From chemistry-request@server.ccl.net Sat Jul 27 04:43:55 2002 Received: from mail.fq.edu.uy (IDENT:0@[164.73.160.197]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6R8hsr15928 for ; Sat, 27 Jul 2002 04:43:54 -0400 Received: from mail.fq.edu.uy (IDENT:2019@localhost [127.0.0.1]) by mail.fq.edu.uy (8.12.4/8.12.4) with ESMTP id g6R8rN8j014028 for ; Sat, 27 Jul 2002 05:53:23 -0300 Received: from localhost (quitel2002@localhost) by mail.fq.edu.uy (8.12.4/8.12.4/Submit) with ESMTP id g6R8rNc3014025 for ; Sat, 27 Jul 2002 05:53:23 -0300 Date: Sat, 27 Jul 2002 05:53:23 -0300 (UYT) From: Quitel 2002 To: CHEMISTRY@ccl.net Subject: Quitel2002/Last call for contributions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues: This is the last call for late registering and contributions for the 28th Congress of Theoretical Chemists of Latin Expression, Montevideo, Uruguay, 1-6 September 2002. Late registration will be open until August 15th, as well as the opportunity to send your scientific contribution (poster or oral presentations). Contributions to this Congress will be published in a special number of Theoretical Chemistry Accounts (Springer). More information can be found at the Web site of the Congress http://quitel2002.fq.edu.uy (only in Spanish) or asking for it at the e-mail address quitel2002@mail.fq.edu.uy Regards ---------- Oscar N. Ventura Organizing Committee 28th Congress of Theoretical Chemists of Latin Expression Quitel2002 --- 1-6 September 2002, Montevideo, Uruguay From chemistry-request@server.ccl.net Sat Jul 27 05:50:53 2002 Received: from web20904.mail.yahoo.com ([216.136.226.226]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6R9oqr17699 for ; Sat, 27 Jul 2002 05:50:52 -0400 Message-ID: <20020727095052.9568.qmail@web20904.mail.yahoo.com> Received: from [62.90.24.137] by web20904.mail.yahoo.com via HTTP; Sat, 27 Jul 2002 02:50:52 PDT Date: Sat, 27 Jul 2002 02:50:52 -0700 (PDT) From: fedaa h Subject: i am a chemistry student need help can you help me? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii dear ccl users: can you help me with information about molecular modeling of apinephrine(adrenaline) my seminar about it and i need some reffrences or artecales about this subject . thanck u . __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Sat Jul 27 01:01:24 2002 Received: from web12804.mail.yahoo.com ([216.136.174.39]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6R51Or11368 for ; Sat, 27 Jul 2002 01:01:24 -0400 Message-ID: <20020727050124.24535.qmail@web12804.mail.yahoo.com> Received: from [203.87.150.242] by web12804.mail.yahoo.com via HTTP; Fri, 26 Jul 2002 22:01:24 PDT Date: Fri, 26 Jul 2002 22:01:24 -0700 (PDT) From: amor san juan Subject: Molecular drawing & optimization To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello all, Have anyone used Alchemy or Spartan softwares to get ligand minimized structure prior docking experiment using AutoDock3? Aside from Sybyl, MOPAC or AMPAC suggested in manual would anyone please suggest other softwares that you successfully used for docking. I appreciate your reply. Amor __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Fri Jul 26 19:22:14 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QNMDr30943 for ; Fri, 26 Jul 2002 19:22:14 -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 g6QNLdg15985 for ; Fri, 26 Jul 2002 16:21:44 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Fri, 26 Jul 2002 16:21:28 -0700 Message-ID: From: Matthew Lee To: "'chemistry@ccl.net'" Subject: partial atomic charges for autodock3 Date: Fri, 26 Jul 2002 16:21:26 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C234FB.29BBBBC0" 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_01C234FB.29BBBBC0 Content-Type: text/plain; charset="iso-8859-1" The Autodock documentation recommends calculating the ligand charges using AMPAC or MOPAC, but to only include *polar* hydrogens. Isn't it incorrect to run QM calculations on molecules that have incomplete valencies, i.e. a carbon without its hydrogen(s)? If one were to add all the hydrogens to a small molecule and do either a single point calculation or a geometry optimization for the partial atomic charges, and then remove the non-polar hydrogens, the molecule would then be far too negative. How are people using AMPAC/MOPAC in conjunction with Autodock? Are you leaving all the non-polar hydrogens there, and designating an additional 'h' atom type to be included for the non-polar hydrogens in the .gpf? Or is everyone using the rule-based Gasteiger-Marsili charges? Also, I am wondering about the hydrogens on the macromolecule. From the documentation, it seems that all hydrogrens, even the non-polar ones, present in a protein's .pdbqs file will be considered H-bond donors (as long as the atom name starts with H). I deduce this from 1) the statement that "When modeling hydrogen bonds explicitly, it is necessary to add polar hydrogens to the macromolecule.", which implies to only add polar hydrogens to the protein and 2) the fact that the .gpf file seems to only allow for C, N, O, S, H, X & M atom types in the macromolecule, without a separate type 'h' for non-polar hydrogens. It seems that the available atom types for the macromolecule are frozen, in contrast to those for the ligands, which can be anything the user wants and can be as many as the user wants. Interestingly, the documentation says under the DPF section of the Appendix: ------------------------ types Atom names for all atom types present in ligand. Each must be a single character, and only one of: C, N, O, S, H, X, or M. ------------------------ This seems erroneous, as I tried using an alternate atom name like P, or even more vaguely like J, and autodock3 has no problem as long as 1) an affinity map was created for that atom name by autogrid3, 2) the atom name appears in the "types" line of the .dpf, and 3) the ATOM_MAPS in "autocomm.h" is sufficiently large. In the AMBER all atom force field, hydrogen bonds are treated implicitly by the electrostatics, with no explicit 12 10 LJ parameters. Are there any thoughts in the community on doing the following for setting up the macromolecule: 1)including all hydrogens in the macromolecule 2)using the AMBER partial atomic charges for all protein atoms 3)turning off all H-bond acceptors in the ligand by switching the ligand's explicit H-bond paramaters for "O-H" and "S-H " in the .gpf from "12 10" to "12 6". Much thanks in advance for any feedback. --Matt Lee ******************************************************************* Matthew Randolph Lee, Ph.D. Computational Scientist phone: (858)410-6534 Lion Bioscience Inc. fax: (858)410-6665 9880 Campus Point Drive e-mail: matthew.lee@lionbioscience.com San Diego, CA 92121 ******************************************************************* ------_=_NextPart_001_01C234FB.29BBBBC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable partial atomic charges for autodock3

