From owner-chemistry@ccl.net Thu Apr 10 04:35:00 2008 From: "Hatice Can alphacan2000_._yahoo.com" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36679-080410040653-12697-CsH4m55u+UQcb7P3ZcTjkQ(0)server.ccl.net> X-Original-From: "Hatice Can" Date: Thu, 10 Apr 2008 04:06:48 -0400 Sent to CCL by: "Hatice Can" [alphacan2000 .. yahoo.com] Dear All, I would be very grateful for pointers/advise etc on especially user-friendly software and reviews/literature suitable for a newcomer to molecular docking (protein/protein/, protein/ligand). Many thanks and kind regards Hatice From owner-chemistry@ccl.net Thu Apr 10 07:06:00 2008 From: "Kevser kevser(0)boun.edu.tr" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36680-080410065926-12855-BSd8U1Mt5/y4jspX7c3bew : server.ccl.net> X-Original-From: Kevser Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 10 Apr 2008 12:50:14 +0300 MIME-Version: 1.0 Sent to CCL by: Kevser [kevser-*-boun.edu.tr] Hi Hatice, I am using Maestro together with VMD for docking purposes. VMD visualizes and divides the protein into smaller segments and Maestro creates the novel ligand (or substrate in my case) and dock it into the corresponding segment of the protein. If you are familiar with your system and its reactive behavior, this is a way to dock a ligand. Hope this helps. Good luck. Quoting "Hatice Can alphacan2000_._yahoo.com" : ~ ~ Sent to CCL by: "Hatice Can" [alphacan2000 .. yahoo.com] ~ Dear All, ~ ~ I would be very grateful for pointers/advise etc on ~ especially user-friendly software and reviews/literature suitable for a ~ newcomer to molecular docking (protein/protein/, protein/ligand). ~ ~ Many thanks and kind regards ~ ~ Hatice ~ ~ ~ ~~~~~ ~~~ ~~~ ~~~ ~~ ~~~ ~~ ~~~ ~~ ~ ~ -- Kevser Gocmen Topal Bogazici University Chemistry Department 34342 Bebek ISTANBUL Phone: +902123597379 Fax: +90 212 287 24 67 http://kevsert.blogspot.com/ From owner-chemistry@ccl.net Thu Apr 10 07:55:01 2008 From: "=?GB2312?B?0vzE/g==?= yin.137 _ gmail.com" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36681-080410075215-3350-gaOP29srW/7rZgIXnEq9eQ[-]server.ccl.net> X-Original-From: "=?GB2312?B?0vzE/g==?=" Content-Type: multipart/alternative; boundary="----=_Part_27271_22159935.1207828324223" Date: Thu, 10 Apr 2008 19:52:04 +0800 MIME-Version: 1.0 Sent to CCL by: "=?GB2312?B?0vzE/g==?=" [yin.137|gmail.com] ------=_Part_27271_22159935.1207828324223 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Hatice, I'm also a new comer in this field, and I am now using AutoDock with AutoDockTools (Mainly protein-ligand docking), many people in my group use it too. It's quite easy to use and it's a free software. You can find the software along with many tutorials at the website of Scripps Institue: http://autodock.scripps.edu best, Ning On Thu, Apr 10, 2008 at 4:06 PM, Hatice Can alphacan2000_._yahoo.com < owner-chemistry]~[ccl.net> wrote: > > Sent to CCL by: "Hatice Can" [alphacan2000 .. yahoo.com] > Dear All, > > I would be very grateful for pointers/advise etc on > especially user-friendly software and reviews/literature suitable for a > newcomer to molecular docking (protein/protein/, protein/ligand). > > Many thanks and kind regards > > Hatice> > > ------=_Part_27271_22159935.1207828324223 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi Hatice,
 I'm also a new comer in this field, and I am now using AutoDock with AutoDockTools (Mainly protein-ligand docking), many people in my group use it too. It's quite easy to use and it's a free software. You can find the software along with many tutorials at the website of Scripps Institue: http://autodock.scripps.edu

best,
Ning
On Thu, Apr 10, 2008 at 4:06 PM, Hatice Can alphacan2000_._yahoo.com <owner-chemistry]~[ccl.net> wrote:

Sent to CCL by: "Hatice  Can" [alphacan2000 .. yahoo.com]
Dear All,

I would be very grateful for pointers/advise etc on
especially user-friendly software and reviews/literature suitable for a
newcomer to molecular docking (protein/protein/, protein/ligand).

