From chemistry-request@ccl.net Tue Jun 15 07:01:48 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5FC1lCj030058 for ; Tue, 15 Jun 2004 07:01:47 -0500 Received: from cornell.edu (67-42-28-75.slkc.qwest.net [67.42.28.75]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i5FC5nTT019004; Tue, 15 Jun 2004 08:06:06 -0400 (EDT) Message-ID: <40CEE61C.9070002..at..cornell.edu> Date: Tue, 15 Jun 2004 06:05:48 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry..at..ccl.net" Subject: converting a -CH3 to a C(CH3)3 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.5.0.92886, Antispam-Core: 4.0.4.93542, Antispam-Data: 2004.6.14.103686 X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS, TO_ADDRESS_EQ_REAL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all This a synthesis question. I've done some computations and converted a methyl group into a t-butyl group with no problem. My question is how can a methyl group be converted synthetically into a t-butyl group? If anyone out there knows how, including reagents, conditions etc. please let me know. Thank you in advance, Richard -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 From chemistry-request@ccl.net Tue Jun 15 08:48:17 2004 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5FDmGvV002636 for ; Tue, 15 Jun 2004 08:48:16 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id i5FDqXjX026338; Tue, 15 Jun 2004 09:52:37 -0400 (EDT) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SAVSMTP 3.1.5.43) with SMTP id M2004061509523608898 ; Tue, 15 Jun 2004 09:52:36 -0400 Received: from sparky.ic.sunysb.edu (sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.10/8.12.10) with ESMTP id i5FDqa7Q026360; Tue, 15 Jun 2004 09:52:36 -0400 (EDT) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id i5FDqYdp019490; Tue, 15 Jun 2004 09:52:36 -0400 (EDT) Date: Tue, 15 Jun 2004 09:52:34 -0400 (EDT) From: Yong Liang Yang To: chemistry|at|ccl.net cc: yonyang|at|ic.sunysb.edu Subject: Prepare the system for Autodock job Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCl users: I am a newbie to Autodock and I want to know if we can prepare a system for Autodock job without using InsightII or Sybyl. Because both of them are commercial and I do not have access to them. I have read a notes about using InsightII to prepare system for Autodock job such as measuring the dimension of the grid or coordinates of ligand pesudo atoms. I have access to ADT but I am not sure ADT can do the same job. Any response will be highly appreciated! I also send this message to ADL list, and I will try to summarize the responses here. Thanks in advance. Cheers From chemistry-request@ccl.net Tue Jun 15 08:08:18 2004 Received: from web60905.mail.yahoo.com (web60905.mail.yahoo.com [216.155.196.81]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5FD8FCj000496 for ; Tue, 15 Jun 2004 08:08:16 -0500 Message-ID: <20040615131236.84787.qmail_at_web60905.mail.yahoo.com> Received: from [195.251.7.66] by web60905.mail.yahoo.com via HTTP; Tue, 15 Jun 2004 14:12:36 BST Date: Tue, 15 Jun 2004 14:12:36 +0100 (BST) From: =?iso-8859-7?q?Aggelos=20Avramopoulos?= Subject: Zinc Cluster;Bonding and NLO Properties To: CHEMISTRY_at_ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1843324867-1087305156=:84436" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1843324867-1087305156=:84436 Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 8bit Hi to everyone Iam currently interested in studing the Bonding, structure and Non Linear Properties of Zn(N) Clusters N=1-20. I have two articles which describe the nature of bonding in Zn(N) N=1-20 but i would like to know if there is something more on Bonding and on NLO properties of these structures as well. Is there anyone who is getting involved on these topics and could offer literature survey to me. Thanks in advance for every help Aggelos Avramopoulos PHD --------------------------------- Do You Yahoo!? Apojt^ste tgm dyqe\m sar_at_yahoo.gr die}humsg sto Yahoo! Mail. --0-1843324867-1087305156=:84436 Content-Type: text/html; charset=iso-8859-7 Content-Transfer-Encoding: 8bit
Hi to everyone
 
Iam currently interested in studing the Bonding, structure and Non Linear
Properties of Zn(N) Clusters N=1-20. I have two articles which describe
the nature of bonding in Zn(N) N=1-20 but i would like to know if there is
something more on Bonding and on  NLO properties  of these structures as well.  Is there anyone who is getting involved on these topics and could offer literature survey to me.
 
