From chemistry-request@server.ccl.net Tue Nov 13 09:20:01 2001 Received: from gatekeeper2.novartis.com ([194.191.169.74]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fADEJuB04204 for ; Tue, 13 Nov 2001 09:19:57 -0500 Received: from mtap1.is.chbs (mtap1.novartis.com [192.37.33.20]) by gatekeeper2.novartis.com (8.11.0/8.11.0) with ESMTP id fADEJhv16763 for ; Tue, 13 Nov 2001 15:19:43 +0100 (MET) Received: from NVCHBS-S0121.is.chbs (nvchbs-s0121.is.chbs [192.37.33.41]) by mtap1.is.chbs (8.11.3/8.11.3) with ESMTP id fADEJhW296022 for ; Tue, 13 Nov 2001 15:19:43 +0100 Subject: Peptide-Database To: chemistry@ccl.net From: maria.brandl@pharma.novartis.com Date: Tue, 13 Nov 2001 15:19:20 +0100 Message-ID: X-MIMETrack: Serialize by Router on CHBSMN12/N1/Novartis(Release 5.0.8 |June 18, 2001) at 11/13/2001 03:19:42 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi CCLers, obviously it's not perfectly trivial to automatically scan the PDB for peptides or peptide-like drug molecules. Thus, I am just trying to compile some sub- databank of peptide structures. With peptides very often being a sequence including both atom and heteroatom- entries, resorting to SEQRES - information seems the only thing that really works. Coordinates are seemingly not accurate enough to determine molecular connectivity based on proximity of atom positions alone. Yet, in 1nqr one chain actually includes two molecules, thus connectivity SEQRES on its own is obviously non- sufficient as well. For the moment I will try to use SEQRES records and check connectivity by measuring atomic distances of neighbouring residues. Is anybody aware of any existing databases of that kind? Any suggestions and comments of how to compile such a data- base are also welcome. Cheers, Maria From chemistry-request@server.ccl.net Tue Nov 13 12:37:29 2001 Received: from t12mail.lanl.gov ([128.165.22.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fADHbSB18071 for ; Tue, 13 Nov 2001 12:37:28 -0500 Received: from MatCha (ts-usr-231.lanl.gov [128.165.7.231]) by t12mail.lanl.gov (8.9.1a/8.9.1) with SMTP id KAA27658 for ; Tue, 13 Nov 2001 10:37:56 -0700 (MST) Content-Type: text/plain; charset="iso-8859-1" From: Matt Challacombe Reply-To: MChalla@LANL.Gov Organization: Group T-12, Los Alamos National Lab To: Subject: Software for viewing periodic systems Date: Tue, 13 Nov 2001 03:27:19 -0700 X-Mailer: KMail [version 1.2] References: <001401c16907$8bf79270$5e40cf9b@chem.auth.gr> In-Reply-To: <001401c16907$8bf79270$5e40cf9b@chem.auth.gr> MIME-Version: 1.0 Message-Id: <01111303271901.28103@MatCha> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fADHbTB18072 Dear CCLrs, I'm asking for your advice on free software for looking for your -- Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ Los Alamos National Laboratory email: MChalla@LANL.Gov Group T-12, Mail Stop B268 phone: (505) 665-5905 Los Alamos, New Mexico 87545 fax: (505) 665-3909 From chemistry-request@server.ccl.net Tue Nov 13 12:40:08 2001 Received: from t12mail.lanl.gov ([128.165.22.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fADHe7B18193 for ; Tue, 13 Nov 2001 12:40:07 -0500 Received: from MatCha (ts-usr-231.lanl.gov [128.165.7.231]) by t12mail.lanl.gov (8.9.1a/8.9.1) with SMTP id KAA27679 for ; Tue, 13 Nov 2001 10:40:35 -0700 (MST) Content-Type: text/plain; charset="iso-8859-1" From: Matt Challacombe Reply-To: MChalla@LANL.Gov Organization: Group T-12, Los Alamos National Lab To: ccl Subject: Free software for viewing periodic systems Date: Tue, 13 Nov 2001 03:29:58 -0700 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <01111303295802.28103@MatCha> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fADHe8B18194 Dear CCLrs, I'm asking your advice for free software that can render systems with non-orthogonal