From chemistry-request@server.ccl.net Sat May 4 00:05:26 2002 Received: from smtpout.mac.com ([204.179.120.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4445PI11322 for ; Sat, 4 May 2002 00:05:25 -0400 Received: from smtp-relay02.mac.com (smtp-relay02-qfe3 [10.13.10.225]) by smtpout.mac.com (8.12.1/8.10.2/1.0) with ESMTP id g4445IW5026429 for ; Fri, 3 May 2002 21:05:19 -0700 (PDT) Received: from asmtp02.mac.com ([10.13.10.66]) by smtp-relay02.mac.com (Netscape Messaging Server 4.15 relay02 Jun 21 2001 23:53:48) with ESMTP id GVKJCP00.727 for ; Fri, 3 May 2002 21:05:13 -0700 Received: from [10.10.130.81] ([142.165.215.236]) by asmtp02.mac.com (Netscape Messaging Server 4.15 asmtp02 Jun 21 2001 23:53:48) with ESMTP id GVKJCP00.R4E for ; Fri, 3 May 2002 21:05:13 -0700 User-Agent: Microsoft-Entourage/10.0.0.1331 Date: Fri, 03 May 2002 22:05:20 -0600 Subject: NMRPipe - Mac OS X From: "H. Martin Gillis" To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, I am curious if anyone has installed NMRPipe on a Mac running OS X. Currently, I have having troubles, but I fear this is simply my lack of understanding the unix realm. If anyone has any helpful comments, I would be very grateful. Thanks in advance, -Martin From chemistry-request@server.ccl.net Sat May 4 06:16:17 2002 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g44AGGI29189 for ; Sat, 4 May 2002 06:16:16 -0400 Received: from PC18 ([202.127.19.225]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id g451Gt5A027181 for ; Sat, 4 May 2002 18:16:55 -0700 (PDT) Message-Id: <200205050116.g451Gt5A027181@mail.shcnc.AC.CN> Date: Sat, 4 May 2002 18:13:24 +0800 From: bxiong To: "chemistry@ccl.net" Subject: how to change background color of SYBYl? X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCL: I want to export a graph from a SYBYL, but the background is black. How can I change the color of background from black to white? Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) From chemistry-request@server.ccl.net Sat May 4 01:35:00 2002 Received: from hotmail.com ([64.4.23.38]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g445Z0I15716 for ; Sat, 4 May 2002 01:35:00 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 3 May 2002 22:34:55 -0700 Received: from 66.31.55.25 by lw15fd.law15.hotmail.msn.com with HTTP; Sat, 04 May 2002 05:34:54 GMT X-Originating-IP: [66.31.55.25] From: "Cameron Banks" To: chemistry@ccl.net Subject: Evaluation of MO's from ab-initio calculations Date: Sat, 04 May 2002 01:34:54 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 04 May 2002 05:34:55.0203 (UTC) FILETIME=[6BE06330:01C1F32D] I'm looking for some code that I can use to compute orbital and density values on a grid from ab-initio (Gaussian/Gamess) calculations. I'm aware of the MOLDEN code but this is not suitable for my purpose. What I'm really after is a Gaussian CUBEGEN like program that I can use like a library. Alternatively if someone can point me to some literature I can probably cook something up. Thanks. Cameron _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp. From chemistry-request@server.ccl.net Sat May 4 01:56:25 2002 Received: from vnuserv.vnuhcm.edu.vn ([203.162.44.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g445uKI17042 for ; Sat, 4 May 2002 01:56:21 -0400 Received: from Services.hcmuns.edu.vn (Services.hcmuns.edu.vn [172.29.16.4]) by vnuserv.vnuhcm.edu.vn (8.9.3/8.8.7) with SMTP id TAA03768; Sat, 4 May 2002 19:56:39 GMT Received: from Server.vnuhcm.edu.vn. by VNU-Gateway with ESMTP Ver (1.1Plus) for recipient addresses : Received: from chemdep.hcmuns.edu.vn (IDENT:root@chemdep.hcmuns.edu.vn [172.29.2.202]) by Services.hcmuns.edu.vn (8.11.2/8.11.2) with ESMTP id g445Xt310938 for ; Sat, 4 May 2002 12:33:55 +0700 Received: from chem5 ([172.29.2.210]) by chemdep.hcmuns.edu.vn (8.9.3/8.9.3) with SMTP id MAA06002 for ; Sat, 4 May 2002 12:27:08 -0700 Message-ID: <001b01c1f4c3$c054af60$d2021dac@chem.hcmuns.edu.vn> From: "dangkhoa" To: Subject: Transition structure Date: Mon, 6 May 2002 13:03:31 +0700 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0017_01C1F4FE.6C2D1950" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0017_01C1F4FE.6C2D1950 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0018_01C1F4FE.6C2D1950" ------=_NextPart_001_0018_01C1F4FE.6C2D1950 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Dear =20 I'm dangkhoa Truong , student of chemistry department of natural = sciences university in Ho Chi Minh city. I'm a new in computational = chemistry. I trying to explore about transition state of reaction = reduction of the succinimide by borohydrure(NaBH4). I don't understand = about geometry of transition structure . Can you help me. thankyou very much.=20 Best regard. =20 ------=_NextPart_001_0018_01C1F4FE.6C2D1950 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
       =
       Dear   =    =20
    I'm dangkhoa Truong ,=20 student of chemistry department of  natural sciences university in = Ho Chi=20 Minh city. I'm a new in computational chemistry. I trying=20 to explore about transition state of reaction  reduction = of the=20 succinimide by borohydrure(NaBH4). I don't understand = about geometry of=20 transition structure . Can you help me.