Many thanks and kind regards

Hatice



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------=_Part_27271_22159935.1207828324223-- From owner-chemistry@ccl.net Thu Apr 10 09:06:01 2008 From: "Hatice Can hcan%%gyte.edu.tr" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36682-080410031428-8638-P4RThcxMw2gmP3S6rwjwkA\a/server.ccl.net> X-Original-From: "Hatice Can" Date: Thu, 10 Apr 2008 03:14:24 -0400 Sent to CCL by: "Hatice Can" [hcan]*[gyte.edu.tr] Dear All, I would be very grateful for pointers/advise etc on especially user-friendly software and reviews/literature suitable for a newcomer to molecular docking (protein/protein/, protein/ligand). Many thanks and kind regards Hatice Can From owner-chemistry@ccl.net Thu Apr 10 09:38:01 2008 From: "Barry Hardy barry.hardy:+:vtxmail.ch" To: CCL Subject: CCL: Bursary Award for eCheminfo Hands-on Drug Discovery Workshop in Oxford Message-Id: <-36683-080410084802-1561-pqxmSJ58Cedb6Fdd/bIJ6w,+,server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 10 Apr 2008 14:47:43 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy{=}vtxmail.ch] We will be accepting academic Bursary Award submissions for attending the eCheminfo Hands-on Drug Discovery Workshop in Oxford through Friday April 18. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com Selection will be based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on the research. We gratefully acknowledge the Bursary sponsorship support of Tripos. The 5 Day Workshop Week will take place this year 21-25 July 2008 at the Medical Sciences Teaching Center, Oxford University, Oxford, UK. Topics to be covered include Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling. The workshop group will study problems with hands-on examples using a range of software methods and will discuss complex issues highlighted by the exercises and case studies presented by instructors. A variety of leading drug discovery software packages and an IT classroom are used by instructors and participants to work through problems. More Information: Web: http://echeminfo.colayer.net/COMTY_training Blog: http://barryhardy.blogs.com/cheminfostream/2008/03/drug-discovery.html Photos: http://echeminfo.com/COMTY_oxfordphotos06 best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Switzerland Tel: +41 61 851 0170 From owner-chemistry@ccl.net Thu Apr 10 10:14:01 2008 From: "Tristan Youngs t.youngs : qub.ac.uk" To: CCL Subject: CCL: Announcing Aten (v0.96) Message-Id: <-36684-080410092406-15778-MKyxP/Z9eYs5OGorScZy1Q(a)server.ccl.net> X-Original-From: "Tristan Youngs" Date: Thu, 10 Apr 2008 09:24:02 -0400 Sent to CCL by: "Tristan Youngs" [t.youngs]|[qub.ac.uk] Dear All, 'Aten' is a new tool for the creation, editing, and visualisation of atomic coordinates for use in molecular computational sciences. The program is still in beta, but creeping towards the golden v1.0 mark. If you have the time or the inclination, please download and try it out. And please write back to me if you force a crash or have a suggestion! Briefly, current capabilities are: * Editing of periodic and non-periodic models * Full spacegroup packing * Generation of disordered models (e.g. liquids) through Monte Carlo methods * Forcefield-driven functions (e.g. energy calculation, minimisation etc.) * Display of volumetric and 2D (map) surfaces, trajectories / sequences of coordinates * Addition of glyphs (cubes, ellipsoids, etc.) at arbitrary coordinates, or linked to atoms * Full GUI (Qt), controllable with full Tcl-like scripting language through interactive or batch interfaces * Support for any file type through user-defined filters * Export of forcefield expressions in addition to coordinates For a more in-depth look at the code, including screenshots and tutorials, go to http://www.projectaten.org. RPMs are available for common Linux distributions, or you can get the source code via SVN or tarball (Aten is free software released under the GPL). Best wishes, Tris. t.youngs%qub.ac.uk tris%projectaten.org From owner-chemistry@ccl.net Thu Apr 10 10:49:00 2008 From: "Gerard Pujadas gerard.pujadas * gmail.com" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36685-080410102456-27903-vwfZl1HNQJqJYsgQ95bsMA!^!server.ccl.net> X-Original-From: "Gerard Pujadas" Content-Type: multipart/alternative; boundary="----=_Part_18709_8363860.1207833888846" Date: Thu, 10 Apr 2008 15:24:48 +0200 MIME-Version: 1.0 Sent to CCL by: "Gerard Pujadas" [gerard.pujadas^-^gmail.com] ------=_Part_18709_8363860.1207833888846 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Hatice, > I would be very grateful for pointers/advise etc on > especially user-friendly software and reviews/literature suitable for a > newcomer to molecular docking (protein/protein/, protein/ligand). we have just published a review on protein-ligand docking that perhaps coul= d be of interest for you: Protein-ligand Docking: A Review of Recent Advances and Future Perspectives= . Montserrat Vaqu=E9, Anna Ard=E9vol, Cinta Blad=E9, M. Josepa Salvad=F3, May= te Blay, Juan Fern=E1ndez-Larrea, Llu=EDs Arola and Gerard Pujadas. Current Pharmaceutical Analysis 4(1):1-19 (2008) Understanding the interactions between proteins and ligands is crucial for the pharmaceutical and functional food industries. The experimental structures of these protein/ligand complexes are usually obtained, under highly expert control, by time-consuming techniques such as X-ray crystallography or NMR. These techniques are therefore not suitable for routinely screening the possible interaction between one receptor and thousands of ligands. To overcome this limitation, computational algorithms (i.e. docking algorithms) have been developed that use the individual structures of the receptor and ligand to predict the structure of their complex. The present review, then, summarizes: (a) the fundamentals of the algorithms of the most commontly used docking programmes (with particular emphasis on their strengths and limitations); (b) how the results from different docking algorithms compare (i.e. which software gives the best predictions); and (c) the future perspectives and challenges for docking techniques. If you are interested in this review, please, contact me Best regards Gerard ------=_Part_18709_8363860.1207833888846 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear Hatice,


