From chemistry-request@server.ccl.net Wed Aug 7 10:16:39 2002 Received: from sas.asc.hpc.mil ([129.48.244.126]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77EGdl06845 for ; Wed, 7 Aug 2002 10:16:39 -0400 Received: from asc.hpc.mil (wk32.asc.hpc.mil [129.48.245.32]) by sas.asc.hpc.mil (8.12.4/8.12.4) with ESMTP id g77EGdDR1971420 for ; Wed, 7 Aug 2002 10:16:39 -0400 (EDT) Sender: duanx@asc.hpc.mil Message-ID: <3D512BC6.CC2D7D3C@asc.hpc.mil> Date: Wed, 07 Aug 2002 10:16:39 -0400 From: XIAOFENG FRANK DUAN Organization: CSC X-Mailer: Mozilla 4.79 [en] (X11; U; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Field strength Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone! when one does calculations of static electric field with most quantum chemistry codes (like Gaussian, GAMESS, DMol3), he/she needs to input the field strength in atomic unit. As I know, the atomic unit of the field strength can be converted to "eV/A". However, I found from papers (and physical text books) that the unit of "V/A" is used for the field strength. Can someone explain the difference between the two "field strength"? Thanks! Frank From chemistry-request@server.ccl.net Wed Aug 7 05:31:54 2002 Received: from delta.cti.unav.es ([159.237.12.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g779Vrl31564 for ; Wed, 7 Aug 2002 05:31:53 -0400 Received: from alumni.unav.es ([159.237.72.47]) by delta.cti.unav.es (8.11.4/8.11.4) with ESMTP id g779Vlf00944 for ; Wed, 7 Aug 2002 11:31:47 +0200 Sender: jj@delta.cti.unav.es Message-ID: <3D50F697.992E5E8F@alumni.unav.es> Date: Wed, 07 Aug 2002 12:29:44 +0200 From: Jose Javier Cuadrado X-Mailer: Mozilla 4.79 [en] (X11; U; IRIX64 6.5 IP30) X-Accept-Language: es, en, it, fr-FR MIME-Version: 1.0 To: chemistry@ccl.net Subject: SUMMARY: Secondary amines Content-Type: multipart/mixed; boundary="------------B0B2566E9E5BAFCAB27B95A1" This is a multi-part message in MIME format. --------------B0B2566E9E5BAFCAB27B95A1 Content-Type: multipart/alternative; boundary="------------7ABB178C083F961DD3CFDE6B" --------------7ABB178C083F961DD3CFDE6B Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Thanks to all who answer my question. My question was: * Hi to all I am working with a molecule that contains a secondary amine group. Its sustituents are: +a benzyl group +a phenyl ring I would like to know if that NH is a possible hydrogen bond acceptor. I have not found two much information. Could anybody tell me any reference about that class of secondary amines and their role as hydrogen bond acceptors? Thanks in advance The answers Ihave got: 1. Dick Caldwell wrote: A weak one. You need to find a list of pKa's of amines - the usual advanced organic texts will be a good start. I guess that yours will have a pKa of about 7, cf. good amine bases (i.e. good H bond acceptors) at about 11-12. good luck, Dick Caldwell 1. Jeremy Greenwood wrote Hi Jose, > > > I am working with a molecule that contains a secondary amine > group. Its sustituents are: > > > +a benzyl group > +a phenyl ring > i.e. :N(H)(CH2Ph)(Ph) <<-->> (H)N+(H)(CH2Ph)(Ph) > I would like to know if that NH is a possible hydrogen bond > acceptor. I have not found two much information. Could anybody tell me > any reference about that class of secondary amines and their role as > hydrogen bond acceptors? (assuming you're interested in hydrogen bond acceptors in the context of biological activity) If it's protonated, it's potentially a double hydrogen bond donor If it's neutral, it's potentially a single hydrogen bond donor and single hydrogen bond acceptor. The pKa is around 10, so it's most likely a potential double hydrogen bond donor at physiogical pH. Whether or not it is protonated in a given receptor will depend on the local environment. The local environment will also determine how many hydrogen bonds it participates in, since it's somewhat sterically crowded. If it's not protonated, then the receptor environment (and/or the rest of the molecule) will determine the chirality of the nitrogen, so you can't say anything a priori about which direction it can donates and accepts in. Hope this helps a little, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy@greenwood.net Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- 1. Richard L. wood wrote: Hi Jose I'm not an expert on this topic. That said, as I recall from my undergraduate sophomore inorganic chemistry, the basicity of amines decreases as you go from primary to secondary to tertiary, as the electron withdrawing power of the R groups pulls the lone pair electrons closer to the nitrogen, making it more difficult to donate those electrons to an acid. I would think it would make it more difficult to act as an H-bond acceptor as well. So I would think that H-bond acceptor strength would go ammonia > primary amine > secondary amine. I hope this helps. Richard 1. Dave Shobe wrote: I don't think the benzyl group would make that much difference. (Unlike the phenyl group which is known to interact strongly with the nitrogen lone pair). Accordingly, if you can't find a study on N-benzylaniline, a study of N-methylaniline or N-ethylaniline would probably be close enough. Hopefully you are in a place with good literature searching tools. :-) --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com --------------7ABB178C083F961DD3CFDE6B Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit   