Thanks in advance for every help
 
Aggelos Avramopoulos PHD  


Do You Yahoo!?
Apojt^ste tgm dyqe\m sar @yahoo.gr die}humsg sto Yahoo! Mail.
--0-1843324867-1087305156=:84436-- From chemistry-request@ccl.net Mon Jun 14 08:57:22 2004 Received: from vsmtp2.tin.it (vsmtp2alice.tin.it [212.216.176.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5EDvGmP028156 for ; Mon, 14 Jun 2004 08:57:19 -0500 Received: from ims1b.cp.tin.it (192.168.70.101) by vsmtp2.tin.it (7.0.027) id 40A2519100443AAF for chemistry:at:ccl.net; Mon, 14 Jun 2004 16:01:30 +0200 Received: from [192.168.70.227] by ims1b.cp.tin.it with HTTP; Mon, 14 Jun 2004 16:01:28 +0200 Date: Mon, 14 Jun 2004 16:01:28 +0200 Message-ID: <40BFCED00000F4EF:at:ims1b.cp.tin.it> From: sa.cosco:at:virgilio.it Subject: Problems with autodock To: "CCL" MIME-Version: 1.0 X-Priority: 1 (Highest) Content-Type: multipart/mixed; boundary="========/40BFCED00000F4EF/ims1b.cp.tin.it" X-Spam-Status: No, hits=3.5 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME, PRIORITY_NO_NAME,X_PRIORITY_HIGH autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --========/40BFCED00000F4EF/ims1b.cp.tin.it Content-Type: text/plain; charset="ISO-8859-15" Content-Transfer-Encoding: quoted-printable Dear CCL I've been usin autodock for plenty of time. At the moment I'm trying to create a .gpf file on a SGI machine and it seems that the program doesn't= assign the right paramaters (all the parameters are set to 0). I tryed to= change the receptor and the ligand but everything went the same. Moreover= , the same ligand and receptor does not give any problems on other machine.= Maybe is a problem of configuration even if I've always run autodock on this machine. I'm attatching the .gpf file to see if you can help me to solve my problem. 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Mon, 14 Jun 2004 10:52:25 -0500 Received: from [165.91.177.61] (HELO yubopclab) by mail.chem.tamu.edu (CommuniGate Pro SMTP 4.1.8) with SMTP id 1723305 for CHEMISTRY)at(ccl.net; Mon, 14 Jun 2004 10:56:40 -0500 Message-ID: <001101c45228$257dfe00$3db15ba5@yubopclab> From: "Yubo Fan" To: Subject: Spin-Spin coupling of NMR Date: Mon, 14 Jun 2004 10:56:24 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C451FE.3C603EA0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C451FE.3C603EA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I've done the NMR calculation with SpinSpin option for propene. The = chemical shifts of the Hs on methyl are slightly different, and the = coupling constants including them are also different. My question is how = I can average them. Namely, how can I compare those values with the = experiment. Thanks in advance. Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=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. Yubo Fan Email: yubofan)at(mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_000E_01C451FE.3C603EA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
 