I would be very grateful for pointers/advise etc on
es= pecially user-friendly software and reviews/literature suitable for a
newcomer to molecular docking (protein/protein/, protein/ligand).

we have just published a review on protein-ligand docking that= perhaps could be of interest for you:


Protein-ligand Docking: A Review of Rece= nt Advances and Future Perspectives. Montserrat Vaqu=E9, Anna Ard=E9vol, Ci= nta Blad=E9, M. Josepa Salvad=F3, Mayte Blay, Juan Fern=E1ndez-Larrea, Llu= =EDs Arola and Gerard Pujadas. Current Pharmaceutical Analysis 4(1):1-19 (2= 008)

Understanding the interactions between proteins and ligands is crucial = for the pharmaceutical and functional food industries. The experimental str= uctures of these protein/ligand complexes are usually obtained, under highl= y expert control, by time-consuming techniques such as X-ray crystallograph= y or NMR. These techniques are therefore not suitable for routinely screeni= ng the possible interaction between one receptor and thousands of ligands. = To overcome this limitation, computational algorithms (i.e. docking algorit= hms) have been developed that use the individual structures of the receptor= and ligand to predict the structure of their complex. The present review, = then, summarizes: (a) the fundamentals of the algorithms of the most common= tly used docking programmes (with particular emphasis on their strengths an= d limitations); (b) how the results from different docking algorithms compa= re (i.e. which software gives the best predictions); and (c) the future per= spectives and challenges for docking techniques.