        The = Autodock documentation recommends calculating the ligand charges using = AMPAC or MOPAC, but to only include *polar* hydrogens.  Isn't it = incorrect to run QM calculations on molecules that have incomplete = valencies, i.e. a carbon without its hydrogen(s)?  If one were to = add all the hydrogens to a small molecule and do either a single point = calculation or a geometry optimization for the partial atomic charges, = and then remove the non-polar hydrogens, the molecule would then be far = too negative. 

        How are = people using AMPAC/MOPAC in conjunction with Autodock?  Are you = leaving all the non-polar hydrogens there, and designating an = additional 'h' atom type to be included for the non-polar hydrogens in = the .gpf? Or is everyone using the rule-based Gasteiger-Marsili = charges?

        Also, I am = wondering about the hydrogens on the macromolecule.  From the = documentation, it seems that all hydrogrens, even the non-polar ones, = present in a protein's .pdbqs file will be considered H-bond donors (as = long as the atom name starts with H).  I deduce this from 1) the = statement that "When modeling hydrogen bonds explicitly, it is = necessary to add polar hydrogens to the macromolecule.", which = implies to only add polar hydrogens to the protein and 2) the fact that = the .gpf file seems to only allow for C, N, O, S, H, X & M atom = types in the macromolecule, without a separate type 'h' for non-polar = hydrogens.  It seems that the available atom types for the = macromolecule are frozen, in contrast to those for the ligands, which = can be anything the user wants and can be as many as the user = wants.  Interestingly, the documentation says under the DPF = section of the Appendix: 

------------------------
types <string>
Atom names for all atom types present in = ligand.  Each must be a single character, and only one of: C, N, = O, S, H, X, or M.

------------------------
This seems erroneous, as I tried using an alternate = atom name like P, or even more vaguely like J, and autodock3 has no = problem as long as 1) an affinity map was created for that atom name by = autogrid3, 2) the atom name appears in the "types" line of = the .dpf, and 3) the ATOM_MAPS in "autocomm.h" is = sufficiently large.