I've done the NMR calculation with = SpinSpin option=20 for propene. The chemical shifts of the Hs on methyl are slightly = different, and=20 the coupling constants including them are also different. My question is = how I=20 can average them. Namely, how can I compare those values with the = experiment.=20 Thanks in advance.
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=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. Yubo=20 Fan           &nbs= p;  =20 Email: yubofan)at(mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-7222
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_000E_01C451FE.3C603EA0-- From chemistry-request@ccl.net Mon Jun 14 23:20:36 2004 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5F4KYgu005142 for ; Mon, 14 Jun 2004 23:20:35 -0500 Received: from yangtze.hku.hk (yangtze.hku.hk [127.0.0.1]) by yangtze.hku.hk (8.12.8/8.12.8) with ESMTP id i5F4CguT031164 for ; Tue, 15 Jun 2004 12:12:42 +0800 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.12.8/8.12.8/Submit) with ESMTP id i5F4CgpT031160 for ; Tue, 15 Jun 2004 12:12:42 +0800 Date: Tue, 15 Jun 2004 12:12:41 +0800 (HKT) From: HU lihong To: chemistry)at(ccl.net Subject: CHARMM QM/MM question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am trying to calculate a biomolecule using QM/MM in c29b2, I need at least 3 link atoms. I don't know if it is ok with multiple link atoms since all of the examples only have one link atom. My calculation could be run but if I use the keyword energy which try to print the energy with QM calculation, it would be failed by segametational fault. Is that because my QM atoms are too much or the script what I wrote is not ok? This is the QM/MM calcultion script in my calculation ------------------------------------------------------------------------------------- nbonds - atom shift vswitch eps 1.0 - cutnb 999.0 ctofnb 998.0 ctonnb 997.0 e14fac 1.0 addl qqh1 pwdm A48 c pwdm A48 c addl qqh2 pwdf A111 c pwdf A111 c addl qqh3 pwdl A300 c pwdl A300 c defind qmset sele segi pwdm .or. segi pwdf .or. segi pwdl end quan sele qmset end am1 --------------------------------------------------------------------------------------- And I want to know if it is all right that I just give the parameters for qqh atom like the example files. If it is not right, where I can find the correct parameters. Or can I find a more complex example of QM/MM than examples? I'll appreciate your any kind help, Yours sincerely, Holly From chemistry-request@ccl.net Mon Jun 14 08:40:50 2004 Received: from hotmail.com (bay22-dav6.bay22.hotmail.com [64.4.16.186]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5EDedmP027790 for ; Mon, 14 Jun 2004 08:40:39 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 14 Jun 2004 06:44:48 -0700 Received: from 210.83.210.9 by bay22-dav6.bay22.hotmail.com with DAV; Mon, 14 Jun 2004 13:44:48 +0000 X-Originating-IP: [210.83.210.9] X-Originating-Email: [liuxin_dut!at!hotmail.com] X-Sender: liuxin_dut!at!hotmail.com From: "li" To: Subject: CCL: Bond structure of semiconductors Date: Mon, 14 Jun 2004 21:44:34 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Message-ID: X-OriginalArrivalTime: 14 Jun 2004 13:44:48.0827 (UTC) FILETIME=[C2BE78B0:01C45215] X-Spam-Status: No, hits=2.0 required=7.5 tests=MIME_BASE64_TEXT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id i5EDeomP027798 Hi! I am starting my project on bond structure of semiconductors synthesised with hydrothermal method. All these semiconductors contains amine, group IV, V, IV elements and some transitional metals to make the frame structure. By trying castep within material studio, we found that the calculation can not converge. So, I wonder with what software or with which method can I carry out the study. As I am new to this field, I do hope that you would not mind giving me some handon instructions. Thank you in advance for your future help! Sincerely yours Xin, Liu From chemistry-request@ccl.net Mon Jun 14 10:00:37 2004 Received: from mailgate01.ctimail.com (mailgate01.ctimail.com [203.186.94.111]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5EF0WmP031203 for ; Mon, 14 Jun 2004 10:00:35 -0500 Received: from patrickwendy (203186034246.ctinets.com [203.186.34.246]) by mailgate01.ctimail.com (8.12.11/8.12.11) with SMTP id i5EF4kfu013601 for ; Mon, 14 Jun 2004 23:04:47 +0800 (HKT) Message-ID: <000d01c45221$f34573b0$f622bacb@patrickwendy> From: "Pang Siu Kwong Patrick" To: Subject: accuracy of solvation models Date: Mon, 14 Jun 2004 23:12:02 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01C45265.0083D1F0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000A_01C45265.0083D1F0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: quoted-printable Dear all, Have you any ROUGH idea about the accuracy of Gibbs free energy = calculated by the following solvation models (i.e. compared with = experimental values)?=20 1. Born model (assumed an ion as a sphere) 2. Kirkwood/Onsager reaction field model (assumed a molecule as a = sphere; not self-consistent reaction field; A.R. Leach, Molecular = Modelling Principles and Applications, 2nd editon, Ch11, p.594-595) 3. Onsager self-consistent reaction field model (assumed a molecule as a = sphere) 4. Pierotti energy of creation of cavity (assumed a molecule as a = sphere; Chem. Rev. 76:717-726) 5. dispersive-repulsive interaction using LJ potential from Pierotti = (assumed a molecule as a sphere; Chem. Rev. 76:717-726) I know the Gibbs free energy of solvation ought to equal to G(Born) + = G(Kirkwood/Onsage) + G(cavity) + G(dis-rep). Do you know any paper test = the accuracy of this whole model when the molecule is assumed to be a = sphere? If you know any idea of one of them, I also welcome.=20 Thank you for your help and attention. Best regards, Patrick ------=_NextPart_000_000A_01C45265.0083D1F0 Content-Type: text/html; charset="big5" Content-Transfer-Encoding: quoted-printable
Dear all,
 