Thanks to all who answer my question.
My question was:
 
  • Hi to all
            I am working with a molecule that contains a secondary amine
group. Its sustituents are:
 

        +a benzyl group
        +a phenyl ring
 

            I would like to know if that NH is a possible hydrogen bond
acceptor. I have not found two much information. Could anybody tell me
any reference about that class of secondary amines and their role as
hydrogen bond acceptors?

            Thanks in advance
 

The answers Ihave got:
 
 

  1. Dick Caldwell wrote:


A weak one. You need to find a list of pKa's of amines - the usual
advanced organic texts will be a good start. I guess that yours will have
a pKa of about 7, cf. good amine bases (i.e. good H bond acceptors) at
about 11-12.
good luck, Dick Caldwell
 
 

  1. Jeremy Greenwood  wrote


Hi Jose,

>
>
>             I am working with a molecule that contains a secondary amine
> group. Its sustituents are:
>
>
>         +a benzyl group
>         +a phenyl ring
>
i.e. :N(H)(CH2Ph)(Ph) <<-->> (H)N+(H)(CH2Ph)(Ph)

>             I would like to know if that NH is a possible hydrogen bond
> acceptor. I have not found two much information. Could anybody tell me
> any reference about that class of secondary amines and their role as
> hydrogen bond acceptors?

(assuming you're interested in hydrogen bond acceptors in the
context of biological activity)

If it's protonated, it's potentially a double hydrogen bond donor
If it's neutral, it's potentially a single hydrogen bond donor
and single hydrogen bond acceptor.

The pKa is around 10, so it's most likely a potential double
hydrogen bond donor at physiogical pH. Whether or not it is protonated
in a given receptor will depend on the local environment.
The local environment will also determine how many hydrogen bonds
it participates in, since it's somewhat sterically crowded.
If it's not protonated, then the receptor environment (and/or
the rest of the molecule) will determine the chirality of the
nitrogen, so you can't say anything a priori about which direction
it can donates and accepts in.

Hope this helps a little,

Jeremy
----------------------------------------------------------------------
Jeremy Greenwood                                  jeremy@greenwood.net
Department of Medicinal Chemistry                      bh +45 35306117
Royal Danish School of Pharmacy                        fx +45 35306040
Universitetsparken 2, DK-2100 Copenhagen, Denmark      ah +45 32598030
----------------------------------------------------------------------
 
 
 

  1. Richard L. wood wrote:
Hi Jose

I'm not an expert on this topic.

