From chemistry-request@ccl.net Thu May 22 21:31:47 2003 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4N1Vlbc027794 for ; Thu, 22 May 2003 21:31:47 -0400 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3p2/8.9.3) with ESMTP id VAA15081; Thu, 22 May 2003 21:31:43 -0400 (EDT) Message-ID: <3ECD79F9.42D8CAFA=at=cornell.edu> Date: Thu, 22 May 2003 20:31:38 -0500 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry=at=ccl.net" Subject: Re: CCL:Periodic system (fwd) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Remove some of the solvent molecules or make the box bigger? Richard Jan Labanowski wrote: > ---------- Forwarded message ---------- > Return-Path: > Date: Wed, 21 May 2003 13:52:56 -0300 > Message-Id: > Subject: Periodic system > From: "ancarauta" > To: jkl=at=ccl.net > > Hi. > I'm calculating a periodic system but the solvent > molecules are blowing up the box. Does anybodry help me? > > Thanks a lot. > > Alexandre Carauta > > > --- > UOL, o melhor da Internet > http://www.uol.com.br/ > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST=at=ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl=at=ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Chemistry Trinity University, San Antonio, TX 78212 From chemistry-request@ccl.net Thu May 22 18:10:56 2003 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4MMAubc022460 for ; Thu, 22 May 2003 18:10:56 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h4MMAux9023028; Thu, 22 May 2003 18:10:56 -0400 (EDT) Date: Thu, 22 May 2003 17:43:17 -0400 From: Rick Venable To: CHEMISTRY.-at-.ccl.net cc: "E.L. Willighagen" Subject: CCL: SUMMARY of MPEG and molecular animation tools Message-ID: ReplyTo: Rick_Venable.-at-.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I recently asked about animation formats in the context of making movies > from simulation trajectories (from CHARMM in my case), and a slightly edited summary of responses follows, along with my original question. Some general comments to the responses: [1] A few suggested GIF animations, but I worry about color information loss in going from TrueColor to a PseudoColor format like GIF; I'll probably try it anyway. [2] I also thought MPEG1 was a standard format, but nonetheless I've had a great deal of trouble trying to use Windows Media Player to play animations created with the venerable mpeg_encode program. [3] I plan to try a couple of the alternate encoders, which allow setting the frame rate (mpeg_encode does not); I've found 10 fps works well for the MD simulation animations I've made. Thanks to everyone for their replies. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable.-at-.nih.gov ALT email: rvenable.-at-.speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= =============== original question ========================= I've been making molecular animations from CHARMM trajectories in MPEG1 format using mpeg_encode* for a while, but I'm having trouble finding good MPEG1 players for M$ Windows and MacOS these days. The only 2 that were decent were VMPEG for M$, and Sparkle on the Mac; in particular, they allow the user to set the frame rate for playback. However, these haven't been updated in some time; I don't think there's a native OSX version of Sparkle, for instance. * from a series of still frames rendered via POV-Ray In contrast, newer apps either don't play MPEG1 at all (M$ Media Player, for instance) and others will play the MPEG1 files, but offer no means of controlling the frame rate (QuickTime, RealPlayer). My questions are: Are there other inexpensive or free media players for M$ and Mac that can handle MPEG1 and can provide a way to set the playback speed? Can anyone recommend other inexpensive animation software for making "movies" in a common format from a series of still frames? Is anyone aware of conversion tools, that might convert MPEG1 to QuickTime or other common format? I prefer Linux tools, but I'll use whatever works. Thanks. ================ summary of responses ==================== From: Jason D. Gans While not the exact solution you were looking for, Qmol (windows only) can directly render DCD files and multi-model pdb files as AVI movies. Both frame rate and compression level can be specified, as well as a host of different graphics and display styles (ribbons, surfaces, clipping plane, etc). The source code and executable can be found at: http://lancelot.bio.cornell.edu/jason/qmol.html ========================================================== From: Bill Ross ImageMagick