Have you any ROUGH idea = about the=20 accuracy of Gibbs free energy calculated by the following solvation = models (i.e.=20 compared with experimental values)? 
1. Born model (assumed an = ion as a=20 sphere)
2. Kirkwood/Onsager = reaction field=20 model (assumed a molecule as a sphere; not self-consistent reaction = field;=20 A.R. Leach, Molecular Modelling Principles and Applications, 2nd editon, = Ch11,=20 p.594-595)
3. = Onsager self-consistent=20 reaction field model (assumed a molecule as a sphere)
4. Pierotti energy of = creation of=20 cavity (assumed a molecule as a sphere; Chem. Rev. = 76:717-726)
5. dispersive-repulsive = interaction=20 using LJ potential from Pierotti (assumed a molecule as a=20 sphere; Chem. Rev. 76:717-726)
 
I know the Gibbs free = energy of=20 solvation ought to equal to G(Born) + G(Kirkwood/Onsage) + = G(cavity) +=20 G(dis-rep).  Do you know any paper test the accuracy of this whole = model=20 when the molecule is assumed to be a sphere?
 
If you know any idea of one = of them,=20 I also welcome. 
 
Thank you for your help and = attention.
 
Best regards,
 
Patrick
------=_NextPart_000_000A_01C45265.0083D1F0-- From chemistry-request@ccl.net Tue Jun 15 16:23:48 2004 Received: from mail2.iitk.ac.in (delhi-203.197.196-2.vsnl.net.in [203.197.196.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5FLNjDC020186 for ; Tue, 15 Jun 2004 16:23:47 -0500 Received: from antivirus.cc.iitk.ac.in (antivirus.cc.iitk.ac.in [172.31.1.102]) by mail2.iitk.ac.in (8.12.8/8.12.8) with SMTP id i5FLm5Bp013568 for ; Wed, 16 Jun 2004 03:18:14 +0530 Received: (from iceman [172.26.80.61]) by antivirus.cc.iitk.ac.in (SAVSMTP 3.1.0.29) with SMTP id M2004061603030815016 for ; Wed, 16 Jun 2004 03:03:08 +0530 Message-ID: <004101c45385$a6aa2220$3d501aac@iceman> From: "Ankit Soni" To: Subject: help regarding Autodock Date: Wed, 16 Jun 2004 15:08:16 +0530 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_003E_01C453B3.C0567740" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=2.9 required=7.5 tests=DATE_IN_FUTURE_06_12, HTML_30_40,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_003E_01C453B3.C0567740 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CClers: I have just started using Autodock3 and don`t have an extensive background of docking theory.could someone please clarify some of my doubts. 1) what is the criteria for docking is it min energy or is it min RMSD?? 2) If we want to calculate the RMSD from a reference file what should be the format of the input reference file and can ADT(Autodock tool kit) = create it..or can we get it from PDB. 3) also can any one suggest some reference for the Directional H-bond implementation in autogrid based on Goodford or explain the theory behind the process. If anyone can help me I would be highly obliged. Thank You Sincerely, Ankit Ankit Soni=20 Junior Undergraduate Department of Computer Science and Engineering, Indian Institute of Technology Kanpur ------=_NextPart_000_003E_01C453B3.C0567740 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi  CClers:

