ) Content-type: text/plain; charset="us-ascii"; format=flowed Hi Everyone, I was wondering if anyone new of some freeware programs that will draw and save structures in the Z-matrix format. Thanks in advanced. **************************************************************** Benjamin J. Moritz home (602) 453-9411 Dept. of Chemistry & Biochemistry work (480) 965-8509 Arizona State University Mailto:bmoritz@asu.edu P. O. Box 871604 Tempe, AZ 85287-1604 **************************************************************** "Karma is justice without the satisfaction." --Boundary_(ID_k3QA1vImrxJN/EHH6ZRCuQ) Content-type: text/html; charset="us-ascii" Hi Everyone,

I was wondering if anyone new of some freeware programs that will draw and save structures in the Z-matrix format. Thanks in advanced.

****************************************************************
Benjamin J. Moritz                                       home (602) 453-9411
Dept. of Chemistry & Biochemistry                 work (480) 965-8509
Arizona State University                                Mailto:bmoritz@asu.edu
P. O. Box 871604
Tempe, AZ 85287-1604
****************************************************************

"Karma is justice without the satisfaction."
--Boundary_(ID_k3QA1vImrxJN/EHH6ZRCuQ)--