If you are interested in this review, please, contact me

B= est regards

Gerard

------=_Part_18709_8363860.1207833888846-- From owner-chemistry@ccl.net Thu Apr 10 11:24:00 2008 From: "Gerard Pujadas gerard.pujadas===gmail.com" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36686-080410103444-2689-lky+hEg5/08k3IUVy/1BDw---server.ccl.net> X-Original-From: "Gerard Pujadas" Date: Thu, 10 Apr 2008 10:34:40 -0400 Sent to CCL by: "Gerard Pujadas" [gerard.pujadas!=!gmail.com] Dear CCL subscribers, > from our own experiences eHiTS (http://simbiosys.ca/ehits) is one of the best, easiest to use docking programs. Moreover, it is free for academic research. This was also suggested by the JACS review in 2005: Sean Michael Kerwin J. Am. Chem. Soc., 2005, 127, (24), pp 88998900. Hope this helps Best regards Gerard From owner-chemistry@ccl.net Thu Apr 10 12:01:01 2008 From: "Duy Le ttduyle^gmail.com" To: CCL Subject: CCL: Visualizing CHGCAR by Origin Message-Id: <-36687-080410110138-22861-S8+5NbUqhf9V3dkSdoioOQ~!~server.ccl.net> X-Original-From: "Duy Le" Date: Thu, 10 Apr 2008 11:01:35 -0400 Sent to CCL by: "Duy Le" [ttduyle[A]gmail.com] Dear CCLers, Does anyone know how to plot CHGCAR file (from VASP calculation) by using Origin? Origin: http://www.originlab.com/ Regards, Duy From owner-chemistry@ccl.net Thu Apr 10 13:11:00 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007-,-yandex.ru" To: CCL Subject: CCL:G: An issue with frequency calculation for polyoxometalate species Message-Id: <-36688-080410130321-18131-LtriY4+D5vnyEXHa/FnwCg ~ server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 10 Apr 2008 20:28:04 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007###yandex.ru] Dear CCL Users, I'd like to ask you for advice and help on the following issue: I try to do frequency calculation (G03 package) for a polyoxometallate species with the stoichiometry H6O42Ru2SiW10, charge -4, multiplicity 3, point group C1; before frequency calculation this species was optimized at the B3LYP/LanL2DZ + d(Si) level, and frequency calculation is being done (for the sake of speed) at the B3LYP/LanL2mb level (376 basis functions in the system, initial guess read from the B3LYP/LanL2DZ + d(Si) level calculation checkpoint file). For other similar species frequency calculations ran smoothly, however, for this one I began to obtain the following output (below is just the part of it): "Symmetry not used in FoFCou. FMM levels: 10 Number of levels for PrismC: 9 PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. Defaulting to unpruned grid for atomic number 44. Defaulting to unpruned grid for atomic number 44. Defaulting to unpruned grid for atomic number 44. Defaulting to unpruned grid for atomic number 44. There are 186 degrees of freedom in the 1st order CPHF. 186 vectors were produced by pass 0. AX will form 186 AO Fock derivatives at one time. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. 186 vectors were produced by pass 1. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3. PrismC: NFx= 2048 NFxT= 3 NFxU= 3." And these passes continue to be generated, which would make the frequency calculation extremely long and unfeasible. Could anybody give me a piece of advice how to avoid such situation? Can something be wrong with the initial guess for frequency calculations? Thanks a lot, With best regards, Aleksey Kuznetsov. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: AlexKuznetsov2007!^!yandex.ru akuznets!^!euch4e.chem.emory.edu ------------------------------------------- From owner-chemistry@ccl.net Thu Apr 10 14:35:01 2008 From: "Durairajan Senthilnathan zenthil03\a/yahoo.co.in" To: CCL Subject: CCL:G: Atom fixing or freezing Message-Id: <-36689-080410143020-18122-zuFBt9uH3taLXj6n3FserA..server.ccl.net> X-Original-From: "Durairajan Senthilnathan" Date: Thu, 10 Apr 2008 14:30:17 -0400 Sent to CCL by: "Durairajan Senthilnathan" [zenthil03:+:yahoo.co.in] Dear CCL'rs Greetings. I want to fix( or freeze) a atom in a 3D space for gaussian calculation. I want to keep this atom as without movement when optimaization and transition state calculation. my input file is %chk=model.chk %mem=6MW %nproc=1 #p opt=modredundant freq am1 Title Card Required 0 1 C -1.04910715 -0.35714285 0.00000000 H -0.69243431 0.14725534 0.87365150 H -0.69243431 0.14725534 -0.87365150 H -2.11910715 -0.35712967 0.00000000 