      =   =20 I have just started using Autodock3 and don`t have an = extensive
background of=20 docking theory.could someone please clarify some of
my doubts.
1) = what is=20 the criteria for docking is it min energy or is it min RMSD??
2) If = we want=20 to calculate the RMSD from a reference file what should be
the format = of the=20 input reference file and can ADT(Autodock tool kit) create it..or = can we=20 get it from PDB.
3) also can any one suggest some reference for the=20 Directional H-bond
implementation  in autogrid based on Goodford = or=20 explain the
theory behind the process.
 
If anyone can=20 help me I would be highly obliged.
 
Thank You
 
Sincerely,
 
Ankit
Ankit Soni
Junior = Undergraduate
Department of Computer Science and=20 Engineering,
Indian Institute of Technology = Kanpur
 
 
------=_NextPart_000_003E_01C453B3.C0567740-- From chemistry-request@ccl.net Wed Jun 16 06:57:27 2004 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5GBvOwE016590 for ; Wed, 16 Jun 2004 06:57:25 -0500 Received: from lctn.uhp-nancy.fr (host5.lctn.uhp-nancy.fr [193.50.239.5]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id OAA15368; Wed, 16 Jun 2004 14:02:54 +0200 Sender: moreau=at=host20.lctn.uhp-nancy.fr Message-ID: <40D0367B.8745704D=at=lctn.uhp-nancy.fr> Date: Wed, 16 Jun 2004 14:01:00 +0200 From: Yohann Moreau Organization: Equipe de Chimie et Biochimie =?iso-8859-1?Q?Th=E9oriques?= X-Mailer: Mozilla 4.7iC-CCK-MCD [en_US] (X11; I; AIX 4.3) X-Accept-Language: fr, en MIME-Version: 1.0 To: Connie Chang CC: chemistry=at=ccl.net Subject: Re: CCL:Help with Gaussian error message References: Content-Type: multipart/alternative; boundary="------------4735CAC11AB40A84A337759C" X-Spam-Status: No, hits=2.0 required=7.5 tests=HTML_MESSAGE,IMPRONONCABLE_1, LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------4735CAC11AB40A84A337759C Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Connie, This message generaly occurs when a geometry optimization has not succeeded (in your case, forces are not yet converged) after the maximum step number allowed by the program has been reached. This is what occured there. You can just change the number of steps allowed for your geometry optimization, but not more than 100, bye keyword : opt=(maxcyc=N) where N is the number of steps but for such a small molecule the reason can be different. In fact I rather think it's a problem of symmetry : the charged specy has perhaps not the same symmetry as the structure you give in input (I think it's a D6h neutral benzene-like strucutre). So, the keyword "nosymm" could help the calculation to succeed. ..Hope this will help you Yohann Connie Chang wrote: > Hi -- > > I'm doing a (what I thought was simple) test job of benzene using B3LYP > and the 6-31G* basis set. > > The neutral case completed without a problem. But when I put a charge on > it, the job terminated with the following error message that I hadn't seen > before: > > No NMR shielding tensors so no spin-rotation constants. > Leave Link 601 at Fri Jun 11 14:36:46 2004, MaxMem= 6291456 cpu: 1.0 > (Enter C:\g03w\l9999.exe) > > BOOKS ARE LIGHTHOUSES ERECTED IN THE GREAT SEA OF TIME. > -- E.P.WHIPPLE > Error termination request processed by link 9999. > Error termination via Lnk1e in C:\g03w\l9999.exe at Fri Jun 11 14:36:47 2004. > Job cpu time: 0 days 1 hours 44 minutes 9.0 seconds. > File lengths (MBytes): RWF= 22 Int= 0 D2E= 0 Chk= 5 Scr= 1 > > I don't understand what's going on. Could this have something to do with > the fact that Gaussian gave up on the optimization? Gaussian had gotten > the RMS Displacement and the Maximum Displacement to converge, but not the > RMS and Maximum Force. It stopped the optimization because the max number > of steps had been reached. > > Any insight would be very helpful. > > Thanks! > > Connie Chang > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST=at=ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow=at=nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Yohann MOREAU, Doctorant Equipe de Chimie et Biochimie Thioriques UMR CNRS-UHP 7565 "SRMSC" BP 239, F-54506 Vandoeuvre-lhs-Nancy http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html --------------4735CAC11AB40A84A337759C Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Connie,

