From antonio@risc2.lrm.fi.cnr.it Sat Apr 15 05:30:02 1995 Received: from risc2.lrm.fi.cnr.it for antonio@risc2.lrm.fi.cnr.it by www.ccl.net (8.6.10/930601.1506) id FAA23795; Sat, 15 Apr 1995 05:19:48 -0400 From: Received: by risc2.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA24370; Sat, 15 Apr 1995 11:13:58 +0200 Date: Sat, 15 Apr 1995 11:13:58 +0200 Message-Id: <9504150913.AA24370@risc2.lrm.fi.cnr.it> To: CHEMISTRY@ccl.net Subject: Deviation of peptide bonds from planarity Dear Netters, I am trying to calculate a structure from NMR data. My approach is as follows: 1) Generate a family of structures using DIANA (a DG program) 2) Use Amber to perform Restrained Energy Minimization on the family The final structures I get often have non planar peptide bonds, the first residue being always the most suffering one. I used PROCHECK to check the peptide bonds planarity. My protein is paramagnetic but I don't think this is a problem. The parameters used for the cluster in Amber are well tested. Has anyone ever faced the same problem? Any suggestion is welcome. Thank you, Antonio e-mail: antonio@risc1.lrm.fi.cnr.it From friedman@tammy.harvard.edu Sat Apr 15 09:45:05 1995 Received: from tammy.harvard.edu for friedman@tammy.harvard.edu by www.ccl.net (8.6.10/930601.1506) id JAA24453; Sat, 15 Apr 1995 09:37:41 -0400 Received: by tammy.harvard.edu (5.64/10.0) id AA15297; Sat, 15 Apr 95 09:40:13 -0400 Date: Sat, 15 Apr 95 09:40:13 -0400 From: friedman@tammy.harvard.edu (Dawn Friedman) Message-Id: <9504151340.AA15297@tammy.harvard.edu> To: chemistry@ccl.net Subject: Re: PSI88: rpsi2 if, Indigo2 Cc: friedman@tammy.harvard.edu I'm sorry to have to take this to the list at large, but I need advice *fast*, and it's hard to catch people on a weekend. The problem is running PSI88 on an SGI Indigo**2. The OS is IRIX. The difficulty is with an if statement in the shell script rpsi2, which I took directly from the UNIX version of psi88.tar.Z. I did, finally, get the compiler flags straightened out. My current problem is not in PSI2, which now compiles without error, but in the shell script rpsi2. It runs fine on my SUN 386i, but on the Indigo**2 it produces the csh error message: if: Malformed file inquiry I've been over all the if statements, and I don't see where there should be a problem with any of them. But the one it seems to object to (after a run with verbose) is the if ($argv[1] == '-pk') statement. It knows what $argv[1] is, because I made it echo; it even verboses the helpful comment: -pk == -pk and then the error message! I've just spent five hours fighting through man pages and online "help", and nowhere can I find a description of error messages for csh commands like 'if'. Has anyone run into this before? Is anyone here sufficiently familiar with shell scripts to tell me what the heck a Malformed file inquiry is? I understand 'file inquiry', sort of, but what would make one 'Malformed'? Can anyone at least tell me where to find descriptions of error messages for csh commands? Or if I should be taking the T over to the MIT Coop to find a csh book? Many thanks, Dawn Friedman friedman@tammy.harvard.edu From dok730@cvx12.inet.dkfz-heidelberg.de Sat Apr 15 10:45:06 1995 Received: from ns.DKFZ-Heidelberg.de for dok730@cvx12.inet.dkfz-heidelberg.de by www.ccl.net (8.6.10/930601.1506) id KAA24685; Sat, 15 Apr 1995 10:30:28 -0400 Received: from cvx12.inet.dkfz-heidelberg.de (cvx12.inet.dkfz-heidelberg.de [192.55.188.1]) by ns.DKFZ-Heidelberg.de (8.6.10/DKFZ-8.6.9) with ESMTP id QAA22516 for ; Sat, 15 Apr 1995 16:30:36 +0200 Received: (from dok730@localhost) by cvx12.inet.dkfz-heidelberg.de (8.6.10/8.6.6) id QAA07118; Sat, 15 Apr 1995 16:30:34 +0200 Date: Sat, 15 Apr 1995 16:30:34 +0200 From: Karl Jalkanen Message-Id: <199504151430.QAA07118@cvx12.inet.dkfz-heidelberg.de> To: chemistry@ccl.net Subject: [cedrick@cml.com: Help On Gortex] To chemistry list at Ohio State Can anyone help this young chemistry student? I received this question on the str-nmr group and though I would forward to the chemists here. Vielen Dank. Please send responses to cedrick@cml.com (Lee Boros) not to me. >To: str-nmr@net.bio.net >From: cedrick@cml.com (Lee Boros) >Subject: Help On Gortex >Date: 14 Apr 1995 16:58:20 GMT >Hi, I'm doing a Chemistry Project on Gortex. I am in Grade 12 and I am >trying to find some informtaion on the internet but am having great >difficulties. Does anyone know where I can search for information on >this molecule? > >-Lee ------------------------------------------------------------------- From dan@sage.syntex.com Sat Apr 15 13:00:08 1995 Received: from sage.syntex.com for dan@sage.syntex.com by www.ccl.net (8.6.10/930601.1506) id MAA25538; Sat, 15 Apr 1995 12:58:40 -0400 Received: by sage.syntex.com (940816.SGI.8.6.9/930416.SGI.AUTO) for CHEMISTRY@ccl.net id QAA09920; Sat, 15 Apr 1995 16:55:01 GMT From: "Dr. Daniel L. Severance" Message-Id: <9504150954.ZM9918@sage.syntex.com> Date: Sat, 15 Apr 1995 09:54:56 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@ccl.net Subject: PSI88: rpsi2 if, Indigo2 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, The problem with the rpsi2 script in PSI88 (originally written on a SUN) has to do with the lines of the form: if ($argv[1] == '-hp') then when $argv[1] is a switch like "-pk". For some reason, it doesn't like having a "-" as the first character in the compare string. The following form works fine (I don't know why, it just works) basically adding a space to the beginning of both strings: if (" $argv[1]" == ' -hp') then Does anyone know why the Suns and SGIs differ in this respect? I have deposited an modified rpsi2 in the incoming directory as "rpsi2.updated". Good luck! Dan -- Dr. Daniel L. Severance dan@sage.syntex.com Staff Researcher Work phone: (415) 354-7509 Syntex Discovery Research Home phone: (415) 969-5818 R6W-002 Fax (Work): (415) 354-7363 3401 Hillview Ave Palo Alto, CA 94303 From lim@rani.chem.yale.edu Sat Apr 15 16:15:11 1995 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.10/930601.1506) id QAA26535; Sat, 15 Apr 1995 16:09:49 -0400 Received: by rani.chem.yale.edu; Sat, 15 Apr 95 16:09:46 -0400 From: Dongchul Lim Message-Id: <9504152009.AA21057@rani.chem.yale.edu> Subject: Re: CCL:PSI88: rpsi2 if, Indigo2 To: chemistry@ccl.net (Computational Chemistry), dan@sage.Syntex.Com (Dan Severance) Date: Sat, 15 Apr 95 16:09:45 EDT In-Reply-To: <9504150954.ZM9918@sage.syntex.com>; from "Dr. Daniel L. Severance" at Apr 15, 95 9:54 am X-Mailer: ELM [version 2.3 PL11] Dr. Daniel L. Severance writes: > > Hi, > The problem with the rpsi2 script in PSI88 (originally written on a SUN) > has to do with the lines of the form: > if ($argv[1] == '-hp') then > when $argv[1] is a switch like "-pk". For some reason, it doesn't like having > a "-" as the first character in the compare string. The following form works > fine (I don't know why, it just works) basically adding a space to the > beginning > of both strings: > if (" $argv[1]" == ' -hp') then > > Does anyone know why the Suns and SGIs differ in this respect? > > I have deposited an modified rpsi2 in the incoming directory as > "rpsi2.updated". > > Good luck! > Dan > If an expression begins with '-' and the next letter is a valid option of 'test', it is assumed that 'test' was omitted at the beginning. E.g., if you say if (-pk == '-pk') the C shell interpretes it as if (test -pk == '-pk'). So, you get a syntax error. To prevent the C shell from interpreting an expression beginning with '-' as an expression for 'test', simply quote the expression, like if ("-pk" == '-pk') --- Dongchul Lim, Dept. of Chemistry, Yale Univ.