C -0.53579143 -1.80907500 0.00000000 H -0.89246389 -2.31347306 0.87365174 H -0.89246472 -2.31347389 -0.87365092 C 1.00420857 -1.80909321 -0.00000123 H 1.36088018 -1.30469693 -0.87365435 H 1.36088208 -1.30469210 0.87364831 C 1.51752428 -3.26102536 0.00000272 H 1.16085397 -3.76542151 0.87365644 H 1.16085150 -3.76542742 -0.87364657 H 2.58752428 -3.26103580 0.00000120 H 2.53166275 -0.48629618 0.52184131 C 2.17500833 0.52251382 0.52184131 H 2.53168117 1.02691201 1.39549281 H 1.10500833 0.52252701 0.52184131 C 2.68835054 1.24847009 -0.73556366 H 2.33009962 2.25671377 -0.73654241 H 3.75834878 1.25015115 -0.73458588 H 2.33327591 0.74294331 -1.60921386 1 F 18 F Here I want to fix or freez atoms 1 and 18. I have error at filanally as error in output finalising step. How can I avoid this error? any one of you give me a better solution for my error. best wishes from Bharathidasan University From owner-chemistry@ccl.net Thu Apr 10 15:09:00 2008 From: "Nuno A. G. Bandeira nuno.bandeira__ist.utl.pt" To: CCL Subject: CCL: An issue with frequency calculation for polyoxometalate species Message-Id: <-36690-080410143726-19427-RQBPSkbaOlh75Erif4aYhg .. server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 10 Apr 2008 19:33:49 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira]~[ist.utl.pt] Is there any reason why you can't use symmetry in your calculation ? POMs are usually highly symmetrical and it would cut down the calculation time for your run by a lot. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ^ IST,Lisbon -- From owner-chemistry@ccl.net Thu Apr 10 15:50:00 2008 From: "Anastassia Alexandrova anastassia.alexandrova^-^yale.edu" To: CCL Subject: CCL:G: An issue with frequency calculation for polyoxometalate species Message-Id: <-36691-080410145118-25229-ONy0kkO/oLyKBxBsU+uX9A * server.ccl.net> X-Original-From: Anastassia Alexandrova Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Thu, 10 Apr 2008 14:19:15 -0400 MIME-Version: 1.0 Sent to CCL by: Anastassia Alexandrova [anastassia.alexandrova|,|yale.edu] Hi Aleksey! may be try changing the grid in DFT. might help. Cheers! AA --------------------------------------- Anastassia Alexandrova, Ph.D. Yale University Department of Chemistry 225 Prospect Street New Haven, CT 06520-8107 Phone: 203-432-6288 Fax: 203-432-6144 anastassia.alexandrova . yale.edu http://zarbi.chem.yale.edu/~anastassia/ --------------------------------------- Go one more mile... Quoting "Aleksey Kuznetsov AlexKuznetsov2007-,-yandex.ru" : > > Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007###yandex.ru] > Dear CCL Users, > > I'd like to ask you for advice and help on the following issue: > > I try to do frequency calculation (G03 package) for a > polyoxometallate species with the stoichiometry H6O42Ru2SiW10, charge > -4, multiplicity 3, point group C1; before frequency calculation this > species was optimized at the B3LYP/LanL2DZ + d(Si) level, and > frequency calculation is being done (for the sake of speed) at the > B3LYP/LanL2mb level (376 basis functions in the system, initial guess > read from the B3LYP/LanL2DZ + d(Si) level calculation checkpoint > file). For other similar species frequency calculations ran smoothly, > however, for this one I began to obtain the following output (below > is just the part of it): > > "Symmetry not used in FoFCou. > FMM levels: 10 Number of levels for PrismC: 9 > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > Defaulting to unpruned grid for atomic number 44. > Defaulting to unpruned grid for atomic number 44. > Defaulting to unpruned grid for atomic number 44. > Defaulting to unpruned grid for atomic number 44. > There are 186 degrees of freedom in the 1st order CPHF. > 186 vectors were produced by pass 0. > AX will form 186 AO Fock derivatives at one time. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > 186 vectors were produced by pass 1. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3. > PrismC: NFx= 2048 NFxT= 3 NFxU= 3." > > And these passes continue to be generated, which would make the > frequency calculation extremely long and unfeasible. Could anybody > give me a piece of advice how to avoid such situation? Can something > be wrong with the initial guess for frequency calculations? > > Thanks a lot, > > With best regards, > > Aleksey Kuznetsov. > ------------------------------------------- > Dr. Aleksey Kuznetsov > Cherry L. Emerson Center for Scientific Computation > Emory University > 1515 Dickey Drive > Atlanta, GA 30322 > USA > > Phone: (404)727-2381 > Email: AlexKuznetsov2007^-^yandex.ru > akuznets^-^euch4e.chem.emory.edu > -------------------------------------------> > From owner-chemistry@ccl.net Thu Apr 10 17:02:01 2008 From: "Chunhui Li baotogo2004*gmail.com" To: CCL Subject: CCL: ab initio calculation for Fe3+ complex Message-Id: <-36692-080410154808-13706-S8amuIXAdzdcqYGF6eavIQ]=[server.ccl.net> X-Original-From: "Chunhui Li" Date: Thu, 10 Apr 2008 15:48:04 -0400 Sent to CCL by: "Chunhui Li" [baotogo2004,gmail.com] Dear All, I need to do an ab initio calculation on a Fe complex. The complex is Fe3+ (H2O)5 with an fluorocarbon which has an COO- end. The total size is about 30-40 atoms. I am using Spartan '06 window to find equilibrium geometry. my first question is to verify that my total charge is +2 and multiplicity is 6, is it right? Since the Fe3+ charge I got from optimization using UHF STO3G is 2.05, not 3, I am confused with the coordination chemistry on Fe3+. my second question is: what method and basis set you think would be appropriate for this system? Will HF method work for just geometry optimization? I tried to use UHF 3-21G to optimize, but SCF failed to converge after 500 cycles. STO-3G did converge. My computer have 512M memory, do you think I need more memory for this calculation? another question is that I don't understand why 6-311G* and 6-311+G** don't work for this system. The output says Basis not supported for the above atom.( I assume it is not working for Fe, isn't it?) My last question is: which one is better, UHF or ROHF in this case? Thank you in advance! Lily From owner-chemistry@ccl.net Thu Apr 10 17:37:01 2008 From: "Peter Oledzki peter[]biosolveit.de" To: CCL Subject: CCL: protein-ligand docking software Message-Id: <-36693-080410115645-9751-PO8CTpabol4ulIBys8l2QA-,-server.ccl.net> X-Original-From: "Peter Oledzki" Date: Thu, 10 Apr 2008 11:56:40 -0400 Sent to CCL by: "Peter Oledzki" [peter#%#biosolveit.de] Hi Hatice, You can use FlexX with it's GUI from BioSolveIT as we designed it to be exactly what you are looking for. It takes you by the hand step by step through the vital part of protein preparation and has simple click and go docking/pharmacophore assignment. We've had comments such as " thats the most straightforward thing i've seen" and one of my favorites "so easy a caveman could use it" ..... i doubt that he would have been able to but it was funny. You can download a copy from here if you wish to give it a try : http://www.biosolveit.de/download/index.html Info on it and tutorial movies are also on this page http://www.biosolveit.de/FlexX/ Best wishes Peter __________________________________________________________________ Dr. Peter Oledzki Peter.Oledzki|-|biosolveit.de Phone: +49-2241-2525-579 / Fax: -525 www.biosolveit.de BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 From owner-chemistry@ccl.net Thu Apr 10 18:20:02 2008 From: "Lukasz Cwiklik cwiklik ~~ gmail.com" To: CCL Subject: CCL:G: Atom fixing or freezing Message-Id: <-36694-080410180917-31379-kK+KbebOfH6BAucR4QS4EQ()server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 11 Apr 2008 01:01:29 +0300 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik:gmail.com] On Thu, Apr 10, 2008 at 9:30 PM, Durairajan Senthilnathan zenthil03a/yahoo.co.in wrote: > > Sent to CCL by: "Durairajan Senthilnathan" [zenthil03:+:yahoo.co.in] > Dear CCL'rs > Greetings. I want to fix( or freeze) a atom in a 3D space for gaussian calculation. I want to keep > this atom as without movement when optimaization and transition state calculation. > my input file is [...] > Here I want to fix or freez atoms 1 and 18. > I have error at filanally as error in output finalising step. > > How can I avoid this error? any one of you give me a better solution for my error. Dear Durairajan, I just took your input and ran it in Gaussian03, everything was fine, the job finished normally. Can you please paste here the error message (or the output file) that your calculation produced at your machine? Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Thu Apr 10 19:13:00 2008 From: "Tristan Youngs t.youngs:+:qub.ac.uk" To: CCL Subject: CCL: Aten (again). Message-Id: <-36695-080410190453-3729-okD5Yr3S8UJDuB29pcPWNQ[A]server.ccl.net> X-Original-From: "Tristan Youngs" Date: Thu, 10 Apr 2008 19:04:49 -0400 Sent to CCL by: "Tristan Youngs" [t.youngs[-]qub.ac.uk] Greetings again, To those unfortunate souls who may have downloaded Aten revision 288 (or 0.96.288) from aten.googlecode.com (either SVN or the latest tarball), my apologies for being rubbish and forgetting to include a crucial file in the distribution. Problems are now fixed! New tarball is available at aten.googlecode.com as of now. Best, Tris. t.youngs+/-qub.ac.uk tris+/-projectaten.org From owner-chemistry@ccl.net Thu Apr 10 23:42:01 2008 From: "Minhaj minhajg%%gmail.com" To: CCL Subject: CCL:G: Atom fixing or freezing Message-Id: <-36696-080410172406-32382-6dnlDDGNaP9xBOCQlmcxng[A]server.ccl.net> X-Original-From: Minhaj Content-Type: multipart/alternative; boundary="----=_Part_4573_23312562.1207862624850" Date: Thu, 10 Apr 2008 16:23:44 -0500 MIME-Version: 1.0 Sent to CCL by: Minhaj [minhajg=-=gmail.com] ------=_Part_4573_23312562.1207862624850 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline If you are using cartesian coordinates in your input (instead of a Z-Matrix), remove modredundant from the route section and include a '-1' in between the atom name and the coordinates of the atom that you want frozen. For eg. The correct input for your system would be ( assuming that you want the first carbon atom and the 18th Hydrogen atom frozen): %chk=model.chk %mem=6MW %nproc=1 #p opt freq am1 Title Card Required 0 1 C -1 -1.04910715 -0.35714285 0.00000000 H -0.69243431 0.14725534 0.87365150 H -0.69243431 0.14725534 -0.87365150 H -2.11910715 -0.35712967 0.00000000 C -0.53579143 -1.80907500 0.00000000 H -0.89246389 -2.31347306 0.87365174 H -0.89246472 -2.31347389 -0.87365092 C 1.00420857 -1.80909321 -0.00000123 H 1.36088018 -1.30469693 -0.87365435 H 1.36088208 -1.30469210 0.87364831 C 1.51752428 -3.26102536 0.00000272 H 1.16085397 -3.76542151 0.87365644 H 1.16085150 -3.76542742 -0.87364657 H 2.58752428 -3.26103580 0.00000120 H 2.53166275 -0.48629618 0.52184131 C 2.17500833 0.52251382 0.52184131 H 2.53168117 1.02691201 1.39549281 H -1 1.10500833 0.52252701 0.52184131 C 2.68835054 1.24847009 -0.73556366 H 2.33009962 2.25671377 -0.73654241 H 3.75834878 1.25015115 -0.73458588 H 2.33327591 0.74294331 -1.60921386 Cheers, Minhaj. On Thu, Apr 10, 2008 at 1:30 PM, Durairajan Senthilnathan zenthil03a/ yahoo.co.in wrote: > > Sent to CCL by: "Durairajan Senthilnathan" [zenthil03:+:yahoo.co.in] > Dear CCL'rs > Greetings. I want to fix( or freeze) a atom in a 3D space for > gaussian calculation. I want to keep this atom as without movement when > optimaization and transition state calculation. > > my input file is > > %chk=model.chk > %mem=6MW > %nproc=1 > #p opt=modredundant freq am1 > > Title Card Required > > 0 1 > C -1.04910715 -0.35714285 0.00000000 > H -0.69243431 0.14725534 0.87365150 > H -0.69243431 0.14725534 -0.87365150 > H -2.11910715 -0.35712967 0.00000000 > C -0.53579143 -1.80907500 0.00000000 > H -0.89246389 -2.31347306 0.87365174 > H -0.89246472 -2.31347389 -0.87365092 > C 1.00420857 -1.80909321 -0.00000123 > H 1.36088018 -1.30469693 -0.87365435 > H 1.36088208 -1.30469210 0.87364831 > C 1.51752428 -3.26102536 0.00000272 > H 1.16085397 -3.76542151 0.87365644 > H 1.16085150 -3.76542742 -0.87364657 > H 2.58752428 -3.26103580 0.00000120 > H 2.53166275 -0.48629618 0.52184131 > C 2.17500833 0.52251382 0.52184131 > H 2.53168117 1.02691201 1.39549281 > H 1.10500833 0.52252701 0.52184131 > C 2.68835054 1.24847009 -0.73556366 > H 2.33009962 2.25671377 -0.73654241 > H 3.75834878 1.25015115 -0.73458588 > H 2.33327591 0.74294331 -1.60921386 > > 1 F > 18 F > > Here I want to fix or freez atoms 1 and 18. > I have error at filanally as error in output finalising step. > > How can I avoid this error? any one of you give me a better solution for > my error. > > best wishes from > Bharathidasan University> > > ------=_Part_4573_23312562.1207862624850 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline If you are using cartesian coordinates in your input (instead of a Z-Matrix), remove modredundant from the route section and include a '-1' in between the atom name and the coordinates of the atom that you want frozen. For eg. The correct input for your system would be ( assuming that you want the first carbon atom and the 18th Hydrogen atom frozen):