That said, as I recall from my undergraduate sophomore inorganic chemistry,
the basicity of amines decreases as you go from
primary to secondary to tertiary, as the electron withdrawing power of the
R groups pulls the lone pair electrons closer to the nitrogen,
making it more difficult to donate those electrons to an acid.  I would
think it would make it more difficult to act as an H-bond acceptor
as well.  So I would think that H-bond acceptor strength would go ammonia >
primary amine > secondary amine.

I hope this helps.

Richard
 
 

  1. Dave Shobe wrote:
I don't think the benzyl group would make that much difference.  (Unlike the
phenyl group which is known to interact strongly with the nitrogen lone
pair).

Accordingly, if you can't find a study on N-benzylaniline, a study of
N-methylaniline or N-ethylaniline would probably be close enough.

Hopefully you are in a place with good literature searching tools. :-)

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com
 
 

--------------7ABB178C083F961DD3CFDE6B-- --------------B0B2566E9E5BAFCAB27B95A1 Content-Type: text/x-vcard; charset=us-ascii; name="jcuasan.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Jose Javier Cuadrado Content-Disposition: attachment; filename="jcuasan.vcf" begin:vcard n:Cuadrado Sanchez;Jose Javier x-mozilla-html:FALSE url:http://www.unav.es/organica/jj/ org:Universidad de Navarra;Dpto. Qca. Organica y Farmaceutica adr:;;C/Irunlarrea 1;Pamplona ;;31080;Espanna version:2.1 email;internet:jcuasan@alumni.unav.es x-mozilla-cpt:;26944 fn:Jose Javier Cuadrado Sanchez end:vcard --------------B0B2566E9E5BAFCAB27B95A1-- From chemistry-request@server.ccl.net Wed Aug 7 08:12:44 2002 Received: from web12804.mail.yahoo.com ([216.136.174.39]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g77CCil03231 for ; Wed, 7 Aug 2002 08:12:44 -0400 Message-ID: <20020807121244.92864.qmail@web12804.mail.yahoo.com> Received: from [61.9.73.249] by web12804.mail.yahoo.com via HTTP; Wed, 07 Aug 2002 05:12:44 PDT Date: Wed, 7 Aug 2002 05:12:44 -0700 (PDT) From: amor san juan Subject: docked output viewer To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all, Someone please kindly share what visualization software is effective in viewing a docked ligand and protein. Thanks, Amor __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Wed Aug 7 10:39:22 2002 Received: from pasteur ([164.2.255.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77EdMl07834 for ; Wed, 7 Aug 2002 10:39:22 -0400 Received: from lrb.ap-hop-paris.fr (localhost [127.0.0.1]) by pasteur.ap-hop-paris.fr (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H0H00DPC9N7RH@pasteur.ap-hop-paris.fr> for chemistry@ccl.net; Wed, 07 Aug 2002 16:30:43 +0200 (MEST) Date: Wed, 07 Aug 2002 15:39:25 -0700 From: Pong Subject: Problem of Raman calculation by Gaussian94w Sender: pong@ap-hop-paris.fr To: chemistry@ccl.net Message-id: <3D51A19D.1FCCC6F2@lrb.ap-hop-paris.fr> Organization: Service de Biochimie et de biologie moleculaire MIME-version: 1.0 X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Dear all, I use Gaussian94w Revision-E.1 for window. I have the problem with frequency caculation. I prefer to calculate both IR and Raman spectra. I used keyword in the input file as following; ********************************************* Gaussian 94: x86-Win32-G94RevE.1 23-Nov-1996 07-Aug-1902 ********************************************* %Chk=D:\g94_outputs\GLYCEROL\water\water_B3LYP_631Gd.chk ---------------------------- # B3LYP/6-31G* Opt Freq Test ---------------------------- But in the output file, it does not have data for Raman intensity (only IR, as shown) Full mass-weighted force constant matrix: Low frequencies --- -49.0895 -47.6951 -20.2841 -.0026 -.0022 -.0018 Low frequencies --- 1712.8715 3727.4009 3849.4834 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A' A' A' Frequencies -- 1712.8715 3727.4009 3849.4834 Red. masses -- 1.0825 1.0453 1.0810 Frc consts -- 1.8713 8.5567 9.4382 IR