From chemistry-request@server.ccl.net Wed Oct 24 14:14:53 2001 Received: from camitros01.camitro.com ([63.97.7.141]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9OIEpB24179 for ; Wed, 24 Oct 2001 14:14:53 -0400 Received: by camitros01.camitro.com with Internet Mail Service (5.5.2653.19) id ; Wed, 24 Oct 2001 11:16:30 -0700 Message-ID: From: "Guo, Jianxin" To: "'chemistry@ccl.net'" Cc: "'christian.pilger@bc.boehringer-ingelheim.com'" Subject: Re: continuum regression Date: Wed, 24 Oct 2001 11:16:24 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi, Christian, You can try matlab to find what you want. Good luck. Jianxin Dear CCLers, is anybody aware of software capable of what is called 'continuum regression' for statistical analysis ? Regards, Christian ________________________________________________________________ Dr. Christian Pilger Dept. Chemical Research / Structural Research J51-00-01 Boehringer Ingelheim Pharma KG D-88397 Biberach/Germany Phone: 07351-545749 Fax: 07351-5497924 mailto: christian.pilger@bc.boehringer-ingelheim.com From chemistry-request@server.ccl.net Wed Oct 24 19:34:53 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9ONYrB30192 for ; Wed, 24 Oct 2001 19:34:53 -0400 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id TAA06929 for ; Wed, 24 Oct 2001 19:37:43 -0400 (EDT) Message-ID: <3BD750C4.4DF0DD81@mindless.com> Date: Wed, 24 Oct 2001 19:37:40 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: isosurface on gopengmol Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To any gOpenMol users, Ive recently been advised to download gopenmol and use it to generate isosurfaces, and have done so. I am using autodock and have generated map files which can be converted to plt files which can be used in gopenmol. However Im not sure which map file is appropriate for mapping electrostatic isosurfaces, Autodock generates a seperate map file for each separate type of atom that exists, i.e.. ACOH etc... Secondly once you have mapped the surface how does one go about getting values to color the isosurface according to electrostatic potential. Basically, what I want to do is generate an affinity isosurface on my macromolecule that is related to the ligand that I have previously docked. If there is an easier way to do this with gopenmol could anyone please let me know. Thanks so much for everyone's suggestions, in the past everyone has bee very generous with there helps... thank you. David From chemistry-request@server.ccl.net Wed Oct 24 03:56:45 2001 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9O7uiB14803 for ; Wed, 24 Oct 2001 03:56:45 -0400 Received: from imim.es (i21.imim.es [193.147.240.127]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id V277DX68; Wed, 24 Oct 2001 10:00:14 +0200 Sender: hteran@ccl.net Message-ID: <3BD673F4.1078799E@imim.es> Date: Wed, 24 Oct 2001 09:55:32 +0200 From: "Hugo G. de Teran" X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: Demetrio Antonio da Silva Filho CC: CHEMISTRY@ccl.net Subject: Re: CCL:Animate sequence of coordinates from TINKER References: <5.1.0.14.0.20011023180348.00b2bc20@deimos.email.arizona.edu> Content-Type: multipart/alternative; boundary="------------F331A60572636AAF16A30922" --------------F331A60572636AAF16A30922 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit VMD (http://www.ks.uiuc.edu/Research/vmd/) uses Babel to convert a series of xyz to a series of PDB files which VMD reads as an animation. I never tried this option, but this is what the documentation of the program says. Hope it helps, Hugo Demetrio Antonio da Silva Filho wrote: > Dear CCL'ers, > > I am using TINKER to perform some MD calculations and I would like > to animate the viewing of sequence of coordinates snapshots from > a dynamic trajectory. > > Does anybody knows a free software able to read the TINKER .xyz > files and animate them ? > > Thanks in advance, > > Demetrio Filho > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Hugo G. de Teran Castaņon G. R. Informatica Biomedica Institut Municipal d'Investigacio Medica - IMIM C/ Dr Aiguader, 80, E-08003/ Barcelona (SPAIN) Ph: +34 93 221 10 09 ext 2340 Fax: Fax: +34 93 221 3237 http://www1.imim.es/modeling/ --------------F331A60572636AAF16A30922 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit VMD (http://www.ks.uiuc.edu/Research/vmd/) uses Babel to convert a series of xyz to a series of PDB files which VMD reads as an animation.
I never tried this option, but this is what the documentation of the program says.
Hope it helps,
Hugo

Demetrio Antonio da Silva Filho wrote:

Dear CCL'ers,

I am using TINKER to perform some MD calculations and I would like
to animate the viewing of sequence of coordinates snapshots from
a dynamic trajectory.

Does anybody knows a free software able to read the TINKER .xyz
files and animate them ?