This message generaly occurs when a geometry optimization has not succeeded (in your case, forces are not yet converged)
after the maximum step number allowed by the program has been reached. This is what occured there.

You can just  change the number of steps allowed for your geometry optimization, but not more than 100, bye keyword : opt=(maxcyc=N)
where N is the number of steps but for such a small molecule the reason can be different.
In fact I rather think it's a problem of symmetry : the charged specy has perhaps not the same symmetry as the structure you give in input (I think
it's a D6h neutral benzene-like strucutre).
So, the keyword "nosymm" could help the calculation to succeed.

..Hope this will help you

Yohann
 

Connie Chang wrote:

Hi --

I'm doing a (what I thought was simple) test job of benzene using B3LYP
and the 6-31G* basis set.

The neutral case completed without a problem.  But when I put a charge on
it, the job terminated with the following error message that I hadn't seen
before:

No NMR shielding tensors so no spin-rotation constants.
Leave Link  601 at Fri Jun 11 14:36:46 2004, MaxMem=    6291456 cpu: 1.0
 (Enter C:\g03w\l9999.exe)

BOOKS ARE LIGHTHOUSES ERECTED IN THE GREAT SEA OF TIME.
     -- E.P.WHIPPLE
Error termination request processed by link 9999.
Error termination via Lnk1e in C:\g03w\l9999.exe at Fri Jun 11 14:36:47 2004.
Job cpu time:  0 days  1 hours 44 minutes  9.0 seconds.
File lengths (MBytes):  RWF=     22 Int=      0 D2E=      0 Chk= 5 Scr=      1

I don't understand what's going on.  Could this have something to do with
the fact that Gaussian gave up on the optimization?  Gaussian had gotten
the RMS Displacement and the Maximum Displacement to converge, but not the
RMS and Maximum Force.  It stopped the optimization because the max number
of steps had been reached.

Any insight would be very helpful.

Thanks!

Connie Chang

-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to:  CHEMISTRY=at=ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST=at=ccl.net
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow=at=nd.edu (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