Inten -- 75.8354 1.6952 19.4360 Raman Activ -- .0000 .0000 .0000 Depolar -- .0000 .0000 .0000 Atom AN X Y Z X Y Z X Y Z 1 8 .00 .07 .00 .00 .05 .00 .07 .00 .00 2 1 -.43 -.56 .00 .58 -.40 .00 -.55 .44 .00 3 1 .43 -.56 .00 -.58 -.40 .00 -.55 -.44 .00 I tried to specify keyword ,Freq Raman to the input file. But it has error message as following; Gaussian 94: x86-Win32-G94RevE.1 23-Nov-1996 07-Aug-1902 ********************************************* %Chk=D:\g94_outputs\GLYCEROL\water\water_B3LYP_631Gd_raman.chk ---------------------------------- # B3LYP/6-31G* Opt Freq Raman Test ---------------------------------- QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. LYP/6-31G* OPT FREQ RAMAN TEST ' Last state="GCL" TCursr= 2963 LCursr= 24 Error termination via Lnk1e in C:\G94W\l1.exe. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 1 Scr= 1 Any-way, I changed to other level of basis set, for example MP2. It still be the same problem, except when I used the HF level of calculation, the program can calculate both IR and Raman. How can i solve this problem? Could you please give me the advises directly to my e-mail address; jaturong.pratuangdejkul@lrb.ap-hop-paris.fr Finally, I would like to thank for all kindness to help me solving my problem. Best regards, Pratuangdejkul J. From chemistry-request@server.ccl.net Wed Aug 7 13:14:54 2002 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77HEsl12094 for ; Wed, 7 Aug 2002 13:14:54 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: docked output viewer Date: Wed, 7 Aug 2002 10:14:43 -0700 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: docked output viewer Thread-Index: AcI+IHQ/tYFSSu2YSNqja2HAU0DZeAAFIRNA From: "DeLano, Warren" To: "amor san juan" , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g77HEsl12095 I'm known to be biased, but this is one of PyMOL's strongpoints. http://pymol.sf.net For multiple ligands (docking results), you'll want to start with a protein in PDB format, and prepare your docked ligands as a 3D SD-file (MDL format). To view them from within PyMOL, issue commands like: load target.pdb show surf, target load docked.sdf show sticks, docked You can then use the arrow keys to step through the docked ligands. Cheers, Warren -- mailto:warren@sunesis.com Warren L. DeLano, Ph.D. > -----Original Message----- > From: amor san juan [mailto:a_juanphd@yahoo.com] > Sent: Wednesday, August 07, 2002 5:13 AM > To: chemistry@ccl.net > Subject: CCL:docked output viewer > > > Hi all, > > Someone please kindly share what visualization > software is effective in viewing a docked ligand and > protein. > > Thanks, > Amor > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.yahoo.com > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | > Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Aug 7 15:17:32 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77JHWl15581 for ; Wed, 7 Aug 2002 15:17:32 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g77JHW113402; Wed, 7 Aug 2002 15:17:32 -0400 (EDT) Date: Wed, 7 Aug 2002 15:17:30 -0400 (EDT) From: Jan Labanowski To: jkl@ccl.net cc: software@asdn.net Subject: 02.09.15 Software Development for Process and Materials Design Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Invitation to a Symposium in Moscow... This is hopefully THE LAST reminder about the Symposium: SOFTWARE DEVELOPMENT FOR PROCESS AND MATERIALS DESIGN, Moscow, September 15-16, 2002 Sorry if you got it before... Check the following URL for more info: http://asdn.net/moscow/software.shtml The symposium is a satellite event of the larger conference: Nano and Giga Challenges in Microelectronics (NGCM) Sept. 10-13, 2002. Our Symposium was originally planned for Cracow as a part of E-MRS Fall meetings. The E-MRS Cracow event was cancelled in late June by E-MRS. Rather than abandon our participants, we moved the Meeting to Moscow and attached it to the other conference which we are coorganizing (we offer substantial discount if you sign up for