will make animated GIFs from a series of stills, and I think it allows frame rate control. ========================================================== From: Lee Woodcock I have used Gimp in the past to do animations. It can do animated gifs well. However, I also have used the animation tool in paint shop pro, it works pretty well. Also, ffmepg in linux can convert from mpeg to avi and there should be plenty of avi players for winblows and macOS. The last thing that may help is imagemagick in linux, it can make some nice animations. I am not sure if you have tried all that I have mentioned above but I have used them to make some animations recently. ========================================================== From: Etienne Derat Currently, I use mencoder from the package MPlayer http://www.mplayerhq.hu There is a lot of options and exportation's types. With PNG or JPEG from Povray you can make movie with command's line like this: mencoder -mf on:w=800:h=600:fps=25 -ovc divx4 -o output.avi \*.jpg It's a little bit complicated at the beginning but very powerful after. Ask me if you have some problems ========================================================== From: Fabian Boes i am using the following windows based software for doing my animations: "Pymol" -> for creating the animation and saving single .png files for each frame "IrfanView" -> for converting the .png into .bmp files "pjBmp2Avi" -> for creating an uncompressed .avi file out of the bitmap (or .tga ) files. frame rate can be specified as well as the keyframes. the resulting animation in uncompressed .avi format is very large (approx. 900 MB for 40 sec. with 640x480 resolution, 25fps). thus i compress it using the programm "Virtualdub" with the open-source video codec "Xvid", which is similar to the popular "DivX" codec. "Virtualdub" is not able to save .mpeg files, but you can use "TMPGEnc" to create .mpeg files out of your uncompressed .avi file. all of the programs i mentioned are - as far as i now - open-source, freeware or shareware, excluding "TMPGEnc" which is free only for personal use (see their website for more details). here are the links: "Pymol" -> http://www.pymol.org "IrfanView" -> http://www.irfanview.com "pjBmp2Avi" -> http://www.cspltd.ndirect.co.uk/graphics/anim.htm "Virtualdub" -> http://www.virtualdub.org/ "XVid" -> http://www.xvid.org (just the source-code, a comiled version can be found here: http://www.roeder.goe.net/%7Ekoepi/xvid.shtml) "TMPGEnc" -> http://www.tmpgenc.net/ ========================================================== From: David F. Green I believe that mencode (the encoder associated with mplayer, one the most functional movie players for linux available) will convert to and > from a number of formats, including MPEG-1, AVI, and Quicktime. I don't have a lot of experience with the encoding side of this software, but > from my experience with the mplayer, it is very good software. Plus, it's open source, and RPMs are available if you're running RedHat. > From the playback under M$/Mac side of things, you also might want to check out some of the DVD players, since they should all read MPEG just fine. I'm not sure if these have adjustable playback speed, but they may. ========================================================== From: Surjit Dixit you could try using "VideoMach" with VMD (VMD has scripts to to use this program). the user can also adjust the frame rate while generating the mpeg file using VideoMach. You can employ videomach with images generated from other sources too. check: http://www.gromada.com/products.html They seem to have other media players that i have not used. it might have the option you are looking for. ========================================================== From: Tru Huynh you might want to check vlc from: http://www.videolan.org/vlc/features.html Although, I don't know if you can set the frame rate. You can also use the MPlayer encoder/player from: http://www.mplayerhq.hu/homepage ========================================================== From: Bogdan Costescu Windows can play MPEG1 files with Media Player with some filter that comes with the OS by default, however there are some limitations that show up especially when embeeding MPEG1 files into PowerPoint presentations for example. The MPEG1 file has to be constrained to some "standard" settings: 720x576 pixels in size (352x288 and 320x240 seem to also work), only in 25 or 30 (possibly 24 and 29.8) frames/second, encoded using constant bit rate, all coming from the