From chemistry-request@server.ccl.net Mon Feb 3 04:03:07 2003 Received: from dire.bris.ac.uk ([137.222.10.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1392qI17902 for ; Mon, 3 Feb 2003 04:02:53 -0500 Received: from eis.bris.ac.uk by dire.bris.ac.uk with SMTP-PRIV with ESMTP; Mon, 3 Feb 2003 09:02:46 +0000 Received: from simpson (simpson.chm.bris.ac.uk [137.222.42.59]) by eis.bris.ac.uk (8.11.6/8.11.6) with SMTP id h1390oJ27620 for ; Mon, 3 Feb 2003 09:00:50 GMT Message-ID: <003c01c2cb63$e3165e50$3b2ade89@chm.bris.ac.uk> From: Chris Arthur To: CHEMISTRY Subject: Protein PDB to Mol2 Date: Mon, 3 Feb 2003 09:08:58 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0039_01C2CB63.E2F7D9D0" 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_0039_01C2CB63.E2F7D9D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi=20 I was wondering if anyone knows how o convert Protein PDB files to MOL2. = I've tried using Babel howver it has problems when it comes to = recognising the CE, NZ, CZ and SG (and varients of) atom codes instead = calling them Du when it gets confused (I assume that...CE - epsilon C , = NZ....zeta nitrogen , CZ .....zeta carbon and SG....gamma Sulfur) Anyone know of a GPL or GNU program that'll do this happily ? Chris=20 ------=_NextPart_000_0039_01C2CB63.E2F7D9D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I was wondering if anyone knows how o = convert=20 Protein PDB files to MOL2. I've tried using Babel howver it has problems = when it=20 comes to recognising the CE, NZ, CZ and SG (and varients of) atom codes = instead=20 calling them Du when it gets confused (I assume that...CE - epsilon C ,=20 NZ....zeta nitrogen , CZ .....zeta carbon and SG....gamma = Sulfur)

Anyone know of a GPL or GNU = program that'll do=20 this happily ?