Thanks in advance,

Demetrio Filho

-= This is automatically added to each message by mailing script =-
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MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
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Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

-- 
Hugo G. de Teran Castañon
G. R. Informatica Biomedica
Institut Municipal d'Investigacio Medica - IMIM
C/ Dr Aiguader, 80, E-08003/ Barcelona (SPAIN)

Ph: +34 93 221 10 09 ext 2340
Fax: Fax: +34 93 221 3237
                    
                    http://www1.imim.es/modeling/
  --------------F331A60572636AAF16A30922-- From chemistry-request@server.ccl.net Tue Oct 23 18:22:38 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NMMbB25992 for ; Tue, 23 Oct 2001 18:22:37 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id f9NMSVx15517 for chemistry@ccl.net; Tue, 23 Oct 2001 15:28:31 -0700 Received: from jnauss1-pc.accelrys.com (jnauss1-pc.sd.accelrys.com [172.30.51.68]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id f9NMSVX15508 for ; Tue, 23 Oct 2001 15:28:31 -0700 Message-Id: <5.1.0.14.0.20011023152404.00ac0e50@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 23 Oct 2001 15:26:16 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Customer Training on Cerius2 in San Diego Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys Inc. will be holding two workshops involving the Cerius2 user interface at the San Diego Supercomputer Center, San Diego, CA. The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on Dec 11-12. This course provides an overview of molecular modeling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modeling experience is not assumed making this course a great place to learn molecular modeling with Cerius2. Also, a week later on Dec 13-14, the "Small Molecule and Drug Design with Cerius2" workshop will be offered. This workshop is aimed at our customers who are involved in drug design or the development of other bioactive compounds and who would like to make more effective use of modeling in their research. The course will focus on QSAR techniques and methodologies as well as structure-based ligand design. Familiarity with the Cerius2 environment is required for attendance to this workshop. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second course. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Thank you very much. Jeffrey L. Nauss 858-799-5555 Chris Arzt 858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc. From chemistry-request@server.ccl.net Wed Oct 24 05:35:21 2001 Received: from fecit-gate.fecit.co.uk (firewall-user@[193.119.134.250]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9O9ZKB16598 for ; Wed, 24 Oct 2001 05:35:21 -0400 Received: by fecit-gate.fecit.co.uk; id KAA24101; Wed, 24 Oct 2001 10:50:16 +0100 Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma024099; Wed, 24 Oct 01 10:49:17 +0100 Received: from wakusei.co.uk (wakusei.fecit.co.uk [192.168.101.54]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id KAA06649; Wed, 24 Oct 2001 10:14:44 +0100 Received: from localhost by wakusei.co.uk (SMI-8.6/SMI-SVR4) id KAA08026; Wed, 24 Oct 2001 10:36:20 +0100 Date: Wed, 24 Oct 2001 10:36:20 +0100 (BST) From: Andrew Horsfield X-Sender: hfield@wakusei.fecit.co.uk Reply-To: Andrew Horsfield To: Computational Chemistry List , Atomic Scale Design Network Subject: Call for announcements Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am preparing the second electronic newsletter of the Institute of Physics Computational Physics Group. If there are any meetings that you are involved with for 2002 that might be of interest to computational physicists and which you would like announced, please send me, by e-mail, in plain text format, the details of the meeting. Please include: o Title of meeting o Venue o Date o URL of web page giving full details of meeting The newsletters can be found at: http://joule.physics.salford.ac.uk/iopcpg Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, Hayes Park Central, Hayes End Road, Hayes, Middlesex UB4 8FE, United Kingdom. phone: +44-(0)20-8606-4653 FAX: +44-(0)20-8606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Wed Oct 24 19:38:03 2001 Received: from smtp1.ndsu.nodak.edu ([134.129.111.146]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9ONc3B30352 for ; Wed, 24 Oct 2001 19:38:03 -0400 Received: from sud8b.pharm.ndsu.NoDak.edu (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) by smtp1.ndsu.nodak.edu (8.11.2/8.11.2) with SMTP id f9ONETf32269; Wed, 24 Oct 2001 18:14:29 -0500 Date: Wed, 24 Oct 2001 18:12:01 -0500 From: "Xin Hu" To: robert@sgmol.bq.ub.es cc: chemistry@ccl.net Subject: Re: CCL:autodock cryst.str. minimisation Message-ID: <3219741142.1003947121@sud8b.pharm.ndsu.NoDak.edu> X-Mailer: Mulberry (Win32) [1.3.3, s/n S-398030] X-Authenticated: xin.hu by imap.ndsu.nodak.edu X-Licensed-To: Mulberry User MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I am very interested in your questions, actually those are what I want to ask for help. I attempted to do local minimization only before and as you said the ligand always moved out the active site. Is there other settings we need to change besides editting the dpf file to do_local_only ? Also I would like to know how to get each energy contribution value because we want to re-calibrate the scoring functions to obtain our own energy coefficient, using the same procedure as Dr. Morris report in the paper.But the two problems are : the do_local_only seems not work properly and we do not know how to get each energy term. If you any answer for these questions, please let me know. I appreciate if someone give me some help. Thanks! xin hu Robert Soliva wrote: Dear Autodock users, I have a couple of questions regarding the use of autodock to minimise with the local search method. I apologise if they seem too obvious (I have just started using the program). 1- I want to minimise a ligand-receptor structure taken from the pdb. I understand I am supposed to use the do_local_only command, but I do not know how to tell the program to optimise without moving the ligand randomly out of the active site. Could anybody send me an example of a dpf input file that can do this? 2-Is is possible once the minimisation has taken place, to have not only the value for the total interaction, but also the value for the different terms of the scoring function (i.e. to have the value and its composition in terms of vdW, electrostatic, H bonding torsion and desolvation?). Is there a command to ask the program for those values? Please reply to robert@sgmol.bq.ub.es Thank you very much for your help. Robert. -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ************************************************* Xin Hu Department of Pharmaceutical Science College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298 (O) 701-231-4360 (H) Fax: 701-231-7781 E-mail: Xin_Hu@ndsu.nodak.edu xxh0541@hotmail.com *************************************************