periodic boundary conditions. I like gopenmol, but it only does 90,90,90... Can someone suggest an alternative? Thx, Matt -- Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ Los Alamos National Laboratory email: MChalla@LANL.Gov Group T-12, Mail Stop B268 phone: (505) 665-5905 Los Alamos, New Mexico 87545 fax: (505) 665-3909 From chemistry-request@server.ccl.net Tue Nov 13 13:05:50 2001 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fADI5oB18779 for ; Tue, 13 Nov 2001 13:05:50 -0500 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: Free software for viewing periodic systems X-MimeOLE: Produced By Microsoft Exchange V6.0.4712.0 Date: Tue, 13 Nov 2001 10:03:53 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Free software for viewing periodic systems Thread-Index: AcFsbCIhJv2DowaGTiiOYlhOD+sVbAAAA03A From: "DeLano, Warren" To: "Matt Challacombe" , "ccl" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fADI5oB18780 Matt, Provided that you can define your system using cell dimensions and angles (alpha, beta, gamma), then any crystallography package should be be able to do this for you. If that you can convert your data into PDB format and define a CRYST record with the above information, then PyMOL is a free option... http://www.pymol.org The latest release (0.68) contains tons of new features, including *transparent surfaces*. Everyone should try PyMOL at least once... Cheers, Warren -- mailto:warren@sunesis.com Warren L. DeLano, Ph.D. Informatics Scientist Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 fax: (650)-266-3501 > -----Original Message----- > From: Matt Challacombe [mailto:MChalla@lanl.gov] > Sent: Tuesday, November 13, 2001 2:30 AM > To: ccl > Subject: CCL:Free software for viewing periodic systems > > > Dear CCLrs, > > I'm asking your advice for free software that can render > systems with non-orthogonal periodic boundary conditions. > I like gopenmol, but it only does 90,90,90... Can someone > suggest an alternative? > > Thx, Matt > > -- > Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ > Los Alamos National Laboratory email: MChalla@LANL.Gov > Group T-12, Mail Stop B268 phone: (505) 665-5905 > Los Alamos, New Mexico 87545 fax: (505) 665-3909 > > -= 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 > > > > > > From chemistry-request@server.ccl.net Tue Nov 13 15:16:15 2001 Received: from odin.cair.du.edu ([130.253.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fADKGFB20964 for ; Tue, 13 Nov 2001 15:16:15 -0500 Received: from CONVERSION-DAEMON.du.edu by du.edu (PMDF V6.1 #37556) id <0GMR06G019MUFN@du.edu> for chemistry@ccl.net; Tue, 13 Nov 2001 13:16:06 -0700 (MST) Received: from fermion ([130.253.176.69]) by du.edu (PMDF V6.1 #37556) with SMTP id <0GMR06G5P9MULS@du.edu> for chemistry@ccl.net; Tue, 13 Nov 2001 13:16:06 -0700 (MST) Date: Tue, 13 Nov 2001 13:16:06 -0700 From: Jim Stoner Subject: Gaussian98, ATLAS, IFC, and RedHat 7.1 To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal Fellow CCLers, I am on the steep accent side of the learning curve when it comes to Linux. I am currently attempting to build Gaussian98 on our new dual P4 workstation. I have managed to install RedHat 7.1 - this choice was made because it is the OS under which another simulation package was built against - with the 2.4.2-2smp kernel. I have installed gcc 2.95.3, Intel's Fortran Complier (fully operational trialware) and ATLAS 3.3.8 as. I modified the build files for these libraries. However, now I am getting an error that I have little intuition how to solve. The build proceeds nicely then crashes and burns here: ml0.f(2) : (col. 0) remark: main has been targeted for automatic cpu dispatch. rm -f ml0.f ml0.c gmake[1]: Leaving directory `/usr/Gaussian98_A6/g98' ifc -O3 -tpp7 -WB -axiMKW -align -Zp8 -o g98 ml0.o libgauutil.so -L/opt/intel/compiler50/ia32/lib -lPEPCF90 ifc: NOTE: You have 29 days left in your evaluation period. ml0.o: In function `main$H': ml0.o(.text+0x643): undefined reference to `upcase_' ml0.o(.text+0xc00): undefined reference to `defbsn_' ml0.o: In function `main$A': ml0.o(.text+0x147f): undefined reference to `upcase_' ml0.o(.text+0x1a03): undefined reference to `defbsn_' libgauutil.so: undefined reference to `defbc2_' libgauutil.so: undefined reference to `qx_' libgauutil.so: undefined reference to `atl_f77wrap_dcopy_' libgauutil.so: undefined reference to `atl_f77wrap_drot_' libgauutil.so: undefined reference to `unpck1_' libgauutil.so: undefined reference to `denmvs_' <...> <...> libgauutil.so: undefined reference to `unrafp_' libgauutil.so: undefined reference to `unpck3_' libgauutil.so: undefined reference to `atl_f77wrap_dscal_' libgauutil.so: undefined reference to `atl_f77wrap_drotg_' libgauutil.so: undefined reference to `derlmat_' libgauutil.so: undefined reference to `dencnt_' libgauutil.so: undefined reference to `pthread_join' libgauutil.so: undefined reference to `decacc_' gmake: *** [g98] Error 1 endif I am not entirely sure what is happening here other than there seems to be links missing from the libgauutil.so. Does anyone have any experiences with this sort of problem or have any intuition where to begin to solve this? Any and all help, comments, and question would greatly be appreciated. Thanks Jim ========================================= | James W. Stoner | Eaton Electron Paramagnetics Laboratory | University of Denver | Department of Chemistry and Biochemistry | Seeley G. Mudd Building, Lab 173 | 2101 East Wesley Avenue | Denver, Colorado 80208 | 303/871-2978 | Fax: 303/871-2254 ========================================= From chemistry-request@server.ccl.net Tue Nov 13 16:53:32 2001 Received: from imo-r09.mx.aol.com ([152.163.225.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fADLrWB22921 for ; Tue, 13 Nov 2001 16:53:32 -0500 Received: from SPEROLEEM@aol.com by imo-r09.mx.aol.com (mail_out_v31_r1.8.) id g.62.16e467b7 (4446) for ; Tue, 13 Nov 2001 16:53:23 -0500 (EST) From: SPEROLEEM@aol.com Message-ID: <62.16e467b7.2922f053@aol.com> Date: Tue, 13 Nov 2001 16:53:23 EST Subject: (no subject) To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="part1_62.16e467b7.2922f053_boundary" X-Mailer: AOL 6.0 for Windows US sub 10540 --part1_62.16e467b7.2922f053_boundary Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Am new to Amber. Have tried running tutorial Protein/Water/counterion/NMR tutorial (plasmocyanin). Made hicu.in and leap.in. On execution I get an error message frcmod.pcy not found. Does anyone know what is wrong? Thanks. Spero M --part1_62.16e467b7.2922f053_boundary Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: 7bit Am new to Amber. Have tried running tutorial Protein/Water/counterion/NMR tutorial (plasmocyanin). Made hicu.in and leap.in. On execution I get an error message frcmod.pcy not found.

Does anyone know what is wrong?

Thanks.

Spero M --part1_62.16e467b7.2922f053_boundary-- From chemistry-request@server.ccl.net Tue Nov 13 15:25:27 2001 Received: from alien.biochem.wfubmc.edu ([152.11.118.46]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fADKPRB21295 for ; Tue, 13 Nov 2001 15:25:27 -0500 Received: from localhost (zhangxd@localhost) by alien.biochem.wfubmc.edu (8.11.6/8.11.6) with ESMTP id fADKPKC6462147; Tue, 13 Nov 2001 15:25:20 -0500 (EST) Date: Tue, 13 Nov 2001 15:25:19 -0500 From: Zhangxd To: Matt Challacombe cc: ccl Subject: question about opt In-Reply-To: <01111303295802.28103@MatCha> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, I want to opt one molecule and I also want to fix some atoms with 0/-1 symbol. keyword opt=? Thx