        In the = AMBER all atom force field, hydrogen bonds are treated implicitly by = the electrostatics, with no explicit 12 10 LJ parameters.  Are = there any thoughts in the community on doing the following for setting = up the macromolecule:

1)including all hydrogens in the macromolecule =
2)using the AMBER partial atomic charges for all = protein atoms
3)turning off all H-bond acceptors in the ligand by = switching the ligand's explicit H-bond paramaters for "O-H" = and "S-H " in the .gpf from "12 10" to "12 = 6".

        Much = thanks in advance for any feedback.

--Matt Lee

***************************************************************= ****
Matthew Randolph Lee, Ph.D.

Computational Scientist =         phone:  = (858)410-6534
Lion Bioscience Inc.    =         fax:    = (858)410-6665
9880 Campus Point Drive =       e-mail:  = matthew.lee@lionbioscience.com
San Diego, CA  92121
***************************************************************= ****

------_=_NextPart_001_01C234FB.29BBBBC0-- From chemistry-request@server.ccl.net Fri Jul 26 18:46:28 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QMkRr27023 for ; Fri, 26 Jul 2002 18:46:28 -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 g6QMjwg15894 for ; Fri, 26 Jul 2002 15:45:58 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Fri, 26 Jul 2002 15:45:47 -0700 Message-ID: From: Matthew Lee To: "'chemistry@ccl.net'" Subject: autodock's autogrid3 > empty map files & 2 other small autodock q uestions Date: Fri, 26 Jul 2002 15:45:43 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C234F6.2CD59830" 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_01C234F6.2CD59830 Content-Type: text/plain; charset="iso-8859-1" Have any of the autodock users ever experienced autogrid3 leading to spurious affinity maps where every grid point energy in each of the macro.X.map files is simply the "constant" as defined in the .gpf (except for the electrostatic potential map, which appears valid)? I'm puzzled by this as there are no errors reported. With one ligand, which is highly rigid (2 rotatable bonds)I can get autogrid3 to run without any problems. On the problem ligand, the only difference I can see is that the ligand is much more flexible. deftors detects 9 rotatable bonds. Does anyone have any ideas on why autogrid3 might not be working properly? In both the working and problematic ligands, I am starting with mol2 files that have the charges defined. As a side discussion, I have two more questions/concerns. 1) I noticed that deftors changes C to A for all the "Active" AKA "Core" carbon atoms, but the 'A' atom type is not discussed at all in the documenttion. Any comments on this? 2) When deftors completes, it says: ---------------------- Checking charges in ... using "chckqs"; ... chckqs - Command not found ---------------------- I looked at deftors and it's calling .../autodock/dist305/share/check-qs. Then I looked at check-qs, which on line 23, is calling for "chckqs", which doesn't seem to exist *anywhere* in the autodock distribution tree. There is a "checkqs", which appears to just be an alternate (antiquated?) version of check-qs. Any comments on this? --Matt Lee ******************************************************************* Matthew Randolph Lee, Ph.D. Computational Scientist phone: (858)410-6534 Lion Bioscience Inc. fax: (858)410-6665 9880 Campus Point Drive e-mail: matthew.lee@lionbioscience.com San Diego, CA 92121 ******************************************************************* ------_=_NextPart_001_01C234F6.2CD59830 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable autodock's autogrid3 > empty map files & 2 other small = autodock questions

Have any of the autodock users ever experienced = autogrid3 leading to spurious affinity maps where every grid point = energy in each of the macro.X.map files is simply the = "constant" as defined in the .gpf (except for the = electrostatic potential map, which appears valid)?  I'm puzzled by = this as there are no errors reported.

With one ligand, which is highly rigid (2 rotatable = bonds)I can get autogrid3 to run without any problems.

On the problem ligand, the only difference I can see = is that the ligand is much more flexible.  deftors detects 9 = rotatable bonds.  Does anyone have any ideas on why autogrid3 = might not be working properly?  In both the working and = problematic ligands, I am starting with mol2 files that have the = charges defined.

As a side discussion, I have two more = questions/concerns. 

1) I noticed that deftors changes C to A for all the = "Active" AKA "Core" carbon atoms, but the 'A' atom = type is not discussed at all in the documenttion.  Any comments on = this?

2) When deftors completes, it says:
----------------------
Checking charges in ... using = "chckqs";
...
chckqs - Command not found
----------------------

I looked at deftors and it's calling = .../autodock/dist305/share/check-qs.  Then I looked at check-qs, = which on line 23, is calling for "chckqs", which doesn't seem = to exist *anywhere* in the autodock distribution tree.  There is a = "checkqs", which appears to just be an alternate = (antiquated?) version of check-qs.  Any comments on = this?