Chris

------=_NextPart_000_0039_01C2CB63.E2F7D9D0-- From chemistry-request@server.ccl.net Mon Feb 3 02:24:31 2003 Received: from mail4.hitachi.co.jp ([133.145.228.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h137OUI15854 for ; Mon, 3 Feb 2003 02:24:31 -0500 Received: from mc1.mcg.hitachi.co.jp by mail4.hitachi.co.jp (8.9.3/3.7W-mail4) id QAA23217; Mon, 3 Feb 2003 16:24:29 +0900 (JST) Received: (from root@localhost) by mc1.mcg.hitachi.co.jp (8.11.6+Sun/8.11.6) id h137ORF07728 for ; Mon, 3 Feb 2003 16:24:28 +0900 (JST) Received: from unknown [192.168.2.1] by mc1.mcg.hitachi.co.jp with SMTP id SAA07727 ; Mon, 3 Feb 2003 16:24:27 +0900 Received: from navsg1.hitachi.co.jp by navsg1.hitachi.co.jp (8.9.3/3.7W-navsg1) id QAA01470; Mon, 3 Feb 2003 16:24:27 +0900 (JST) Received: from missun1.musashi.hitachi.co.jp ([158.212.213.198]) by navsg1.hitachi.co.jp (NAVGW 2.5.2.17) with SMTP id M2003020316242711070 for ; Mon, 03 Feb 2003 16:24:27 +0900 Received: from hul3.hitachi-ul.co.jp (hul3.hitachi-ul.co.jp [158.211.18.102]) by missun1.musashi.hitachi.co.jp (8.9.3/3.7W/SIC-MAILGW_arai) with ESMTP id QAA28373 for ; Mon, 3 Feb 2003 16:24:21 +0900 (JST) Received: (from root@localhost) by hul3.hitachi-ul.co.jp (8.11.6/3.7W) id h137MEr25730 for ; Mon, 3 Feb 2003 16:22:14 +0900 (JST) Received: from hul2.hitachi-ul.co.jp [158.211.18.118] by hul3.hitachi-ul.co.jp with SMTP id SAA25729 ; Mon, 3 Feb 2003 16:22:14 +0900 Received: from k5jk-ux-09.hitachi-ul.co.jp (localhost [127.0.0.1]) by hul2.hitachi-ul.co.jp (8.8.8+Sun/3.6W-hul2) with ESMTP id QAA17360 for ; Mon, 3 Feb 2003 16:24:20 +0900 (JST) Received: from hitachi-ul.co.jp ([202.19.63.88]) by k5jk-ux-09.hitachi-ul.co.jp (8.11.4/8.11.4) with ESMTP id h137OH501318 for ; Mon, 3 Feb 2003 16:24:17 +0900 (JST) Message-ID: <3E3E1905.626032BF@hitachi-ul.co.jp> Date: Mon, 03 Feb 2003 16:23:57 +0900 From: "k.watanabe" X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: ja,en MIME-Version: 1.0 To: Chemistry@ccl.net Subject: How to calculate new force field parameter? Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit hi, We need to calculate a MD of the protein with a small molecule. So, We calculated point charges of small molecule using gaussian and resp (in amber) . To run MD, We also need bond, angle, torsion, improper torsion and VDW parameters of a small molecule. Does anyone know any information (e.g. web or paper) for beginners that indicate how to calculate it? K, Watanabe. Hitachi ulsi systems co. ltd. From chemistry-request@server.ccl.net Mon Feb 3 13:20:17 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h13IKFI25572 for ; Mon, 3 Feb 2003 13:20:15 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.5/jtpda-5.4) with SMTP id h13IK5YY045185 for ; Mon, 3 Feb 2003 19:20:06 +0100 (CET) Date: Mon, 3 Feb 2003 19:20:05 +0100 Message-Id: <03020319200514@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: chemistry@ccl.net Subject: CCL:Symmetry, Asymmetry and Similarity / call for papers X-VMS-To: SMTP%"chemistry@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr Subj="Symmetry, Asymmetry and Similarity / call for papers" /* sorry if multiple receipts */ Dear Colleague, The journal ENTROPY has planned a special issue about: Symmetry, Asymmetry and Similarity. As guest editor for this issue, let me invite you to submit some paper(s) for this special issue. http://www.mdpi.org/entropy http://www.mdpi.org/entropy/specialissues.htm I hope to hear from you soon. Best regards, Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html From chemistry-request@server.ccl.net Mon Feb 3 12:41:11 2003 Received: from smtp.uh.cu ([216.72.24.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h13HegI19959 for ; Mon, 3 Feb 2003 12:41:04 -0500 Received: from fq.uh.cu (canaria.qct.fq.oc.uh.cu [192.168.3.4]) by smtp.uh.cu (Postfix) with ESMTP id A7BAF34036 for ; Mon, 3 Feb 2003 13:44:12 -0500 (CST) Received: from localhost (rachel@localhost) by fq.uh.cu (8.9.0/8.8.7) with SMTP id MAA11293 for ; Mon, 3 Feb 2003 12:42:10 -0500 Date: Mon, 3 Feb 2003 12:42:09 -0500 (CST) From: Rachel Crespo Otero To: chemistry@ccl.net Subject: About TS calculation with g94 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCL members! We are calculating a transition state with gaussian 94, calculation stop and output said: The smallest eigenvalue of the overlap matrix is 1.952E-02 Floating Exception Somebody can help me? Rachel From chemistry-request@server.ccl.net Mon Feb 3 08:23:31 2003 Received: from vscan1-eur.ext.dsm.com ([163.175.162.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h13DNTI05659 for ; Mon, 3 Feb 2003 08:23:30 -0500 Received: from nlgln20ntms920.GLN20.DSM-GROUP.COM (localhost [127.0.0.1]) by vscan1-eur.ext.dsm.com (8.9.3/8.8.5-1.2.2m-19990317) with ESMTP id OAA11009 for ; Mon, 3 Feb 2003 14:23:27 +0100 (MET) Received: by nlgln20ntms920.gln20.dsm-group.com with Internet Mail Service (5.5.2653.19) id <1B395Z9W>; Mon, 3 Feb 2003 14:22:51 +0100 Message-ID: <6D47A7D05774D411959200508BDF739A024386E9@nlgln50ntms001.gln51.dsm-group.com> From: "Coussens, Betty" To: "'chemistry@ccl.net'" Subject: calculating NMR spectra for crystal structures Date: Mon, 3 Feb 2003 14:22:47 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear all, I would like to calculate NMR chemical shifts for a number of crystal structures containing H, C, N, O and P atoms. I know that this is possible using e.g. plane wave codes like CPMD but I would like to hear the opinion of you who have a lot of experience with this type of computations. Can anybody tell me what type of codes are most suitable for my purpose and give me an idea about typical CPU timings for these type of calculations? Thanks a lot! Betty Disclaimer 1. This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. 2. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. This e-mail is confidential and may be legally privileged. DSM does not guarantee that the information sent and/or received by or with this e-mail is correct and does not accept any liability for damages related thereto. From chemistry-request@server.ccl.net Mon Feb 3 16:15:13 2003 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h13LFDI14717 for ; Mon, 3 Feb 2003 16:15:13 -0500 Received: from cornell.edu (kili.ccmr.cornell.edu [128.84.241.146]) by cornell.edu (8.9.3/8.9.3) with ESMTP id QAA12061 for ; Mon, 3 Feb 2003 16:15:12 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3E3EDBE1.8F0B102C@cornell.edu> Date: Mon, 03 Feb 2003 16:15:13 -0500 From: Connie Chang X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Question about the use of COOR=CART in GAMESS (Linux-pc) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I entered a molecule in GAMESS using the keyword COOR=CART The coordinates follow the exact symmetry I am using (C2h) which I declare, but it is in no particular orientation. I thought that COOR=CART would allow me to enter the molecule in full and that GAMESS would then figure out the symmetry unique atoms and orient them appropriately if I give it the right symmetry. I enter the 140 atoms of my moelcule, but I get an error saying that GAMESS cannot process more than 500 atoms! I am guessing GAMESS is taking my 140 atoms and using the fact that the molecule is C2h symmetric, it is getting 140*4=560 atoms. But my molecule just has 140 atoms and I'm not using COOR=UNIQUE. Does anyone know what I am doing wrong? Thanks, Connie Chang