From Sandra.Wauters@rug.ac.be Tue Mar 10 03:16:55 1998 Received: from mserv.rug.ac.be for Sandra.Wauters@rug.ac.be by www.ccl.net (8.8.3/950822.1) id CAA25504; Tue, 10 Mar 1998 02:44:30 -0500 (EST) Received: from elptrs5.rug.ac.be by mserv.rug.ac.be with SMTP id AA09316 (5.67b/IDA-1.5 for ); Tue, 10 Mar 1998 08:44:25 +0100 Received: by elptrs5.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA15778; Tue, 10 Mar 1998 08:40:59 +0100 Date: Tue, 10 Mar 1998 08:40:59 +0100 From: Sandra.Wauters@rug.ac.be (Sandra Wauters) Message-Id: <9803100740.AA15778@elptrs5.rug.ac.be> To: chemistry@www.ccl.net Subject: Error message with G94 Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Md5: FKLK4BFZvXJkD71WzuIPHQ== Hi, I am dealing with a problem concerning a G94 calculation. I am running a frequency job on a RISC 6000 system for a system of 164 basis functions. The job aborts with the following error message : (Enter /udd06.2/udd06/sw/g94/l1002.exe) Minotr: UHF wavefunction. Direct CPHF calculation. Solving linear equations simultaneously. Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum. Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum. Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. MDV= 4000000 Integrals replicated using symmetry in FoFDir. MinBra= 0 MaxBra= 2 MinRaf= 0 MaxRaf= 2. IRaf= 0 NMat= 54 IRICut= 54 DoRegI=T DoRafI=T ISym2E= 2 JSym2E=2. Not enough memory for a single radius per batch: NAngPt= 302 MaxPt= 224. Error termination via Lnk1e in /udd06.2/udd06/sw/g94/l1002.exe. Job cpu time: 0 days 11 hours 2 minutes 3.1 seconds. File lengths (MBytes): RWF= 72 Int= 0 D2E= 0 Chk= 3 Scr= 1 I tried to change the available memory, but it doesn't make any difference. Is there anyone who has encountered this problem too, or knows how to deal with it ? I would be very grateful if someone could help me with this problem. With kind regards, Sandra Sandra Wauters PhD student Laboratorium voor Petrochemische Techniek Krijgslaan 281, S5 9000 Gent e-mail : Sandra.Wauters@rug.ac.be From root@liposome.genebee.msu.su Fri Mar 6 07:16:06 1998 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id GAA24470; Fri, 6 Mar 1998 06:49:50 -0500 (EST) Received: from localhost (root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) with SMTP id OAA04514 for ; Fri, 6 Mar 1998 14:58:24 +0300 Date: Fri, 6 Mar 1998 14:58:24 +0300 (MSK) To: chemistry@www.ccl.net From: root Reply-To: root cc: CHEMISTRY@www.ccl.net Subject: generating polypeptide oligos with X-PLOR; Re: CCL:Dear SIRS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, On Fri, 6 Mar 1998, Renate Griffith wrote: > [...] The mindset that can not even conceive of scientists being other > than male (as in "Dear Sirs, ...) is extremely hurtful. Quite apart from > being wrong. [...] I think this would give us a fascinating opportunity to conduct an informal poll -- what is the percentile of nonmales in the computational chemistry field? While certainly being multiply biased, this would at least supply ballpark figures. If nobody else will, I volunteer to count the voices. To make this post somewhat less off-topic: relatively recently I've asked the list about methods to generate pdb and psf files for polypeptide oligos. To complete the mini-summary I already provided: Andrew Atkinson via bionet.software.x-plor kindly supplied the following solution: first generate a psf file e.g. with the following X-PLOR script (polylys50mer): topology @TOPPAR:topallhdg.pro end segment name="BLAH" chain link pept head - * tail + * end first nter tail + * end last ctn head - * end sequence LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS LYS end end end write structure output=polylysine.psf end stop And feed the shiny new .psf blob into the the script coming with the X-PLOR tutorial (tutorial/nmr/generate_template.inp). The resulting pdb structure is steepest descent minimized and already subjected to some MD relaxation. Helmut Grubmueller's Solvate can handle the resulting structure. However, when using salt water for solvating matrix, it inserts references to toph19.nacl into the generated mkpsf.inp X-PLOR script. This parameter file is is not part of Solvate nor comes with X-PLOR nor is visible by AltaVista. As Helmut is currently on the move -- does anybody have a pointer to toph19.nacl? Polylysine made thusly is totally ionized, and lacks counterions. While counterions should be easy to add, estimating the dissociation coefficient of a protein polyelectrolyte appears difficult. I understand forcefields used in biochemistry do not allow for bond breakage/formation as e.g. MM2 is purported to be able to do, so a polyelectrolyte must enter the MD arena sensibly dissociated. Apart from extracting these data from an experiment, e.g. via electrophoretic mobility, is there a sofware package capable of predicting peptide polyelectrolyte dissociation coefficients under roughly physiological conditions? Regards, Eugene Leitl From georg.schmeer@chemie.uni-regensburg.de Tue Mar 10 09:16:57 1998 Received: from rrzs2.rz.uni-regensburg.de for georg.schmeer@chemie.uni-regensburg.de by www.ccl.net (8.8.3/950822.1) id JAA02093; Tue, 10 Mar 1998 09:06:51 -0500 (EST) Received: from ngate.ngate.uni-regensburg.de (ngate.rz.uni-regensburg.de [132.199.3.13]) by rrzs2.rz.uni-regensburg.de (8.8.8/8.8.8) with SMTP id PAA08216 for ; Tue, 10 Mar 1998 15:06:42 +0100 (MET) Received: from chemie.uni-regensburg.de by ngate.ngate.uni-regensburg.de; Tue, 10 Mar 98 15:07 MET Received: from ALF2/SpoolDir by alf2.ngate.uni-regensburg.de (Mercury 1.31); 10 Mar 98 15:06:39 +0100 Received: from SpoolDir by ALF2 (Mercury 1.31); 10 Mar 98 15:06:33 +0100 From: "Georg Schmeer" Organization: Universitaet Regensburg To: CHEMISTRY@www.ccl.net Date: Tue, 10 Mar 1998 15:06:25 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: alkaline hydrolysis of picryl acetate Return-receipt-to: "Georg Schmeer" Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-ID: <1F1B86D4D5C@alf2.ngate.uni-regensburg.de> Dear CCLers! I am seeking for the value of the rate constant of the alkaline hydrolysis of PICRYL ACETATE in water at 25C. Surely, my question lies on the borderline of CCLers' interest, I need however this value for the comparison with computed results of solvolysis reactions. I would be very happy if someone can help me. Many thanks for the effort Georg Schmeer. Prof. Dr. Georg Schmeer Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg Georg.Schmeer@chemie.uni-regensburg.de