-- 

               Yohann MOREAU, Doctorant                 
       Equipe de Chimie et Biochimie Théoriques   
               UMR CNRS-UHP 7565 "SRMSC"        
          BP 239, F-54506 Vandoeuvre-lès-Nancy  
http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html
  --------------4735CAC11AB40A84A337759C-- From chemistry-request@ccl.net Wed Jun 16 08:20:48 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5GDKlwE018516 for ; Wed, 16 Jun 2004 08:20:47 -0500 Received: from cornell.edu (67-42-28-75.slkc.qwest.net [67.42.28.75]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i5GDOscj014817; Wed, 16 Jun 2004 09:25:10 -0400 (EDT) Message-ID: <40D04A25.6060106(at)cornell.edu> Date: Wed, 16 Jun 2004 07:24:53 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: Re: CCL:converting a -CH3 to a C(CH3)3 References: <40CEE61C.9070002(at)cornell.edu> In-Reply-To: <40CEE61C.9070002(at)cornell.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.6.0.99824, Antispam-Core: 4.6.0.101390, Antispam-Data: 2004.6.15.103927 X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all I didn't get a satisfactory answer, so I'll try again. I would like to replace an -O-C(CH3)2-COOH group with an -O-C(C(CH3)3))2-COOH group. I know it can be done, because the group that is on the molecule now replaced a methyl group. In other words, the molecule I have is a derivative of a previously made one. I can't say more than this about my molecule. Those of you that work for a company will understand this. Richard Richard Wood wrote: > Hi all > > This a synthesis question. I've done some computations and converted > a methyl group into a t-butyl group with no problem. > > My question is how can a methyl group be converted synthetically into > a t-butyl group? If anyone out there knows how, including reagents, > conditions etc. please let me know. > > Thank you in advance, > Richard > -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 From chemistry-request@ccl.net Wed Jun 16 02:13:08 2004 Received: from mailfilter.diszk.unideb.hu ([193.6.138.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5G7D7sM007889 for ; Wed, 16 Jun 2004 02:13:07 -0500 Received: from mailfilter.diszk.unideb.hu (localhost [127.0.0.1]) by mailfilter.diszk.unideb.hu (Postfix) with SMTP id 2A5E7A0273; Wed, 16 Jun 2004 09:05:31 +0200 (CEST) Received: from Cthulhu (anti309.chem.klte.hu [193.6.133.108]) by delfin.unideb.hu (Postfix) with SMTP id E08AAC80E; Wed, 16 Jun 2004 09:05:21 +0200 (DFT) Message-ID: <003e01c45370$4bd8abb0$6c8506c1@Cthulhu> From: "Tamas E. Gunda" To: "Richard Wood" , References: <40CEE61C.9070002-.at.-cornell.edu> Subject: Re: CCL: converting a -CH3 to a C(CH3)3 Date: Wed, 16 Jun 2004 09:05:24 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=4.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Richard, Without knowing the structure it cannot be said. Is the Me group bonded to C? Or to N or O? Is it an ester? An enolate? etc etc... there are a huge number of possibilities. Tamas ================== Dr. Tamas E. Gunda University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry POBox 36 H-4010 Debrecen Hungary e-mail: tgunda (AT) puma*unideb*hu ----- Original Message ----- From: "Richard Wood" To: Sent: Tuesday, June 15, 2004 2:05 PM Subject: CCL:converting a -CH3 to a C(CH3)3 > Hi all > > This a synthesis question. I've done some computations and converted a > methyl group into a t-butyl group with no problem. > > My question is how can a methyl group be converted synthetically into a > t-butyl group? If anyone out there knows how, including reagents, > conditions etc. please let me know. > > Thank you in advance, > Richard > > -- > Richard L. Wood, Ph. D. > Computational Chemist > SynVax, Inc. > N. Logan, UT 84341 > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY-.at.-ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Wed Jun 16 08:12:56 2004 Received: from chaos.egr.duke.edu (chaos.egr.duke.edu [152.3.195.82]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5GDCtwE018367 for ; Wed, 16 Jun 2004 08:12:56 -0500 Received: from chaos.egr.duke.edu (localhost.localdomain [127.0.0.1]) by chaos.egr.duke.edu (8.12.8/8.12.8) with ESMTP id i5GDHIwc031324; Wed, 16 Jun 2004 09:17:18 -0400 Received: from localhost (jlb@localhost) by chaos.egr.duke.edu (8.12.8/8.12.8/Submit) with ESMTP id i5GDHHvt031320; Wed, 16 Jun 2004 09:17:17 -0400 X-Authentication-Warning: chaos.egr.duke.edu: jlb owned process doing -bs Date: Wed, 16 Jun 2004 09:17:17 -0400 (EDT) From: Joshua Baker-LePain X-X-Sender: jlb.