From owner-chemistry@ccl.net Thu Jun 7 06:35:01 2007 From: "Vladimir Chupakhin chupvl#,#gmail.com" To: CCL Subject: CCL: Metabolic rules handling Message-Id: <-34431-070607061750-12054-P4RThcxMw2gmP3S6rwjwkA:-:server.ccl.net> X-Original-From: "Vladimir Chupakhin" Date: Thu, 7 Jun 2007 06:17:46 -0400 Sent to CCL by: "Vladimir Chupakhin" [chupvl~~gmail.com] Dear All! I wondering how do the metabolic rules are stored in metabolites prediction software? and how they applied? Do open source metabolites prediction software exists? Yours, Chupakhin Vladimir From owner-chemistry@ccl.net Thu Jun 7 08:35:01 2007 From: "Paritosh Mondal paritos]~[tezu.ernet.in" To: CCL Subject: CCL: Computational Chemistry Message-Id: <-34432-070607081604-14449-RuevA3fbAOXR1V3c5MO9Hg]|[server.ccl.net> X-Original-From: "Paritosh Mondal" Date: Thu, 7 Jun 2007 08:16:01 -0400 Sent to CCL by: "Paritosh Mondal" [paritos^^tezu.ernet.in] In calculating transition state using DMOL3 program with PWC/DNP basis set, I am unable to get the desire structure for the formation titanium hydroperoxo complex from Hydrogen peroxide and TS-1 zeolites. Paritosh Mondal paritos a tezu.ernet.in Department of Chemical Sciences Tezpur University Tezpur Assam India-784028 From owner-chemistry@ccl.net Thu Jun 7 09:09:01 2007 From: "Marco Neves marco.neves^^icrm.cnr.it" To: CCL Subject: CCL: Using Metals with AutoDockTools Message-Id: <-34433-070607081523-14366-+rWKkXBrzPIeh0pjOJhYaw*|*server.ccl.net> X-Original-From: Marco Neves Content-transfer-encoding: 7bit Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Jun 2007 12:09:56 +0200 MIME-version: 1.0 Sent to CCL by: Marco Neves [marco.neves-,-icrm.cnr.it] Check your .pdbqs file. Zinc atoms must be identified with an M (3rd column). If not, change it manually. I recently started using autodock4. It seems to recognize better metal atom types. Hope this help. marco M K Creber mary.creber||rmc.ca wrote: > Sent to CCL by: "M K Creber" [mary.creber|,|rmc.ca] > I am a new user to AutoDock (version 3.0.5), currently attempting to use the GUI AutoDockTools to set up, launch and analyze AutoDockruns. My macromolecule of interest, MMP-2 (Gelatinase-a) contains 2 Zinc molecules. The program prompts me to input the ionic radius and potential energy well depth for Zn to create the .pdbqs file, but when I run autogrid I get the following error message: > > autogrid3: WARNING! Atom type error, can't find type for "Zn" in typelist "CNOSHXM" > > Does anyone with AD/ADT experience have any suggestions for where I might be going wrong or where to edit in the file to get it to recognize Zn as a type "M" (metal)? > > Thank you in advance, > > MK Creber > Royal Military College of Canada> > > > > From owner-chemistry@ccl.net Thu Jun 7 15:32:00 2007 From: "Rob Paton rsp25(_)cam.ac.uk" To: CCL Subject: CCL: babel conversion of batchmin output Message-Id: <-34434-070607131119-25613-uIdCwhjue3SaaKUi8ai+qw..server.ccl.net> X-Original-From: "Rob Paton" Date: Thu, 7 Jun 2007 13:11:16 -0400 Sent to CCL by: "Rob Paton" [rsp25-.-cam.ac.uk] Hi, I'm trying to use babel to convert the output of a batchmin (macromodel) job into a jaguar format input file. However, the output file is sufficiently esoteric that babel complains of a segmentation error. I have tried using the mmod, out, mmd and dat flags to no avail. Any helpful suggestions? Is there an option for batchmin to write to a different file format? Many thanks in advance, Rob Paton rsp25 at cam dot ac dot uk Cambridge University, UK From owner-chemistry@ccl.net Thu Jun 7 16:08:00 2007 From: "Peter Nielsen peter#,#daylight.com" To: CCL Subject: CCL: Release Announcement: Daylight v.4.93 Message-Id: <-34435-070607134641-28997-NYAd8w2awG3ZSdlhihae2g]*[server.ccl.net> X-Original-From: "Peter Nielsen" Date: Thu, 7 Jun 2007 13:46:38 -0400 Sent to CCL by: "Peter Nielsen" [peter{:}daylight.com] ------------------------------------------------------------- Daylight Chemical Information Systems, Inc. Release Announcement DAYLIGHT CIS SOFTWARE, VERSION 4.93 www.daylight.com ------------------------------------------------------------- Daylight Chemical Information Systems, Inc. is pleased to announce that Daylight Software v.4.93 is now released and available for downloading at www.daylight.com. New products in v.4.93 include Daylight Web Services and a fully- supported Daylight Java Wrapper. The web services facilitate the rapid development and deployment of discovery-oriented web applications to a broad audience. Also included in v.4.93 are new multi-threading capabilities of DayCart and Daylight Toolkits, resulting in up to a ten-fold improvement in performance of the cartridge on multiprocessor systems. Daylight v.4.93 also includes the capability to derive a SMARTS- based scaffold from a group of molecules as both a Web Service and as a feature of the SMARTS Toolkit. In addition, a new algorithm partitions structures into clusters, each with a common substructure single or multi-fragment covering a large proportion of every molecule in the cluster. This scaffold-directed clustering algorithm is offered as a Web Service or as part of the the Daylight Clustering Package. Thank you, Daylight CIS, Inc. http://www.daylight.com From owner-chemistry@ccl.net Thu Jun 7 17:36:01 2007 From: "Geoffrey Hutchison geoffh-x-pitt.edu" To: CCL Subject: CCL: babel conversion of batchmin output Message-Id: <-34436-070607173229-31127-rDZ+NNnoYQUAirXSZG9J9w[A]server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 7 Jun 2007 16:28:30 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Geoffrey Hutchison [geoffh**pitt.edu] > I'm trying to use babel to convert the output of a batchmin > (macromodel) job into a jaguar format > input file. However, the output file is sufficiently esoteric that > babel complains of a segmentation > error. I have tried using the mmod, out, mmd and dat flags to no > avail. Well, they're all the same underlying format code, so if one fails, the rest certainly will. Of course, Open Babel should never crash. So if you're using, e.g. Open Babel version 2.1, then please file a bug report and include the appropriate output file for us to test. http://sourceforge.net/projects/openbabel Thanks, -Geoff ------------------------------------------- Geoff Hutchison Assistant Professor University of Pittsburgh, Department of Chemistry 219 Parkman Avenue Pittsburgh, PA 15260 From owner-chemistry@ccl.net Thu Jun 7 19:52:00 2007 From: "Nihan Aldis naldis!^!gmail.com" To: CCL Subject: CCL:G: Oniom and Si Cluster Message-Id: <-34437-070607175847-9577-VB1IWMwKp9CaTN+XfQazMg-$-server.ccl.net> X-Original-From: "Nihan Aldis" Date: Thu, 7 Jun 2007 17:58:43 -0400 Sent to CCL by: "Nihan Aldis" [naldis . gmail.com] Dear CCLers, I am using three layer oniom to optimize silicon cluster which has 80 Si (10 of them are surface silicons) and 52 H atoms. Since it is a big cluster, first, I wanted to optimize medium and low layers, my input is: p opt oniom(hf/3-21g*:am1/sparse) geom=connectivity gfinput iop(6/7=3) 0 1 0 1 0 1 Si- 0 -0.000761 -5.424092 -1.239365 M Si- 0 -0.002617 -5.425100 1.229628 M Si-Si3 0 1.920222 -4.149714 -1.782543 M Si-Si3 0 -1.922267 -4.149970 -1.780334 M . . and I end up with convergence error. The output is: The electronic state of the initial guess is 1-A. Leave Link 401 at Tue Jun 5 11:34:49 2007, MaxMem= 131072000 cpu: 19.8 (Enter /home/g03/l502.exe) Closed shell SCF: Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Using DIIS extrapolation, IDIIS= 1040. Integral symmetry usage will be decided dynamically. IEnd= 770023 IEndB= 770023 NGot= 131072000 MDV= 130532524 LenX= 130532524 Fock matrices will be formed incrementally for 20 cycles. Integral accuracy reduced to 1.0D-05 until final iterations. Cycle 1 Pass 0 IDiag 1: Petite list used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1. E= -6336.12178000983 DIIS: error= 7.14D-02 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -6336.12178000983 IErMin= 1 ErrMin= 7.14D-02 ErrMax= 7.14D-02 EMaxC= 1.00D-01 BMatC= 1.30D+00 BMatP= 1.30D+00 IDIUse=3 WtCom= 2.86D-01 WtEn= 7.14D-01 Coeff-Com: 0.100D+01 Coeff-En: 0.100D+01 Coeff: 0.100D+01 Gap= 0.028 