television standards. I have had no problems playing such files with Media Player in Windows98SE, Windows2000 (Pro and Server) and WinXP, without installing any extra players/filters. MEncoder for Linux (http://www.mplayerhq.hu) can import still frames and output AVI and (experimental) MPEG; the content of AVI can be compressed with a variety of codecs. The drawback of this method is that the respective codec has to be installed on the Windows/MacOS/whatever machine in order to play back the movie, which is sometimes impossible (administrative reasons, inexistance of the codec for a particular platform, etc.). What do you call a "common format" ? I'd call MPEG1 a common format because it's an industry (video) standard. TMPGEnc has profiles for generating movies in VCD format (MPEG1-based) that can be played by the majority of standalone DVD players ! MEncoder can import MPEG1 (and MPEG2) files and convert them to AVI. There are lots of Windows tools for importing MPEG1/2 files and exporting AVI (and some of them offer much more functionality, like video editting in VirtualDub (http://www.virtualdub.org)) mainly used for DVD backup, one starting point is http://www.doom9.org. ================ end of summary ====================== From chemistry-request@ccl.net Thu May 22 19:03:05 2003 Received: from zephyr.meteo.McGill.CA (zephyr.Meteo.McGill.CA [132.206.43.13]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h4MN35bc023864 for ; Thu, 22 May 2003 19:03:05 -0400 Received: from kinetic.Meteo.McGill.CA by zephyr.meteo.McGill.CA (AIX 4.1/UCB 5.64/4.03) id AA21872; Thu, 22 May 2003 18:51:51 -0400 Date: Thu, 22 May 2003 18:59:56 -0400 From: Andrew Ryzhkov X-Mailer: The Bat! (v1.61) Reply-To: Andrew Ryzhkov Organization: Dep. of Atm. & Oc. Sci. McGill Univ. X-Priority: 3 (Normal) Message-Id: <121602121734.20030522185956.-at-.zephyr.meteo.mcgill.ca> To: chemistry.-at-.ccl.net Subject: ViewMol3D new version is available Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL people, I glad to present for your attention the new version of my program - the ViewMol3D 4.02 In short, it is a very small OpenGL viewer of molecular structures from output files of some quantum chemical packages like Gaussain and GAMESS. It is possible to view various models (e.g. ball'n'stick, CPK), vectors (gradient and oscillation), measure parameters (bond length, angles), etc. The main page of the ViewMol3D http://redandr.tripod.com/vm3/ Changes history of the program can be found at http://redandr.tripod.com/vm3/viewmol3d_history.htm Download sites: http://redandr.tripod.com/vm3/viewmol3d_download.htm Best regards, Andrew Dr. Andrei Ryjkov Departments of Chemistry, and Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West #808 Montreal, Quebec, CANADA, H3A 2K6. -------------------------------------- Phone: +1(514)398-8867 Fax: +1(514)398-6115 -------------------------------------- E-mail: Andrew.-at-.Zephyr.Meteo.McGill.Ca Internet: http://RedAndr.tripod.com From chemistry-request@ccl.net Thu May 22 21:40:08 2003 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4N1e7bc027942 for ; Thu, 22 May 2003 21:40:07 -0400 Received: from laquicom02 ([148.223.46.1]) by yakko.cimav.edu.mx (8.12.3/8.12.3/Debian-6.3) with SMTP id h4N1cIgR029123 for ; Thu, 22 May 2003 19:38:21 -0600 Message-ID: <001b01c320c3$d42e6df0$8400000a@laquicom02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: condensed Fukui functions Date: Thu, 22 May 2003 19:39:54 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0018_01C32099.EAF1DBF0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0018_01C32099.EAF1DBF0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: Is there any way (exact or an approximation) to estimate molecular condensed Fukui functions, without resorting to the calculation of the atomic charges of the anion and cation ? That is, something based only on the neutral molecule ? Thanks in advance Dr. Daniel Glossman-Mitnik ********************************************************************** Dr. Daniel Glossman-Mitnik Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Qu=EDmica Computacional Miguel de Cervantes 120 - Comp. Ind. Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel.: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman.-at-.cimav.edu.mx glossman.-at-.hotmail.com dglossman.-at-.yahoo.com ********************************************************************** ------=_NextPart_000_0018_01C32099.EAF1DBF0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
Dear netters:
 