--Matt Lee

***************************************************************= ****
Matthew Randolph Lee, Ph.D.

Computational Scientist =         phone:  = (858)410-6534
Lion Bioscience Inc.    =         fax:    = (858)410-6665
9880 Campus Point Drive =       e-mail:  = matthew.lee@lionbioscience.com
San Diego, CA  92121
***************************************************************= ****

------_=_NextPart_001_01C234F6.2CD59830-- From chemistry-request@server.ccl.net Fri Jul 26 22:16:19 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g6R2GJT09167 for chemistry@ccl.net; Fri, 26 Jul 2002 22:16:19 -0400 Received: from roadkill.chemcomp.com ([209.226.194.165]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6PNG0r21101 for ; Thu, 25 Jul 2002 19:16:01 -0400 Received: from chemcomp.com (firewall.chemcomp.com [209.226.194.162]) by roadkill.chemcomp.com (8.9.3/8.9.3) with ESMTP id TAA06719 for ; Thu, 25 Jul 2002 19:15:57 -0400 Message-ID: <3D4087E2.86792497@chemcomp.com> Date: Thu, 25 Jul 2002 19:21:06 -0400 From: Pamela Newton Organization: CCG X-Mailer: Mozilla 4.77 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCG Excellence Awards winners Content-Type: multipart/mixed; boundary="------------4DEC85AE862AEF8E8075C04A" Status: RO X-Status: X-Keywords: This is a multi-part message in MIME format. --------------4DEC85AE862AEF8E8075C04A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The American Chemical Society's (ACS) Division of Computers and Chemistry (COMP) and Chemical Computing Group (CCG), are pleased to announce the winners of the CCG Excellence Awards for the Fall ACS National Meeting, to be held in Boston, MA from August 19-21, 2002. The CCG Excellence Awards have been created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Winners will receive a one-year software license of CCG's MOE (Molecular Operating Environment) for their academic research groups, in addition to travel costs associated with attending an ACS National Meeting to present their research. In alphabetical order, the winners are: Srikanth Kidambi from the University of Michigan, for the paper entitled: "Quantum chemical calculations of cadmium chemical shielding tensors in biologically relevant molecules" Qiong Luo from Rensselaer Polytechnic Institute, for the paper entitled: "Prediction of Glass Transition Temperatures for Polymers Using TAE/RECON Method" Nathan R. McElroy from Pennsylvania State University, for the paper entitled: "Classification of Cytogenetic Toxicity of Organic Compounds from Molecular Structure" Suhas J. Patankar from Pennsylvania State University, for the paper entitled: "Classification of HIV Protease Inhibitors and Prediction of Their Antiviral Potency from Molecular Structure" Minghu Song from Rensselaer Polytechnic Institute, for the paper entitled: "Prediction of Protein Retention Times in Anion-exchange System using Support Vector Machine Regression" Send all application materials to: Prof. Curt M. Breneman Treasurer, ACS COMP Division RPI Department of Chemistry 110 8th St.; Troy, NY 12180. brenec@rpi.edu For more information please contact: Bill Hayden Vice President, Chemical Computing Group 1010 Sherbrooke Street West, Suite 910 Montreal, Quebec, Canada H3A 2R7 hayden@chemcomp.com -- ________________________ Pamela Newton Account Manager Chemical Computing Group T: 1.514.393.1055 x 28 F: 1.514.874.9538 --------------4DEC85AE862AEF8E8075C04A Content-Type: text/x-vcard; charset=us-ascii; name="pnewton.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Pamela Newton Content-Disposition: attachment; filename="pnewton.vcf" begin:vcard n:Newton;Pamela tel;cell:(514) 945-9230 tel;fax:(514) 874-9538 tel;work:(514) 393-1055 x 28 x-mozilla-html:FALSE url:http://www.chemcomp.com org:Chemical Computing Group, Inc.;Sales/Marketing version:2.1 email;internet:pnewton@chemcomp.com title:Account Manager adr;quoted-printable:;;1010 Sherbrooke St. West=0D=0ASuite 910;Montreal;Quebec;H3A 2R7;Canada fn:Pam Newton end:vcard --------------4DEC85AE862AEF8E8075C04A--