the two conferences). We are quite happy that the risk we undertook to move the symposium was a good bet. We have a great 2-day program (over 40 submitted abstracts), and we are forced to run 3 sessions per day. We still can squeeze a few oral presentations, and of course take more posters. If you want to contribute, we would have to see your abstract submitted within a day or two, since we are firming up the program. Please hurry if you want to be a part of this exciting event. The topics of interest are listed on the home page of the meeting, but in short: we give priority to methodology development and software development for process and materials design. Excellent application papers are also considered. We plan to publish the proceedings of this meeting. We were lucky to get support and sponsors on a short notice, and we are able to waive registration fees and subsidize local accommodations for our speakers. Please check our site, for latest information and details. THERE IS ALSO A PROSPECT OF SUPPORT FOR EUROPEAN BASED GRAD STUDENTS AND YOUNG RESEARCHERS (it is still in works, though), so register and fill the financial aid form. Note that we also have some small, optional component in Cracow (details on the Web). Please register today, if you want to come. There is a reason for rushing you to do it now!!!. Getting Russian Visa is easy but it TAKES MUCH TIME (up to a month). If you want to come, you have to start the process NOW!!!. Thank you for your time... Yours as always... Jan K. Labanowski Ohio Supercomputer Center 1224 Kinnear Rd Columbus, OH 43221-1163 For the Organizing Committe: Jim Greer, National Microelectronics Research Centre, Cork, Ireland Anatoli A. Korkin, Motorola, Mesa, AZ, USA Stanislaw A. Kucharski, University of Silesia, Katowice, Poland Boris V. Potapkin, Russian Research Ctr "Kurchatov Institute", Moscow, Russia Jerzy M Rudzinski, FQS Poland Sp. z o.o., Cracow, Poland Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ From chemistry-request@server.ccl.net Wed Aug 7 15:04:55 2002 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77J4tl15260 for ; Wed, 7 Aug 2002 15:04:55 -0400 Received: from dhcp.csuohio.edu (scifac209-53.dhcp.csuohio.edu [137.148.209.53]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0H0H00B04MCFS3@sims.csuohio.edu> for CHEMISTRY@ccl.net; Wed, 7 Aug 2002 15:05:03 -0400 (EDT) Date: Wed, 07 Aug 2002 15:04:09 -0400 From: "David W. Ball" Subject: freqchk utility X-Sender: d.ball@popmail.csuohio.edu To: CHEMISTRY@ccl.net Message-id: <5.1.0.14.0.20020807150209.00a45480@popmail.csuohio.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT After some experimentation with G98's freqchk utility, I have concluded that the utility does not work if the molecule has imaginary (negative) vibrational frequencies. Is that correct? (If it isn't, then I haven't found out why I'm having trouble with it!) Thanks, David ************************************* David W. Ball, Ph.D. Professor of Chemistry President, Cleveland Technical Societies Council Treasurer, CSU-AAUP Councilor, Cleveland Section of the American Chemical Society Department of Chemistry Cleveland State University Cleveland OH 44115 d.ball@csuohio.edu 216-687-2456, fax 216-687-9298 www.csuohio.edu/chemistry/dwb.html Personal web pages: academic.csuohio.edu/ball (CAUTION! Includes lots of baby pictures!) ************************************* From chemistry-request@server.ccl.net Wed Aug 7 13:53:17 2002 Received: from sgofims02.ccs.ppg.com ([141.189.251.