Is there any way (exact or an = approximation) to=20 estimate
molecular condensed Fukui functions, without resorting to
the calculation of the atomic = charges of the=20 anion and cation ?
That is, something based only on the = neutral=20 molecule ?
 
Thanks in advance
 
          &nbs= p;            = ;           =20 Dr. Daniel Glossman-Mitnik
 
****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigaci=F3n en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Qu=EDmica Computacional
Miguel = de=20 Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih. 31109 - = MEXICO
Tel.:=20 (52) 614 4391151
FAX: (52) 614 4391112
E-mail: daniel.glossman.-at-.cimav.edu.mx=
           = ;=20 glossman.-at-.hotmail.com
 &n= bsp;         =20 dglossman.-at-.yahoo.com
**********= ************************************************************
= ------=_NextPart_000_0018_01C32099.EAF1DBF0-- From chemistry-request@ccl.net Fri May 23 07:19:29 2003 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4NBJSbc009007 for ; Fri, 23 May 2003 07:19:28 -0400 Received: from mail-e.bcc.ac.uk by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 23 May 2003 12:18:56 +0100 Received: from D270CN0J (actually host chem120.chem.ucl.ac.uk) by mail-e.bcc.ac.uk with SMTP (Mailer); Fri, 23 May 2003 12:15:09 +0100 Message-ID: <003401c3211d$5f80f180$784c2880@D270CN0J> From: Tom Lewis To: chemistry Subject: G98 error Date: Fri, 23 May 2003 12:20:52 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0031_01C32125.C0DA1490" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0031_01C32125.C0DA1490 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, Just a quick question regarding Gaussian. I don't have much = experience with it, and I have a structure for which I have constrained = four dihedral angles for an optimisation. It accepts all the = constraints, but errors with a ' Curvilinear step not converged. Error = imposing constraints'. Is this because of a problem with the torsion = angles selected, and is there a way around this? Thanks in advance Tom -------------------------------------------------------------------------= ------ Thomas C Lewis Centre of Theoretical and Computational Chemistry University College London Thomas.lewis:at:ucl.ac.uk (020) 76794665 ------=_NextPart_000_0031_01C32125.C0DA1490 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,
    Just a quick = question regarding=20 Gaussian. I don't have much experience with it, and I have a structure = for which=20 I have constrained four dihedral angles for an optimisation. It accepts = all the=20 constraints, but errors with a ' Curvilinear step not converged. Error = imposing=20 constraints'. Is this because of a problem with the torsion angles = selected, and=20 is there a way around this?
 
Thanks in advance
 
Tom
 
----------------------------------------------------------------= ---------------
Thomas=20 C Lewis
Centre of Theoretical and Computational = Chemistry
University=20 College London
Thomas.lewis:at:ucl.ac.uk
(020= )=20 76794665
------=_NextPart_000_0031_01C32125.C0DA1490-- From chemistry-request@ccl.net Fri May 23 15:03:22 2003 Received: from ms1.usu.edu (ms1.usu.edu [129.123.104.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4NJ3Lbc018178 for ; Fri, 23 May 2003 15:03:22 -0400 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by ms1.usu.edu (8.12.8/8.12.8) with SMTP id h4NJ7r4P026248 for ; Fri, 23 May 2003 13:07:53 -0600 Reply-To: From: "Tapas Kar" To: "CCL" Subject: MNDO/PM3/AM1 parameters for Transition metals Date: Fri, 23 May 2003 13:00:24 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0002_01C3212B.46628D40" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MailScanner: Found to be clean This is a multi-part message in MIME format. ------=_NextPart_000_0002_01C3212B.46628D40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear Colleagues, Where can I find MNDO/PM3/AM1 parameters for fist-row transition metals, especially for Fe and Mn? Tapas *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar=at=cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html ------=_NextPart_000_0002_01C3212B.46628D40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 Colleagues,
Where can=20 I find  MNDO/PM3/AM1 parameters for fist-row transition metals, = especially=20 for Fe and Mn?
Tapas

***********************************************
"We owe a lot to the Indians, who taught = us how to=20 count, without
which no worthwhile scientific discovery could have = been=20 made."
         &n= bsp;           &nb= sp;           &nbs= p;        =20 - Albert Einstein=20 -
--------------------------------------------------------------------= ------------
Tapas=20 Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State=20 University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax:=20 435-797-3390
Email: tapaskar=at=cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html

 
------=_NextPart_000_0002_01C3212B.46628D40-- From chemistry-request@ccl.net Fri May 23 09:58:59 2003 Received: from tocsy.utmb.edu (tocsy.utmb.edu [129.109.73.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4NDwxbc012395 for ; Fri, 23 May 2003 09:58:59 -0400 Received: from tocsy.utmb.edu (localhost [127.0.0.1]) by tocsy.utmb.edu (SGI-8.9.3p2/8.9.3) with ESMTP id IAA13262; Fri, 23 May 2003 08:59:43 -0500 (CDT) Sender: dpower-.at.-tocsy.utmb.edu Message-ID: <3ECE294F.3DF557F1-.at.-tocsy.utmb.edu> Date: Fri, 23 May 2003 08:59:43 -0500 From: David Power Organization: Sealy Center for Structural Biology X-Mailer: Mozilla 4.78C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Tom Lewis CC: chemistry Subject: Re: CCL:G98 error References: <003401c3211d$5f80f180$784c2880@D270CN0J> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Tom, This usually happens when the fixed torsional or dihedral angles are far from that of the starting geometry. This can also happen if you fix too many redundant coordinates at once causing Gaussian to have a difficult time funneling the forces in the remaining coordinates. In the case of the latter problem, the code will go through the first energy cycle and then crash. In the first example, the code will crash in the first few ms of the clock time. Have a look at the starting geometry and make sure that Gaussian can move the coordinates easily without atoms coming into close proximity. Cheers, David Tom Lewis wrote: > Hi, Just a quick question regarding Gaussian. I don't have much > experience with it, and I have a structure for which I have > constrained four dihedral angles for an optimisation. It accepts all > the constraints, but errors with a ' Curvilinear step not converged. > Error imposing constraints'. Is this because of a problem with the > torsion angles selected, and is there a way around this? Thanks in > advance Tom > ------------------------------------------------------------------------------- > > Thomas C Lewis > Centre of Theoretical and Computational Chemistry > University College London > Thomas.lewis-.at.-ucl.ac.uk > (020) 76794665 -- ( @ @ ) -------------o00o----(_)----o00o----------------------------------- | Dr. David Power | | | Department of Human | Never Teach A Pig To Sing. | | Biological Chemistry | It Wastes Your Time & | | & Genetics | Annoys The Pig. | | University of Texas | | | Medical Branch | Office: (409)-747-6822 | |301 University Blvd., Rt 1157 | Main Office: (409)-747-6800 | | Galveston, TX 77555-1157 | Fax: (409)-747-6850 | | .ooo0 | Email: dpower-.at.-tocsy.utmb.edu | | ( ) 0ooo.| | ------------------\ (-----( )------------------------------------ \_) ) / (_/ From chemistry-request@ccl.net Fri May 23 09:15:31 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4NDFUbc011632 for ; Fri, 23 May 2003 09:15:31 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Fri, 23 May 2003 10:17:54 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B39-.at.-correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: CCL: Connect 2 benzene rings and optimise Date: Fri, 23 May 2003 10:17:52 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4NDFVbc011635 Dear CCLers, If you connect two aromatic rings with a short hydrocarbon chain (3 carbons) and put it to optimise using HF/3-21g in gaussian98 it does not finish. There must be a simple explaination but I can't see it at the moment. Any ideas? Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell-.at.-cetem.gov.br From chemistry-request@ccl.net Fri May 23 22:21:12 2003 Return-Path: Received: from mbu.iisc.ernet.in (mail.mbu.iisc.ernet.in [144.16.74.32]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h4O03Xt06280 for ; Fri, 23 May 2003 20:03:33 -0400 (EDT) Received: from mbu.iisc.ernet.in (localhost.localdomain [127.0.0.1]) by mbu.iisc.ernet.in (8.12.8/8.12.5) with ESMTP id h4O0bXST003278 for ; Sat, 24 May 2003 06:07:33 +0530 Received: from localhost (gyan@localhost) by mbu.iisc.ernet.in (8.12.8/8.12.5/Submit) with ESMTP id h4O0bW8s003274 for ; Sat, 24 May 2003 06:07:33 +0530 Date: Sat, 24 May 2003 06:07:31 +0530 (IST) From: Gyanendra kumar To: chemistry[at]ccl.net Subject: Autodock_segmentation_fault Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.2 required=6.0 tests=SPAM_PHRASE_00_01,USER_AGENT_PINE version=2.43 hi all, could anybody tell me, how large a ligand can autodock handle? Even after setting the stacksize to unlimited, the autotors is giving segmentation fault, when I am running it on a molecule like CoA. Is this problem because of the big size of ligand (bigger than normal small organic molecules). Is there any subroutine in autodock which can automatically define the torsions in a ligand. I have using Autodock on my PC running on Linux Red-hat 7.3 OS. Thanks in advance, Gyan.