  thankyou very = much. 
  Best regard. =20
------=_NextPart_001_0018_01C1F4FE.6C2D1950-- ------=_NextPart_000_0017_01C1F4FE.6C2D1950 Content-Type: application/octet-stream; name="reactant.ent" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="reactant.ent" HETATM 1 O 1 3.823 1.016 0.188 HETATM 2 C 2 0.488 -0.250 0.204 HETATM 3 C 3 0.488 1.270 0.204 HETATM 4 C 4 1.995 -0.575 0.204 HETATM 5 C 5 2.620 0.811 0.196 HETATM 6 N 6 1.710 1.764 0.198 HETATM 7 O 7 -0.524 1.952 0.209 HETATM 8 H 8 2.277 -1.142 -0.683 HETATM 9 H 9 2.279 -1.132 1.096 HETATM 10 H 10 1.923 2.752 0.195 HETATM 11 C 11 -0.195 -0.802 1.445 HETATM 12 C 12 -0.195 -0.802 -1.037 HETATM 13 C 13 -0.722 0.074 -1.994 HETATM 14 C 14 -0.298 -2.186 -1.223 HETATM 15 C 15 -1.350 -0.434 -3.137 HETATM 16 C 16 -0.926 -2.693 -2.367 HETATM 17 C 17 -1.453 -1.818 -3.323 HETATM 18 C 18 -0.722 0.074 2.402 HETATM 19 C 19 -0.298 -2.186 1.631 HETATM 20 C 20 -0.926 -2.693 2.774 HETATM 21 C 21 -1.350 -0.434 3.545 HETATM 22 C 22 -1.453 -1.818 3.731 HETATM 23 H 23 -0.643 1.142 -1.851 HETATM 24 H 24 0.109 -2.861 -0.485 HETATM 25 H 25 -1.756 0.242 -3.875 HETATM 26 H 26 -1.005 -3.761 -2.510 HETATM 27 H 27 -1.938 -2.209 -4.205 HETATM 28 H 28 -0.643 1.142 2.258 HETATM 29 H 29 0.109 -2.861 0.893 HETATM 30 H 30 -1.005 -3.761 2.918 HETATM 31 H 31 -1.756 0.242 4.283 HETATM 32 H 32 -1.938 -2.209 4.613 CONECT 1 5 CONECT 2 3 4 11 12 CONECT 3 2 6 7 CONECT 4 2 5 8 9 CONECT 5 1 4 6 CONECT 6 3 5 10 CONECT 7 3 CONECT 8 4 CONECT 9 4 CONECT 10 6 CONECT 11 2 18 19 CONECT 12 2 13 14 CONECT 13 12 15 23 CONECT 14 12 16 24 CONECT 15 13 17 25 CONECT 16 14 17 26 CONECT 17 15 16 27 CONECT 18 11 21 28 CONECT 19 11 20 29 CONECT 20 19 22 30 CONECT 21 18 22 31 CONECT 22 20 21 32 CONECT 23 13 CONECT 24 14 CONECT 25 15 CONECT 26 16 CONECT 27 17 CONECT 28 18 CONECT 29 19 CONECT 30 20 CONECT 31 21 CONECT 32 22 END ------=_NextPart_000_0017_01C1F4FE.6C2D1950 Content-Type: application/octet-stream; name="principal product.ent" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="principal product.ent" HETATM 1 C 1 0.548 -0.433 0.375 HETATM 2 C 2 0.548 1.110 0.375 HETATM 3 C 3 2.043 -0.805 0.375 HETATM 4 C 4 2.678 0.433 -0.229 HETATM 5 N 5 1.846 1.454 -0.224 HETATM 6 H 6 2.232 -1.686 -0.238 HETATM 7 H 7 2.407 -0.982 1.387 HETATM 8 H 8 2.073 2.368 -0.589 HETATM 9 C 9 -0.144 -0.974 1.616 HETATM 10 C 10 -0.144 -0.974 -0.866 HETATM 11 C 11 -0.672 -0.089 -1.814 HETATM 12 C 12 -0.252 -2.356 -1.061 HETATM 13 C 13 -1.309 -0.587 -2.957 HETATM 14 C 14 -0.889 -2.854 -2.204 HETATM 15 C 15 -1.417 -1.969 -3.152 HETATM 16 C 16 -0.672 -0.089 2.565 HETATM 17 C 17 -0.252 -2.356 1.811 HETATM 18 C 18 -0.889 -2.854 2.954 HETATM 19 C 19 -1.309 -0.587 3.708 HETATM 20 C 20 -1.417 -1.969 3.903 HETATM 21 H 21 -0.588 0.977 -1.664 HETATM 22 H 22 0.155 -3.038 -0.329 HETATM 23 H 23 -1.716 0.095 -3.689 HETATM 24 H 24 -0.973 -3.920 -2.354 HETATM 25 H 25 -1.909 -2.353 -4.034 HETATM 26 H 26 -0.588 0.977 2.414 HETATM 27 H 27 0.155 -3.038 1.080 HETATM 28 H 28 -0.973 -3.920 3.105 HETATM 29 H 29 -1.716 0.095 4.439 HETATM 30 H 30 -1.909 -2.353 4.784 HETATM 31 O 31 0.448 1.622 1.707 HETATM 32 O 32 3.817 0.478 -0.665 