From chemistry-request@server.ccl.net Mon May 3 03:25:15 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA01969 for ; Mon, 3 May 1999 03:25:15 -0400 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA03229 Mon, 3 May 1999 03:20:58 -0400 (EDT) Message-Id: <199905030720.DAA03229@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Mon, 03 May 1999 09:19:43 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: CHEMISTRY@www.ccl.net Date: Mon, 3 May 1999 09:21:07 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re:CCL:POAV analysis Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) > Hello everybody, > I'm looking for the QCMP044 program for the > calculation of pyramidalization angle in > nonplanar conjugated organic molecules. > R.C Haddon was interested in POAV Analysis. > Have you ever heard something about this? > > Thank you, > Francesca Dear Franceska, I do not know about the QCPE program. However, the program Mol2Mol can calculate POAV and a few other pyramidality indices as well. Have a look on http://www.compuchem.com/mol2mol.html Tamas ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ From chemistry-request@server.ccl.net Mon May 3 05:44:43 1999 Received: from cfalfa.chfi.unipd.it (cfalfa.chfi.unipd.it [147.162.53.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA03202 for ; Mon, 3 May 1999 05:44:40 -0400 Received: by cfalfa.chfi.unipd.it; (5.65v3.2/1.1.8.2/02Nov95-0925AM) id AA26873; Mon, 3 May 1999 10:42:09 GMT Date: Mon, 3 May 1999 10:42:09 +0000 (GMT) From: Steve Todd To: chemistry@ccl.net Subject: multipart xyz visualisation... In-Reply-To: <199904252134.RAA04553@alchemy.chem.utoronto.ca> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there... I am looking for a piece of software that allows you to visualise and animate multipart xyz files. I have used software such as Re_View from Dr Gosper but it appears to have a limit of 50 "sections" and my output files are around 500-1000 "sections" ... Does anyone know of any software capable of animating files this big ? Cheers for any advice and I will sumarise later... Steve Email: S.Todd@chfi.unipd.it Snailmail: Dr Stephen Todd c/o Gruppo di Chimica Teorica Dipartimento di Chimica Fisica Universita' degli Studi di Padova Via Loredan 2 I-35131 Padova Italy From chemistry-request@server.ccl.net Mon May 3 08:43:43 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA04854 for ; Mon, 3 May 1999 08:43:43 -0400 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA03627 Mon, 3 May 1999 08:39:20 -0400 (EDT) Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.8.7/8.8.7) with ESMTP id QAA00421 for ; Mon, 3 May 1999 16:43:17 +0400 Sender: val@nmr-v.ioc.ac.ru Message-ID: <372D99E5.84A493BE@cacr.ioc.ac.ru> Date: Mon, 03 May 1999 16:43:17 +0400 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.30 i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL_post Subject: PCM Geometry Optimization Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I have some problems with PCM geometry optimization of transition metal complexes (ECP bases set) in GAMESS program. First 5 or 6 steps it goes like a normal geometry optimization, but during all the rest cycles gradient doesn't change leading to unconverged geometry search (an example attached below). Does anybody know how to solve the problem (or just a hint ;) ? It would be nice to hear if anybody were successful in obtaining PCM geometries of TM complexes with other programs. In addition, any references concerning PCM calculations on platinum group metal complexes are very appreciated. It is of interest whether PCM optimization is a problem of the particular software or a general one. Thanks! The summary will be sent. best regards, Valentin. PCM geometry optimization example: step=1 MAXIMUM GRADIENT = 0.0029642 RMS GRADIENT = 0.0010251 step=2 MAXIMUM GRADIENT = 0.0020712 RMS GRADIENT = 0.0006788 step=3 MAXIMUM GRADIENT = 0.0014879 RMS GRADIENT = 0.0005576 step=4 MAXIMUM GRADIENT = 0.0007580 RMS GRADIENT = 0.0003812 step=5 MAXIMUM GRADIENT = 0.0004269 RMS GRADIENT = 0.0001639 step=6 MAXIMUM GRADIENT = 0.0001744 RMS GRADIENT = 0.0000857 step=7 MAXIMUM GRADIENT = 0.0001727 RMS GRADIENT = 0.0000677 step=8 MAXIMUM GRADIENT = 0.0001685 RMS GRADIENT = 0.0000617 step=9 MAXIMUM GRADIENT = 0.0001604 RMS GRADIENT = 0.0000706 step=10 MAXIMUM GRADIENT = 0.0001525 RMS GRADIENT = 0.0000608 step=11 MAXIMUM GRADIENT = 0.0001546 RMS GRADIENT = 0.0000611 ................... step=60 MAXIMUM GRADIENT = 0.0001495 RMS GRADIENT = 0.0000628 step=61 MAXIMUM GRADIENT = 0.0001502 RMS GRADIENT = 0.0000598 step=62 MAXIMUM GRADIENT = 0.0001495 RMS GRADIENT = 0.0000592 step=63 MAXIMUM GRADIENT = 0.0001533 RMS GRADIENT = 0.0000718 step=64 MAXIMUM GRADIENT = 0.0001493 RMS GRADIENT = 0.0000593 ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Mon May 3 09:25:59 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA05485 for ; Mon, 3 May 1999 09:25:59 -0400 Received: from f04n01.cac.psu.edu (f04s01.cac.psu.edu [128.118.141.31]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA03810 Mon, 3 May 1999 09:21:45 -0400 (EDT) Received: from [146.186.73.41] (I1S.OZ.PSU.EDU [146.186.73.41]) by f04n01.cac.psu.edu (8.8.7/8.6.12) with SMTP id JAA77256 for ; Mon, 3 May 1999 09:21:42 -0400 Message-Id: <199905031321.JAA77256@f04n01.cac.psu.edu> X-Sender: i1s@email.psu.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 3 May 1999 10:53:52 -0400 To: chemistry@www.ccl.net From: i1s@psu.edu (Inge Schuster) Subject: Xl structures Hi! Is there a program out there for the Mac or PC to convert X-ray info.( unit cell dimensions, fractional coordinates) to info on bond lengths, angles, etc.together with graphics representation of the systems. From chemistry-request@server.ccl.net Mon May 3 11:38:42 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06902 for ; Mon, 3 May 1999 11:38:42 -0400 Received: from ns.dsm.nl (ns.dsm.nl [163.175.153.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA04093 Mon, 3 May 1999 11:34:25 -0400 (EDT) From: Steven.Creve@dsm-group.com Received: from dsm-fw1. (dsm-fw1.dsm.nl [163.175.153.254]) by ns.dsm.nl (8.8.6/MQT) with SMTP id RAA12696 for ; Mon, 3 May 1999 17:43:16 +0200 (METDST) Received: from localhost (root@localhost) by dsm-om1.dsm.nl (8.8.6/MQT) with SMTP id RAA28604 for CHEMISTRY@www.ccl.net;Mon, 3 May 1999 17:31:31 +0200 (METDST) X-OpenMail-Hops: 5 Date: Mon, 3 May 1999 17:32:43 +0200 X-OpenMail-Transport-Id: <04717372DC19B003/NL/400net/DSM/372DBF86.10DD.4908.000> Message-Id: <"372DBF86.10DD.4908.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Subject: CCL: program for equilibria MIME-Version: 1.0 TO: CHEMISTRY@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi, does anyone know about a program to calculate the equilibrium composition of a mixture of about 5-10 compounds, where the K's, DeltaG's, ... are known. (In fact, this is a straightforward calculation task, but it would be nice if a simple program is at hand...) Regards, Steven Creve From chemistry-request@server.ccl.net Sat May 1 21:08:47 1999 Received: from out4.ibm.net (out4.ibm.net [165.87.194.239]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA18135 for ; Sat, 1 May 1999 21:08:46 -0400 Received: from jm (slip-32-100-189-144.in.us.ibm.net [32.100.189.144]) by out4.ibm.net (8.8.5/8.6.9) with ESMTP id BAA20356; Sun, 2 May 1999 01:04:52 GMT Message-ID: <000101be9438$38eeb500$90bd6420@jm> Reply-To: "jerome f. baker" From: "jerome f. baker" To: Cc: "Mary O'Sullivan" Subject: problem with AutoDock 3.0 example files Date: Sat, 1 May 1999 20:07:57 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-7" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Hello CCL subscribers, We have just compiled AutoDock 3.0 for Linux, and are attempting to run the two sets of example docking files which are included in the distribution. There does not seem to be an electrostatics map in either set, so we have removed all of the map files and have run AutoGrid to produce a complete set of map files for both examples. This works perfectly. However, when we attempt to run AutoDock, as soon as it has read in the various .map files and attempts to +ACI-move+ACI- the ligand (the .pdbq file), it aborts and returns a +ACI-segmentation fault+ACI- message. Any suggestions from more experienced AutoDock users? Thanks very much, Sincerely, Jerry Baker jfbaker+AEA-ibm.net