Goal= None Shift= 0.000 GapD= 0.028 DampG=0.250 DampE=0.500 DampFc=0.2500 IDamp=-1. Damping current iteration by 2.50D-01 RMSDP=3.88D-03 MaxDP=1.66D-01 OVMax= 7.00D-01 . . .. Cycle 127 Pass 1 IDiag 4: ZThr: 1.000000D-08 Final acc: 1.000000D-08 E= 1.57401277029328 Delta-E= -0.000166891521 Rises=F Damp=F CGDMS It:127 Delta Func: -5.20D-08 Grad: 2.36D-03 Idemp: 1.25D-03 RMSDP=1.76D-04 MaxDP=5.78D-03 DE=-1.67D-04 OVMax= 0.00D+00 Cycle 128 Pass 1 IDiag 4: ZThr: 1.000000D-08 Final acc: 1.000000D-08 E= 1.57389538984853 Delta-E= -0.000117380445 Rises=F Damp=F CGDMS It:128 Delta Func: -4.24D-08 Grad: 2.36D-03 Idemp: 1.25D-03 RMSDP=1.77D-04 MaxDP=6.24D-03 DE=-1.17D-04 OVMax= 0.00D+00 >>>>>>>>>> Convergence criterion not met. SCF Done: E(RHF) = 1.57389538985 A.U. after 129 cycles Convg = 0.1770D-03 -V/T = 1.0014 S**2 = 0.0000 KE=-1.116528443604D+03 PE= 2.149081086145D-03 EE= 5.344349071435D+02 Convergence failure -- run terminated. Error termination via Lnk1e in /home/g03/l502.exe at Tue Jun 5 13:07:52 2007. Job cpu time: 0 days 1 hours 38 minutes 49.8 seconds. File lengths (MBytes): RWF= 270 Int= 0 D2E= 0 Chk= 27 Scr= To fix this problem, I changed the iop command to iop(5/32=1). This one has been running for more than two days and still running, it seems to oscillate, nothing more. Any suggestions are welcome. I am not subscribed to CCL and will appreciate if you send/copy your response to my e.mail address Thank you Nihan Aldis naldis/./gmail.com From owner-chemistry@ccl.net Thu Jun 7 23:13:00 2007 From: "Jian computationalboy]^[gmail.com" To: CCL Subject: CCL: fragment filtering Message-Id: <-34438-070607223721-4277-Qn44Ow1BkozJxo+aF3a7ng+*+server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_38073_23154574.1181269847811" Date: Fri, 8 Jun 2007 10:30:47 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy.:.gmail.com] ------=_Part_38073_23154574.1181269847811 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline You can try 3dfs, ligbuilder, etc. They are both free. Regards! On 6/4/07, Mingyue Zheng myzheng ~ gmail.com wrote: > > you may try openbabel, good luck! > > 2007/6/4, Thomas Joseph alabarae+/-yahoo.com : > > > > > > Sent to CCL by: "Thomas Joseph" [alabarae..yahoo.com] > > Hi all, > > > > Do any of you know about any FREE softwares which can identify fragments > > in a chemical database that wil run under Windows? > > I want to identify specific fragments in a chemical database > > > > thank you in advance > > > > > > > > > > E-mail to subscribers: CHEMISTRY**ccl.net or use:> > > > E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use> > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > > > > > > > > > > -- > -------------------------------------------------------------------------------- > > Dr. Mingyue Zheng > Research Associate, Drug Discovery and Design Center (DDDC) > Box 1201, Shanghai Institute of Materia Medica. > 555 Rd. Zuchongzhi, Shanghai, China > Tel: 86-021-50806600-1201 > Web: http://dddc.ac.cn > Email: myzheng**mail.shcnc.ac.cn ------=_Part_38073_23154574.1181269847811 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You can try 3dfs, ligbuilder, etc.
They are both free.
Regards!


On 6/4/07, Mingyue Zheng myzheng ~ gmail.com <owner-chemistry{:}ccl.net> wrote:
you may try openbabel, good luck!

2007/6/4, Thomas Joseph alabarae+/-yahoo.com < owner-chemistry**ccl.net>:

Sent to CCL by: "Thomas  Joseph" [alabarae..yahoo.com]
Hi all,

Do any of you know about any FREE softwares which can identify fragments in a chemical database that wil run under Windows?
I want to identify specific fragments in a chemical database

thank you in advance




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--
--------------------------------------------------------------------------------
Dr. Mingyue Zheng
Research Associate, Drug Discovery and Design Center (DDDC)
Box 1201, Shanghai Institute of Materia Medica.
555 Rd. Zuchongzhi, Shanghai, China
Tel:      86-021-50806600-1201
Web:   http://dddc.ac.cn
Email: myzheng**mail.shcnc.ac.cn

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