HETATM 33 H 33 -0.274 1.500 -0.226 HETATM 34 H 34 0.450 2.581 1.683 CONECT 1 2 3 9 10 CONECT 2 1 5 31 33 CONECT 3 1 4 6 7 CONECT 4 3 5 32 CONECT 5 2 4 8 CONECT 6 3 CONECT 7 3 CONECT 8 5 CONECT 9 1 16 17 CONECT 10 1 11 12 CONECT 11 10 13 21 CONECT 12 10 14 22 CONECT 13 11 15 23 CONECT 14 12 15 24 CONECT 15 13 14 25 CONECT 16 9 19 26 CONECT 17 9 18 27 CONECT 18 17 20 28 CONECT 19 16 20 29 CONECT 20 18 19 30 CONECT 21 11 CONECT 22 12 CONECT 23 13 CONECT 24 14 CONECT 25 15 CONECT 26 16 CONECT 27 17 CONECT 28 18 CONECT 29 19 CONECT 30 20 CONECT 31 2 34 CONECT 32 4 CONECT 33 2 CONECT 34 31 END ------=_NextPart_000_0017_01C1F4FE.6C2D1950 Content-Type: application/octet-stream; name="secondary product.ent" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="secondary product.ent" HETATM 1 O 1 -1.175 2.245 -1.622 HETATM 2 C 2 0.335 -0.144 -0.131 HETATM 3 C 3 0.952 1.111 0.458 HETATM 4 C 4 0.213 0.225 -1.622 HETATM 5 C 5 0.174 1.768 -1.622 HETATM 6 N 6 0.859 2.130 -0.372 HETATM 7 O 7 1.470 1.170 1.561 HETATM 8 H 8 -0.702 -0.186 -2.049 HETATM 9 H 9 1.073 -0.141 -2.184 HETATM 10 H 10 1.217 3.053 -0.173 HETATM 11 C 11 1.241 -1.349 0.068 HETATM 12 C 12 -1.027 -0.428 0.481 HETATM 13 C 13 -1.549 0.430 1.457 HETATM 14 C 14 -1.760 -1.547 0.068 HETATM 15 C 15 -2.803 0.168 2.020 HETATM 16 C 16 -3.015 -1.808 0.631 HETATM 17 C 17 -3.536 -0.951 1.607 HETATM 18 C 18 2.468 -1.201 0.725 HETATM 19 C 19 0.847 -2.605 -0.407 HETATM 20 C 20 1.681 -3.715 -0.225 HETATM 21 C 21 3.302 -2.311 0.907 HETATM 22 C 22 2.909 -3.568 0.433 HETATM 23 H 23 -0.983 1.293 1.776 HETATM 24 H 24 -1.358 -2.208 -0.685 HETATM 25 H 25 -3.206 0.829 2.773 HETATM 26 H 26 -3.580 -2.672 0.313 HETATM 27 H 27 -4.504 -1.153 2.042 HETATM 28 H 28 2.771 -0.232 1.091 HETATM 29 H 29 -0.099 -2.719 -0.914 HETATM 30 H 30 1.378 -4.685 -0.591 HETATM 31 H 31 4.249 -2.197 1.414 HETATM 32 H 32 3.552 -4.424 0.573 HETATM 33 H 33 -1.175 3.205 -1.622 HETATM 34 H 34 0.702 2.171 -2.486 CONECT 1 5 33 CONECT 2 3 4 11 12 CONECT 3 2 6 7 CONECT 4 2 5 8 9 CONECT 5 1 4 6 34 CONECT 6 3 5 10 CONECT 7 3 CONECT 8 4 CONECT 9 4 CONECT 10 6 CONECT 11 2 18 19 CONECT 12 2 13 14 CONECT 13 12 15 23 CONECT 14 12 16 24 CONECT 15 13 17 25 CONECT 16 14 17 26 CONECT 17 15 16 27 CONECT 18 11 21 28 CONECT 19 11 20 29 CONECT 20 19 22 30 CONECT 21 18 22 31 CONECT 22 20 21 32 CONECT 23 13 CONECT 24 14 CONECT 25 15 CONECT 26 16 CONECT 27 17 CONECT 28 18 CONECT 29 19 CONECT 30 20 CONECT 31 21 CONECT 32 22 CONECT 33 1 CONECT 34 5 END ------=_NextPart_000_0017_01C1F4FE.6C2D1950-- From chemistry-request@server.ccl.net Sat May 4 18:38:55 2002 Received: from mail.rochester.edu (root@[128.151.224.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g44MctI19083 for ; Sat, 4 May 2002 18:38:55 -0400 Received: from wei (vpn1-1.utd.rochester.edu [128.151.103.1]) by mail.rochester.edu (8.12.1/8.12.1) with SMTP id g44McJAF7845918 for ; Sat, 4 May 2002 18:38:20 -0400 (EDT) Message-Id: <200205042238.g44McJAF7845918@mail.rochester.edu> Date: Sat, 4 May 2002 18:38:35 -0500 From: wei zhuang To: "chemistry@ccl.net" Subject: help about opls_aa force field X-mailer: FoxMail 3.11 Release [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit X-Filter-Version: 1.7 (mail1) Dear friends: I would like to use opls_aa force field to simulate a system that one HCl molecule soaked in glycol solvent molecules.my question is if I choose Cl-, how can I choose H. since there is no H+. can I choose HW(H on TIP3P, TIP4P or TIP5P water )? I guess I have to choose a H( with a positive charge)to keep the system neutral,right? regards wei zhuang From chemistry-request@server.ccl.net Sat May 4 20:37:07 2002 Received: from rwcrmhc52.attbi.com ([216.148.227.88]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g450b3I25081 for ; Sat, 4 May 2002 20:37:06 -0400 Received: from C1353359A ([12.228.119.53]) by rwcrmhc52.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020505003658.FZJJ4412.rwcrmhc52.attbi.com@C1353359A>; Sun, 5 May 2002 00:36:58 +0000 Reply-To: From: "Mark Thompson" To: "Cameron Banks" , Subject: RE: Evaluation of MO's from ab-initio calculations Date: Sat, 4 May 2002 17:41:47 -0700 Message-ID: <000001c1f3cd$a373e010$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Cameron, If you subsequently want to view surfaces derived from the grids you generate, you might try ArgusLab (www.arguslab.com) It handles both gaussian output files and cube files. See http://www.arguslab.com/gallery.htm for some examples. Cheers, Mark ================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA. http://www.arguslab.com ================================= > > I'm looking for some code that I can use to compute orbital and density > values on a grid from ab-initio (Gaussian/Gamess) calculations. > I'm aware > of the MOLDEN code but this is not suitable for my purpose. What > I'm really > after is a Gaussian CUBEGEN like program that I can use like a library. > > Alternatively if someone can point me to some literature I can > probably cook > something up. > > Thanks. > > Cameron > From chemistry-request@server.ccl.net Sat May 4 21:29:43 2002 Received: from donkeykong.gpcc.itd.umich.edu (smtp@[141.211.2.163]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g451ThI27536 for ; Sat, 4 May 2002 21:29:43 -0400 Received: from rastan.gpcc.itd.umich.edu (rastan.gpcc.itd.umich.edu [141.211.2.215]) by donkeykong.gpcc.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id VAA22058 for ; Sat, 4 May 2002 21:29:43 -0400 (EDT) Received: from localhost (brupalf@localhost) by rastan.gpcc.itd.umich.edu (8.9.1a/5.1-client) with ESMTP id VAA13838 for ; Sat, 4 May 2002 21:29:43 -0400 (EDT) Precedence: first-class Date: Sat, 4 May 2002 21:29:43 -0400 (EDT) From: Bruce Allan Palfey X-X-Sender: brupalf@rastan.gpcc.itd.umich.edu To: CHEMISTRY@ccl.net Subject: amides in AM1/GAMESS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi I want to minimize some structures containing amides at the AM1 level using GAMESS. I know that in MOPAC the MMOK keyword is necessary in order to properly treat amides. Is there a corresponding keyword to apply a molecular mechanics correction in GAMESS, or is the correction applied automatically? ciao, Bruce Palfey Department of Biological Chemistry University of Michigan Ann Arbor, MI 48109-0606