%chk=model.chk
%mem=6MW
%nproc=1
#p opt freq am1

Title Card Required

0 1
 C     -1         -1.04910715   -0.35714285    0.00000000
 H                 -0.69243431    0.14725534    0.87365150
 H                 -0.69243431    0.14725534   -0.87365150
 H                 -2.11910715   -0.35712967    0.00000000
 C                 -0.53579143   -1.80907500    0.00000000
 H                 -0.89246389   -2.31347306    0.87365174
 H                 -0.89246472   -2.31347389   -0.87365092
 C                  1.00420857   -1.80909321   -0.00000123
 H                  1.36088018   -1.30469693   -0.87365435
 H                  1.36088208   -1.30469210    0.87364831
 C                  1.51752428   -3.26102536    0.00000272
 H                  1.16085397   -3.76542151    0.87365644
 H                  1.16085150   -3.76542742   -0.87364657
 H                  2.58752428   -3.26103580    0.00000120
 H                  2.53166275   -0.48629618    0.52184131
 C                  2.17500833    0.52251382    0.52184131
 H                  2.53168117    1.02691201    1.39549281
 H        -1       1.10500833    0.52252701    0.52184131
 C                  2.68835054    1.24847009   -0.73556366
 H                  2.33009962    2.25671377   -0.73654241
 H                  3.75834878    1.25015115   -0.73458588
 H                  2.33327591    0.74294331   -1.60921386

Cheers,
Minhaj.



On Thu, Apr 10, 2008 at 1:30 PM, Durairajan Senthilnathan zenthil03a/yahoo.co.in <owner-chemistry#,#ccl.net> wrote:

Sent to CCL by: "Durairajan  Senthilnathan" [zenthil03:+:yahoo.co.in]
Dear CCL'rs
         Greetings. I want to fix( or freeze) a atom in a 3D space for gaussian calculation. I want to keep this atom as without movement when optimaization and transition state calculation.

my input file is

%chk=model.chk
%mem=6MW
%nproc=1
#p opt=modredundant freq am1

Title Card Required

0 1
 C                 -1.04910715   -0.35714285    0.00000000
 H                 -0.69243431    0.14725534    0.87365150
 H                 -0.69243431    0.14725534   -0.87365150
 H                 -2.11910715   -0.35712967    0.00000000
 C                 -0.53579143   -1.80907500    0.00000000
 H                 -0.89246389   -2.31347306    0.87365174
 H                 -0.89246472   -2.31347389   -0.87365092
 C                  1.00420857   -1.80909321   -0.00000123
 H                  1.36088018   -1.30469693   -0.87365435
 H                  1.36088208   -1.30469210    0.87364831
 C                  1.51752428   -3.26102536    0.00000272
 H                  1.16085397   -3.76542151    0.87365644
 H                  1.16085150   -3.76542742   -0.87364657
 H                  2.58752428   -3.26103580    0.00000120
 H                  2.53166275   -0.48629618    0.52184131
 C                  2.17500833    0.52251382    0.52184131
 H                  2.53168117    1.02691201    1.39549281
 H                  1.10500833    0.52252701    0.52184131
 C                  2.68835054    1.24847009   -0.73556366
 H                  2.33009962    2.25671377   -0.73654241
 H                  3.75834878    1.25015115   -0.73458588
 H                  2.33327591    0.74294331   -1.60921386

 1 F
 18 F

Here I want to fix or freez atoms 1 and 18.
I have error at filanally as error in output finalising step.

How can I avoid this error? any one of you give me a better solution for my error.

best wishes from
Bharathidasan University



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