From chemistry-request@server.ccl.net Tue Sep 26 02:17:47 2000 Received: from aurora.balcab.ch (aurora.balcab.ch [213.200.1.126]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA03132 for ; Tue, 26 Sep 2000 02:17:46 -0400 Received: from sigma.balcab.ch (sigma.balcab.ch [213.200.1.125]) by aurora.balcab.ch (8.9.1/8.9.1) with ESMTP id IAA01610 for ; Tue, 26 Sep 2000 08:17:23 +0200 (MET DST) Received: from ubaclu.unibas.ch ([213.200.8.206]) by sigma.balcab.ch (Netscape Messaging Server 3.6) with ESMTP id AAA5C2B; Tue, 26 Sep 2000 08:17:22 +0200 Message-ID: <39D03FD3.23356555@ubaclu.unibas.ch> Date: Tue, 26 Sep 2000 08:18:59 +0200 From: Shu-Kun Lin Reply-To: lin@mdpi.org Organization: MDPI (http://www.mdpi.org) X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en-US,zh,zh-CN MIME-Version: 1.0 Subject: ECSOC-4 is running at http://www.mdpi.org/ecsoc-4.htm Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You are kindly invited to visit our ECSOC-4 conference halls at http://www.mdpi.org/ecsoc-4.htm. The 4th International Electronic Conference on Synthetic Organic Chemistry is held during September 1-30, 2000. ECSOC-4 has been running this month in September, 2000. It has 150 papers presented. We have installed the search engine and the BBS for discussion. Please make comments. We are grateful to the financial support from 9 sponsors. Sincerely yours Shu-Kun Lin, ECSOC-4 Secretary E-mail: lin@mdpi.org -- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland Tel. +41 79 322 3379, Fax +41 61 302 8918 E-mail: lin@mdpi.org http://www.mdpi.org/lin/ From chemistry-request@server.ccl.net Tue Sep 26 11:29:52 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA06182 for ; Tue, 26 Sep 2000 11:29:51 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Tue, 26 Sep 2000 17:32:48 +0200 Sender: zhang@ccl.net Message-ID: <39D0BFAE.6DCADBC8@mail.biokemi.su.se> Date: Tue, 26 Sep 2000 17:24:30 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Autodock: autotors References: <39CB8291.73206A75@mail.biokemi.su.se> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, A few days ago, I posted a question about "autotors" in autodock package (see following). I haven't got any answer yet. But I found that this problem is related to the presence of cysteine residue in the ligand peptide. I tried the "autotors" from both autodock 3.0 and 3.0.5 release. It seems that the "autotors" on my machine (PC Linux) can not handle the -SH group of cysteine. "Autotors" either crashes or skips the atoms in -SH group and add a symbol (^) in a few places and move the ENDROOT to end of the line which contains the symbol. Off course you can not get a grid map file for S atom if you don't edit the new pdbq file. I wonder if this is a bug in "autotors" code or the problem of my compilation? Does any body tried to run autotors with a ligand which contains S atom or -SH group? Any suggestions are highly appreciated. Sincerely yours, Xiao-Ping Zhang Xiao-Ping Zhang wrote: > > Dear autodock experts, > > I got a problem to run "autotors" on some of my peptide > models (the conformation of the peptide might not be > realistic, but everyone was refined in molecular modeling > program). I got the following error message: > > mol2flag = 0 > hflag = 1 > offset = 70 > aflag = 1 > bflag = 1 > > bnd format:94 records read in > unable to attach all pieces of bond data > > Does anybody encountered a similar problem before? How to > solve it? > > Thank you advance for any suggestions. > > Have a nice weekend? > > Sincerely, > > Zhang > > ****************************** > Xiao-Ping Zhang > Department of Biochemistry > Arrhenius Laboratories of Natural Sciences > Stockholm Universities > 106 91 Stockholm > Sweden > > Phone: 046-08-162472 /162582 > Fax: 046-08-153679 > e-mail: zhang@biokemi.su.se > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Tue Sep 26 17:24:11 2000 Received: from stripe.Colorado.EDU (stripe.Colorado.EDU [128.138.129.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA07821 for ; Tue, 26 Sep 2000 17:24:11 -0400 Received: from stripe.colorado.edu (chem103-19-dhcp.Colorado.EDU [128.138.103.19]) by stripe.Colorado.EDU (8.9.3/8.9.3/ITS-5.0/standard) with ESMTP id PAA02161; Tue, 26 Sep 2000 15:24:08 -0600 (MDT) Message-ID: <39D114A0.D9ADCABF@stripe.colorado.edu> Date: Tue, 26 Sep 2000 15:26:57 -0600 From: Neil Whittemore Organization: University of Colorado, Boulder X-Mailer: Mozilla 4.73 [en] (Win98; U) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net, Neil Whittemore Subject: AMBER forcefield and thioglycosides Content-Type: multipart/mixed; boundary="------------4403887138E9CF26A2F5DA9F" This is a multi-part message in MIME format. --------------4403887138E9CF26A2F5DA9F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am using the AMBER forcefield with the Homans carbohydrate parameters (AMBER*) in the InsightII2000 package from MSI to model glycosides. I would like to compare these models with models of their thio-counterparts. What are people's experience using AMBER * on thioglycosides? The major issue with using these parameters is that there does not seem to be a suitable parameter set/potential type for the sulfur atom in the glycosidic linkage---the only ones relating to sulfur I could find were for disulfides/methionine and cystine. Any advice/comments would be greatly appreciated. Neil Whittemore whittemo@stripe.colorado.edu --------------4403887138E9CF26A2F5DA9F Content-Type: text/x-vcard; charset=us-ascii; name="whittemo.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Neil Whittemore Content-Disposition: attachment; filename="whittemo.vcf" begin:vcard n:Whittemore;Neil tel;work:(303) 492-4935 x-mozilla-html:FALSE org:University of Colorado;Dept. of Chem. and Biochem. version:2.1 email;internet:whittemo@stripe.colorado.edu adr;quoted-printable:;;Campus Box 215=0D=0A;Boulder;CO;80303-0215;USA fn:Neil Whittemore end:vcard --------------4403887138E9CF26A2F5DA9F--