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77HrHl13208 for ; Wed, 7 Aug 2002 13:53:17 -0400 Received: by sgofims02.ccs.ppg.com with Internet Mail Service (5.5.2653.19) id ; Wed, 7 Aug 2002 13:53:13 -0400 Message-ID: <2195C52A2E0BD41190CB0090273F72E504390659@sgofusr09.ccs.ppg.com> From: "Deng, Jun" To: chemistry@ccl.net Subject: TDDFT question Date: Wed, 7 Aug 2002 13:53:11 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi, Does anyone has experience in TDDFT calculation on a charged molecule? I found that for neutral compounds, TDDFT generally gives smaller excitation energy than experiment for neutral compounds. However, for charged molecules, it gives much, much higher energy. Why? Any suggestion? Thank you all in advance! *********************************************************************** Jun Deng 440 College Park Drive Senior Research Chemist Monroeville, PA 15146 Applied Scientific Computing Tel: (724) 325-5243 Monroeville Technical Center Fax: (724) 325-5225 PPG Industries, Inc. E-mail: jdeng@ppg.com *********************************************************************** From chemistry-request@server.ccl.net Wed Aug 7 14:21:50 2002 Received: from pasteur ([164.2.255.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77ILnl14195 for ; Wed, 7 Aug 2002 14:21:49 -0400 Received: from lrb.ap-hop-paris.fr (localhost [127.0.0.1]) by pasteur.ap-hop-paris.fr (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H0H00E4XKEI2I@pasteur.ap-hop-paris.fr> for chemistry@ccl.net; Wed, 07 Aug 2002 20:23:06 +0200 (MEST) Date: Wed, 07 Aug 2002 19:31:48 -0700 From: Pong Subject: program to generate pharmacophore Sender: pong@ap-hop-paris.fr To: chemistry@ccl.net Message-id: <3D51D814.B8362B3F@lrb.ap-hop-paris.fr> Organization: Service de Biochimie et de biologie moleculaire MIME-version: 1.0 X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Dear all, I'm Mr. PRATUANGDEJKUL Jaturong. I'm a student in Faculty of Pharmacy, Paris V University, France. My thesis is the field of mollecular modeling in drug design. I'm the beginner for this field. Now I have many ligands. I would like to find out the pharmacophore. I read many papers, they used program to automatically generate pharmacophore, such as APEX, Catalyst, RAPID, GASP. But all is commercial program. I don't have enough money to buy those one. So, could you please give me any idea, where I can find the free of charge for academic or trial version of pharmacophore generating program. Finally, I would like to thank for your kind helping. Best regards, Jaturong From chemistry-request@server.ccl.net Wed Aug 7 11:17:52 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g77FHql09067 for ; Wed, 7 Aug 2002 11:17:52 -0400 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g77FHFg10602; Wed, 7 Aug 2002 08:17:15 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Wed, 7 Aug 2002 08:17:05 -0700 Message-ID: From: Stephen Bowlus To: "'amor san juan'" , chemistry@ccl.net Subject: RE: docked output viewer Date: Wed, 7 Aug 2002 08:16:57 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C23E25.788F8960" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C23E25.788F8960 Content-Type: text/plain; charset="iso-8859-1" I use VMD from the TBG at UI: http://www.ks.uiuc.edu/#over Input is a pdb file with the ligand identified in HETATM records. sb > -----Original Message----- > From: amor san juan [mailto:a_juanphd@yahoo.com] > Sent: Wednesday, August 07, 2002 5:13 AM > To: chemistry@ccl.net > Subject: CCL:docked output viewer > > > Hi all, > > Someone please kindly share what visualization > software is effective in viewing a docked ligand and > protein. > > Thanks, > Amor > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.yahoo.com > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | > Jan: jkl@ccl.net > > > > > ------_=_NextPart_001_01C23E25.788F8960 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: docked output viewer

I use VMD from the TBG at UI: http://www.ks.uiuc.edu/#over

Input is a pdb file with the ligand identified in = HETATM records.

sb

> -----Original Message-----
> From: amor san juan [mailto:a_juanphd@yahoo.com]
> Sent: Wednesday, August 07, 2002 5:13 AM
> To: chemistry@ccl.net
> Subject: CCL:docked output viewer
>
>
> Hi all,
>
> Someone please kindly share what = visualization
> software is effective in viewing a docked = ligand and
> protein.
>
> Thanks,
> Amor
>
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