From chemistry-request@server.ccl.net Fri Nov 2 03:45:23 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA28jJB05437 for ; Fri, 2 Nov 2001 03:45:20 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 15zZzs-0000SV-00; Fri, 02 Nov 2001 10:48:16 +0200 Received: from vejas (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id LAA05558; Fri, 2 Nov 2001 11:27:43 +0200 (GMT) Date: Fri, 2 Nov 2001 10:48:19 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <1691560133.20011102104819@vaidila.vdu.lt> To: Wibke Sudholt CC: CHEMISTRY@ccl.net Subject: Re: CCL:Adding hydrogens In-reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Try Swiss-PDB viewer as well. Good luck Arturas ----------------------------> WS> I am searching for free programs that are able to add hydrogens to a given WS> xyz or pdb structure (organic molecule, protein). It would be great if one WS> has some control over this process, e.g. at which atoms how many hydrogens WS> are attached. From chemistry-request@server.ccl.net Fri Nov 2 07:58:52 2001 Received: from serwis ([193.91.0.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA2CwqB10898 for ; Fri, 2 Nov 2001 07:58:52 -0500 Received: from mgroth by serwis with local (Exim 3.12 #1 (Debian)) id 15zeuP-0000V7-00 for ; Fri, 02 Nov 2001 15:02:57 +0100 Date: Fri, 2 Nov 2001 15:02:57 +0100 From: Malgorzata Groth To: chemistry@ccl.net Subject: avoided crossing Message-ID: <20011102150257.K1094@serwis> Reply-To: m.groth@miasto.gdynia.pl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Organization: Wydzial informatyki UM Gdyni Sender: Malgorzata Groth Hi everyone :D Does anyone of you know any free software by means of which I could start to searching for avoided crossing of some photochemical reactions? I have acces to Gaussian (not free of course), but the mcscf algorithm is too slowly for this case. In Gamess it is not possible as I know. Does somebody knows such program ? Thanks for your help Malgorzata Groth -- --- _/ _/ _/_/_/ _/_/ _/_/ _/ _/ _/ _/ _/ _/_/ "No one can give you wiser advice _/ _/ _/ _/ than yourself" - Cicero _/ _/ _/_/_/ From chemistry-request@server.ccl.net Fri Nov 2 03:42:41 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA28geB05355 for ; Fri, 2 Nov 2001 03:42:40 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 15zZxP-0000SN-00; Fri, 02 Nov 2001 10:45:43 +0200 Received: from vejas (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id LAA05545; Fri, 2 Nov 2001 11:25:05 +0200 (GMT) Date: Fri, 2 Nov 2001 10:45:41 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <921401965.20011102104541@vaidila.vdu.lt> To: Yubo Fan CC: CHEMISTRY@ccl.net Subject: Re: CCL:GIF file with frequency animation In-reply-To: <3BE02988.6A340C96@mail.chem.tamu.edu> References: <3BE02988.6A340C96@mail.chem.tamu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Yubo, There is some soft - known as video grabbers - which is capabele to take the snapshots from your monitor, while vibratin animations play. Better way - in my mind - use gOpenmol. There is option to export normal modes vibrations into MPEG, via making TGA files. Later you can convert TGA to GIF files for each frame. Then you can bring all frames together in any GIF animation sotware (there is sharaware as well). That's all. Good luck - I think it'll help you :-) Arturas ----------------------------> YF> Hi, YF> Guassview and HyperChem can visualize vibrational modes calculated by YF> G98, to my knowledge. But, they can't export the animations to any YF> format that common programs, such as Windows MediaPlayer, can load. In YF> fact, I want to create some animated GIF files for some frequencies. I YF> mean if I can capture 4 or 5 pictures from Guassview or HyperChem's YF> animation, these GIF files can be created correctly. YF> Any advice? Thanks in advance YF> Yubo <--------------------------- Arturas From chemistry-request@server.ccl.net Fri Nov 2 08:21:09 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA2DL8B11505 for ; Fri, 2 Nov 2001 08:21:09 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 15zeIt-0000jd-00; Fri, 02 Nov 2001 15:24:11 +0200 Received: from vejas (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id QAA07668; Fri, 2 Nov 2001 16:03:41 +0200 (GMT) Date: Fri, 2 Nov 2001 15:24:10 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <43247335.20011102152410@vaidila.vdu.lt> To: sanner@scripps.edu CC: CCL Subject: ADT error .. need help Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I installed ADT undr linux (Suse 7.0, kernel 2.4.x). My python runs (/usr/bin/env python). I have corrected 'adt' executable first line: #!/usr/bin/env python1.5.2 -> #!/usr/bin/env python in oder it could run at all. My ADT package was decompressed as follos : /home/'my dir'/share/lib/python1.5/site-packages/AutoDockTools /home/'my dir'/i86linux2/.... Made alias to 'adt' as well. But when I run in bash prompt 'adt' I get the following error: > '...my path to adt...' line 40, in ? import AutoDockTools ImportError: No modules named AutoDockTools hit any .... What is wrong ? I got another directory i86linux2. What is the relation with 'adt' ? From chemistry-request@server.ccl.net Fri Nov 2 16:28:27 2001 Received: from dagger.nd.edu ([129.74.250.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA2LSQB21950 for ; Fri, 2 Nov 2001 16:28:26 -0500 Received: from mahler (mahler.chem.nd.edu [129.74.80.173]) by dagger.nd.edu (8.10.2/8.10.2) with ESMTP id fA2LVVC12428 for ; Fri, 2 Nov 2001 16:31:31 -0500 (EST) From: "Nicolas Saettel" To: Subject: SCIPCM Problem in Gaussian Date: Fri, 2 Nov 2001 16:34:03 -0500 Message-ID: <000001c163e6$17e02d00$ad504a81@mahler> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C163BC.2F0BABA0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C163BC.2F0BABA0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi all, I am trying to run a SCIPCM calculation with Gaussian98, but I get this error message: WARNING! Serious error in surface integrals. It is probable that some of the solute is outside the cavity and/or parts of the cavity surface cannot be reached from the origin. Try more integration points or a different set of integration origins. Surface Problems in SciFoc Do you know how to set more integration points, or any other fix? Thanks in advance, Nicolas SAETTEL http://www.nd.edu/~nsaettel University of Notre Dame Department of Chemistry and Biochemistry NOTRE DAME, IN 46556 tel: +1 (219) 631-4007 ------=_NextPart_000_0001_01C163BC.2F0BABA0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Message
Hi=20 all,
I am trying to run a SCIPCM calculation with=20 Gaussian98, but I get this error message:
 
 WARNING!  Serious error in surface = integrals.
 It is=20 probable that some of the solute is outside the cavity and/or
parts = of the=20 cavity surface cannot be reached from the origin.
 Try more = integration=20 points or a different set of  integration origins.
 Surface = Problems in SciFoc
Do you = know how to=20 set more integration points, or any other fix?
Thanks = in=20 advance,
 

      Nicolas=20 SAETTEL           =            =20 http://www.nd.edu/~nsaettel = ;
  =20 University of Notre=20 Dame           &nb= sp;    
Department=20 of Chemistry and = Biochemistry   
    =20 NOTRE DAME, IN=20 46556           &n= bsp;       =20 tel: +1 (219) 631-4007

 
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