-at-.chaos.egr.duke.edu To: Eugen Leitl cc: Beowulf.-at-.beowulf.org, chemistry.-at-.ccl.net, Marc Noguera Julian Subject: Re: [Beowulf] CCL:Experiences with 64 bits AMD processors (fwd from marc.-at-.klingon.uab.es) In-Reply-To: <20040616042135.GH12847.-at-.leitl.org> Message-ID: References: <20040616042135.GH12847.-at-.leitl.org> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, 16 Jun 2004 at 6:21am, Eugen Leitl wrote > ----- Forwarded message from Marc Noguera Julian ----- > > From: Marc Noguera Julian > Date: Tue, 10 Jun 2003 19:09:00 +0200 > To: chemistry.-at-.ccl.net > Subject: CCL:Experiences with 64 bits AMD processors > User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 > > Hello, > we are interested in buying some more computational resources. In our > group we are interested in 64 bit AMD processors, but we do not know > about their compatibility. They are supposed, as AMD says, to be32 bit > compatible and therefore AMD 64 bit processor should be able to run any > 32 bit application. Is that true? Any experience about this will help us > a lot. I have several Opterons running RHEL 3 WS for AMD64, and I run a mix of 32 and 64bit apps on them with no problem. For commercial codes, this includes Matlab (32bit) and LS-DYNA (I've run both 32 and 64bit versions of this). It just works, and the chips are quite fast. -- Joshua Baker-LePain Department of Biomedical Engineering Duke University From chemistry-request@ccl.net Wed Jun 16 05:38:31 2004 Received: from life.ai.mit.edu (ai.mit.edu [128.52.32.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5GAcUwE014641 for ; Wed, 16 Jun 2004 05:38:30 -0500 Received: from horsepower.csail.mit.edu (horsepower.csail.mit.edu [128.30.2.64]) by life.ai.mit.edu (8.12.10/8.12.9/BASENAME(ai.master.life-8.12.9.mc,.mc):RCS_REVISION(Revision: 1.23)) with ESMTP id i5GAghDH003817; Wed, 16 Jun 2004 06:42:48 -0400 (EDT) Received: from localhost (dfgreen@localhost) by horsepower.csail.mit.edu (8.9.1/8.8.4AI/ai.client:1.5) with ESMTP id GAA08765; Wed, 16 Jun 2004 06:42:43 -0400 (EDT) X-Authentication-Warning: horsepower.csail.mit.edu: dfgreen owned process doing -bs Date: Wed, 16 Jun 2004 06:42:42 -0400 (EDT) From: "David F. Green" X-Sender: dfgreen[at]horsepower.csail.mit.edu To: Richard Wood cc: "chemistry[at]ccl.net" Subject: Re: CCL:converting a -CH3 to a C(CH3)3 In-Reply-To: <40CEE61C.9070002[at]cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This depends entirely on the details of the molecule, and the current synthetic scheme being used for it. In some cases, the reagent initially containing the methyl is also available (or easily synthesized) with a t-butyl, and the alternate synthesis may be straightforward (although differences in reactivity can still lead to difficulties). However, in other cases the synthetic stragety must be changed to make the substitution. In any case, it's not at all straightforward to convert a methyl to a t-butyl in the context of a larger molecule, and thus the conversion should be done early on in the synthetic process. +--------------------------------------------------------------------+ | David F. Green | | | Postdoctoral Associate | Phone: 617-253-5438 | | Division of Bioengineering and Computer | Mobile: 617-953-3922 | | Science & Artificial Intelligence Lab | Fax: 617-258-8682 | | Massachusetts Institute of Technology | | | 32 Vassar St., 32-211 | E-mail: dfgreen[at]mit.edu | | Cambridge, MA 02139 | | +--------------------------------------------------------------------+ On Tue, 15 Jun 2004, Richard Wood wrote: > Hi all > > This a synthesis question. I've done some computations and converted a > methyl group into a t-butyl group with no problem. > > My question is how can a methyl group be converted synthetically into a > t-butyl group? If anyone out there knows how, including reagents, > conditions etc. please let me know. > > Thank you in advance, > Richard > > -- > Richard L. Wood, Ph. D. > Computational Chemist > SynVax, Inc. > N. Logan, UT 84341 > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >