From owner-chemistry@ccl.net Wed May 13 01:00:01 2009 From: "Tirtha mukherjee mukherjeetirtha===yahoo.co.in" To: CCL Subject: CCL: Searching for a free software to calculate pK, Stability constant etc Message-Id: <-39304-090513003615-20952-MZ732kqUyE/FTta659nByA---server.ccl.net> X-Original-From: "Tirtha mukherjee" Date: Wed, 13 May 2009 00:36:11 -0400 Sent to CCL by: "Tirtha mukherjee" [mukherjeetirtha _ yahoo.co.in] Respected members I am searching fro a free soft ware to calculate pka and stability constant form potentiometric data. Can any please help? From owner-chemistry@ccl.net Wed May 13 01:34:00 2009 From: "Shikha Varma-O Brien shikha ~~ accelrys.com" To: CCL Subject: CCL: Accelrys announces new release of Discovery Studio Message-Id: <-39305-090513012006-15548-0D3mwmnFJdmfLiQv9SJ1uw[A]server.ccl.net> X-Original-From: "Shikha Varma-O Brien" Date: Wed, 13 May 2009 01:20:02 -0400 Sent to CCL by: "Shikha Varma-O Brien" [shikha^accelrys.com] Accelrys is pleased to announce the release of Discovery Studio 2.5. As part of this release, we are offering a series of eight webinars to highlight whats new in this version by Accelrys scientists as well as share success stories by our customers. Hear from leading researchers in the industry, academia, and Accelrys scientists to learn: 1) How scientists are solving computational drug discovery problems in the industry 2) About the latest trends and modern methods in lead identification and optimization 3) How you can access and use a combination of computational chemistry and biology tools, and effectively communicate your findings to your group 4) How you can introduce and use CADD as an educational tool in academia Discovery Studio 2.5 is packaged with solutions for modern day computational challenges - all within a customizable workflow environment and a customizable interface! See the latest advancements in: Please click on the following link to register for FREE webinars: http://accelrys.com/events/webinars/discovery-studio-25/index-ccl.html Webinars will highlight: Fragment-based & structure-based design methods, Transmembrane protein and antibody modeling methods, X-ray data analysis tools, Pharmacophore modeling tools Virtual screening, QSAR, & data mining tools, Predictive ADMET, and much more Sincerely, _________________________________ Shikha Varma-O'Brien, Ph.D. Director, LS Modeling and Simulations Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego CA, 92121 Office: (858)799-5607 http://accelrys.com __________________________________ From owner-chemistry@ccl.net Wed May 13 02:45:00 2009 From: "Andreas Klamt klamt:-:cosmologic.de" To: CCL Subject: CCL: Scaffold-Hopping software Message-Id: <-39306-090513024128-2870-9PZycwjsC6/SVpmAn/4uhA]_[server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 13 May 2009 08:41:17 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt(_)cosmologic.de] Dear Alberto, you may try COSMOsim for this task. COSMOsim only uses the similarity of the surface polarization charges (sigma profiles) from COSMO, which - according to COSMO-RS - are the essential descriptors for the quantitative evaluation of all kinds of interactions in the liquid state and in the ligand-receptor complex. Hence it avoids any bias ariasing > from classifying and counting certain structural features which happens in most other techniques for drug similarity definitions. For more information see: - www.cosmologic.de - "COSMOsim: Bioisosteric Similarity Based on COSMO-RS s-Profiles", Michael Thormann, Andreas Klamt, Martin Hornig and Michael Almstetter, /J. Chem. Inf. Model./ *46*, 1040 -1053 (2006). , Article-DOI: 10.1021/ci050464m . - or the recent presentation of Michael Thormann given on our COSMO-RS Symposium 2009 "COSMO-RS & COSMOsim - Valuable Tools for Drug Discovery" (you can download the presentation from www.cosmologic.de/symposium 2009 (under program) Andreas Alberto Pasamontes alberto.pasamontes:+:gmail.com schrieb: > Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes#,#gmail.com] > Dear, > > We are planning a Scaffold-Hopping step (ligand based) in a virtual screening procedure. We know about LASSO and CODESSA. Any others suggestions about which software could we use to calculate descriptors and make a statistical analysis? > > thanks in advance > > > > -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt%%cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed May 13 04:05:01 2009 From: "Sten Nilsson Lill stenil]*[chem.gu.se" To: CCL Subject: CCL: Generating symmetry from where it almost exists... Message-Id: <-39307-090513040234-4915-ZsxcWKXTt4YFD/so/1XTvA[*]server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 13 May 2009 10:02:19 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil=-=chem.gu.se] John, > from my experience Chemcraft is very useful for symmetrizing molecules. You can download the program at http://www.chemcraftprog.com/ and it works for Windows and Linux. If you go to the Edit menu there's an option called "Set Point Group". I normally let the program suggest the symmetry by using the "Auto" function. There you will get a few point group options to select from. If the program doesn't include your specific symmetry you can directly define it to set the point group you are searching for, just pick it in the menu. Hope that helps, Sten > Folks, > > I have a bunch of cartesian geometries that have "almost" C2 symmetry. > Graphical inspection says yhey should be C2 but the code I'm using won't > generate C2, even with large "out-of-symmetry" threshold values. Can > anyone > point me to a simple utility that could be used to clean these structures > up? > > Thanks! > > John McKelvey > Ph. D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg Kemigården 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2873 Fax: +46-31-772 3840 E-mail: stenil%a%chem.gu.se Alternative e-mail: stenil%a%physto.se From owner-chemistry@ccl.net Wed May 13 05:45:01 2009 From: "Jerry Chan chanjcc(_)ntu.edu.tw" To: CCL Subject: CCL: Checking for hydrogen bonding Message-Id: <-39308-090513050300-2881-cpVtY1nfkdK+w2bJutoBqw#,#server.ccl.net> X-Original-From: Jerry Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=Big5 Date: Wed, 13 May 2009 16:03:33 +0800 MIME-Version: 1.0 Sent to CCL by: Jerry Chan [chanjcc^^^ntu.edu.tw] Dear colleagues, I need to find out if there are any intermolecular hydrogen bondings in an aggregate of peptides. I suppose some NH and CO will form better hydrogen bonding and some do not. Is there any freeware that can analyze such system and has a scoring function for H-bonding? Even pointers to references would be greatly appreciated. Million thanks, Jerry -- Jerry C. C. Chan phone: 886-2-33662994 Chemistry Department fax: 886-2-23636359 National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei, Taiwan http://spin.ch.ntu.edu.tw From owner-chemistry@ccl.net Wed May 13 07:35:01 2009 From: "Reaz Uddin riaasuddin|,|yahoo.com" To: CCL Subject: CCL: problem with FRED -refine lig_mmff Message-Id: <-39309-090513053853-11005-HybR70warnFuzggT78d34w-$-server.ccl.net> X-Original-From: Reaz Uddin Content-Type: multipart/alternative; boundary="0-845520504-1242203920=:69838" Date: Wed, 13 May 2009 01:38:40 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Reaz Uddin [riaasuddin-,-yahoo.com] --0-845520504-1242203920=:69838 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello ccls,.=20 You know I have a little problem with FRED. Whenever I use option -refine l= ig_mmff=A0with Zap job, it doesn't work. It shows all docking failed. I am = using ~8000=A0compounds for docking. But no single compound is docked succe= ssfully.=A0 Without -refine option the job runs well=A0and no=A0trouble. Does anybody have any idea.?? I appreciate for your time. Thanks =A0 FRED Parameter file looks like: # -exhaustive_scoring chemgauss3 -opt chemgauss3 -assign_protein_charges true -refine lig_mmff # -pose_select_weight_shapegauss 1=20 -pose_select_weight_plp 1=20 -pose_select_weight_chemgauss3 1=20 -pose_select_weight_oechemscore 1=20 -pose_select_weight_chemscore 1 -pose_select_weight_screenscore 1 # -pose_select_weight_chemgauss2 1 #-pose_select_weight_cgo 0=20 #-pose_select_weight_cgt 0=20 # -shapegauss true -plp true -chemgauss3 true -oechemscore true # -screenscore true -zapbind true -consensus true -chemgauss2 true #-cgo false #-cgt false # -shapegauss_masc true -plp_masc true -chemgauss3_masc true -chemscore_masc true -oechemscore_masc true -screenscore_masc true -zapbind_masc true -consensus_masc true # -chemgauss2_masc true #-cgo-masc false #-cgt-masc false #-report_masc_failures true -pvmconf hosts -prefix ZAP-withAll-MASC- REAZUDDIN=20 Research Scholar=20 HEJ Research Institute of Chemistry University of Karachi Karachi, Pakistan Email: riaasuddin#%#yahoo.com, mriazuddin#%#iccs.edu=0A=0A=0A --0-845520504-1242203920=:69838 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello ccls,= .
You know I have a little problem with FRED. Whenever I use option -refine lig_mmff with Z= ap job, it doesn't work. It shows all docking failed. I am using ~8000 = ;compounds for docking. But no single compound is docked successfully. = ;
Without -refine option the job runs well an= d no trouble.
Does anybody have any idea.??
I appreciate for your time.
Thanks
 
FRED Parameter file looks like:
#
-exhaustive_scoring chemgauss3
-opt chemgauss3
-assign_prot= ein_charges true
-refine lig_mmff
#
-pose_select_weight_shapegauss= 1
-pose_select_weight_plp 1
-pose_select_weight_chemgauss3 1
-= pose_select_weight_oechemscore 1
-pose_select_weight_chemscore 1
-po= se_select_weight_screenscore 1
#
-pose_select_weight_chemgauss2 1
= #-pose_select_weight_cgo 0
#-pose_select_weight_cgt 0
#
-shapega= uss true
-plp true
-chemgauss3 true
-oechemscore true
#
-scr= eenscore true
-zapbind true
-consensus true

-chemgauss2 true#-cgo false
#-cgt false
#
-shapegauss_masc true
-plp_masc tru= e
-chemgauss3_masc true
-chemscore_masc true
-oechemscore_masc tru= e
-screenscore_masc true
-zapbind_masc true
-consensus_masc true#
-chemgauss2_masc true
#-cgo-masc false
#-cgt-masc false
#-r= eport_masc_failures true
-pvmconf hosts
-prefix ZAP-withAll-MASC-


REA= ZUDDIN
Research Scholar
HEJ Research Institute of Chemistry
University of Karachi
Karachi, Pakistan=
Email: riaasuddin#%#y= ahoo.com, mriazuddin#%#iccs.edu

=0A=0A= --0-845520504-1242203920=:69838-- From owner-chemistry@ccl.net Wed May 13 10:08:01 2009 From: "Sangeetha Subramaniam srdshigella|a|gmail.com" To: CCL Subject: CCL: How to add missing residues Message-Id: <-39310-090513043939-21494-cyn5crIZaOSk0BpA6k/20w,server.ccl.net> X-Original-From: Sangeetha Subramaniam Content-Type: multipart/alternative; boundary=0016367fbb82d1643d0469c6bb0f Date: Wed, 13 May 2009 12:39:22 +0430 MIME-Version: 1.0 Sent to CCL by: Sangeetha Subramaniam [srdshigella__gmail.com] --0016367fbb82d1643d0469c6bb0f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thank you all for your kind reply and suggestions. Regards Sangeetha. On Mon, May 11, 2009 at 11:08 PM, Deepangi Pandit deepangi.pandita/gmail.com wrote: > > Sent to CCL by: Deepangi Pandit [deepangi.pandit!A!gmail.com] > Hi Sangeetha: > Adding missing residues before simulation is an important task and > people have their own preferences about the methodology. You could try > the free program SWISS PDBViewer/DeepView program (Link 1) and follow > the second link which explains the procedure with help of tutorials > listed on the second link > > 1. http://spdbv.vital-it.ch/index.html > > > 2. http://spdbv.vital-it.ch/build.html > > Best, > Deepa > > > > On Mon, May 11, 2009 at 12:49 PM, Sangeetha Vimal > srdshigella!A!gmail.com wrote: > > > > Sent to CCL by: "Sangeetha Vimal" [srdshigella]^[gmail.com] > > Hello everyone, > > > > Can someone post the tools/methods available for building missing > residues in the crystal structure. I need the complete structure for > carrying out simulation studies. > > > > thanks > > sangeetha.> > > > > > > > > - This is automatically added to each message by the mailing script -> > > --0016367fbb82d1643d0469c6bb0f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you all for your kind reply and suggestions.

Regards
Sangee= tha.

On Mon, May 11, 2009 at 11:08 PM, De= epangi Pandit deepangi.pandita/gmail.com <owner-chemistry!=!ccl.net> wrote:

Sent to CCL by: Deepangi Pandit [deepangi.pandit!A!gmail.com]
Hi Sangeetha:
Adding missing residues before simulation is an important task and
people have their own preferences about the methodology. You could try
the free program SWISS PDBViewer/DeepView program (Link 1) and follow
the second link which explains the procedure with help of tutorials
listed on the second link

1. http:/= /spdbv.vital-it.ch/index.html


2. http:/= /spdbv.vital-it.ch/build.html

Best,
Deepa



On Mon, May 11, 2009 at 12:49 PM, Sangeetha Vimal
srdshigella!A!gmail.com = <owner-chemistry^ccl.net> wrote:
>
> Sent to CCL by: "Sangeetha =A0Vimal" [srdshigella]^[gmail.com]
> Hello everyone,
>
> Can someone post the tools/methods available for building missing resi= dues in the crystal structure. I need the complete structure =A0for carryin= g out simulation studies.
>
> thanks
> sangeetha.
>
>
>
> -=3D This is automatically added to each message by the mailing script= =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message= > =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> = =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 = =A0http://www= .ccl.net/spammers.txt>
>
>



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--0016367fbb82d1643d0469c6bb0f-- From owner-chemistry@ccl.net Wed May 13 11:02:00 2009 From: "Beatriz Carolina Ramirez bea_ucv*o*yahoo.com" To: CCL Subject: CCL:G: Method question Message-Id: <-39311-090513091533-23445-943p0lG8lT2Wmd2K5i+QEA#server.ccl.net> X-Original-From: "Beatriz Carolina Ramirez" Date: Wed, 13 May 2009 09:15:29 -0400 Sent to CCL by: "Beatriz Carolina Ramirez" [bea_ucv!=!yahoo.com] Im performing a calculation un gaussian 03 and it fails in the same point despite I change some settings. I want to optimize two large molecules (thiamine and CoA) as reactants for a reaction with an oniom calculation b3lyp/6-31g:pm3 level of theory, but after a while I got this message: . . . It=199 PL= 2.12D-12 DiagD=TT ESCF= -313.681008 Diff=-3.98D-07 RMSDP= 2.43D-02. It=199 PL= 2.12D-12 DiagD=TT ESCF= -313.681008 Diff=-3.98D-07 RMSDP= 2.43D-02. It=200 PL= 2.12D-12 DiagD=TT ESCF= -313.681008 Diff=-1.46D-07 RMSDP= 2.43D-02. """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE DELTAE= -0.3362E-05 DELTAP= 0.2118E-11 Error termination via Lnk1e in C:\G03W\l402.exe at Tue May 13 00:12:47 2008. Job cpu time: 0 days 15 hours 4 minutes 24.0 seconds. File lengths (MBytes): RWF= 99 Int= 0 D2E= 0 Chk= 36 Scr= 1 If someone knows how can I fix this error.. plese shed me some light. Thanks From owner-chemistry@ccl.net Wed May 13 11:32:00 2009 From: "Uwe Huniar uwe.huniar**cosmologic.de" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39312-090513111648-942-Fbx80C5mJa6X5Wl7w61t4Q++server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 13 May 2009 17:16:40 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar(0)cosmologic.de] Hello, Turbomole has an implemented genetic algorithm for global geometry optimizations in its latest version 6.0. The problem with such an algorithm is the amount of calculations that have to be done to get a reasonable number of generations. So while the program for the genetic algorithm comes with Turbomole 6.0, the scripts for job submissions (preferable in a queuing system) are not part of the official distribution - but Turbomole users can get a copy upon request. However, they have to be adapted to the user's queuing system. Publications: The main publication: M. Sierka, J. Döbler, J. Sauer, G. Santambrogio, M. Brümmer, L. Wöste, E. Janssens, G. Meijer and K. R. Asmis Unexpected Structures of Aluminum Oxide Clusters in the Gas Phase Angew. Chem. Int. Ed. 46 (2007) 3372-3375. Applications: D. Santambrogio, E. Janssens, S. Li, T. Siebert, G. Meijer, K.R. Asmis, J. Döbler, M. Sierka and J. Sauer Identification of Conical Structures in Small Aluminium Oxide Clusters: Infrared Spectroscopy of (Al_2 O_3 )_1-4 (AlO)+ J. Am. Chem. Soc. 130 (2008) 15143–15149 G. Santambrogio, M. Brümmer, L. Wöste, J. Döbler, M. Sierka, J. Sauer, G. Meijer and K. R. Asmis Gas Phase Vibrational Spectroscopy of Mass-Selected Vanadium Oxide Cluster Anions Phys. Chem. Chem. Phys. 10 (2008) 3992 - 4005 Oger E, Kelting R, Weis P, et al.Small tin cluster anions: Transition > from quasispherical to prolate structures J. Chem. Phys. 130 (2009) 124305 Nava P, Ahlrichs R Theoretical investigation of clusters of phosphorus and arsenic: Fascination and temptation of high symmetries Chemistry - A European Journal 14 (2008) 4039-4045 Esther Oger, Nathan R. M. Crawford, Rebecca Kelting, Patrick Weis, Manfred M. Kappes, Reinhart Ahlrichs Boron Cluster Cations: Transition from Planar to Cylindrical Structures Angew. Chem. Int. Ed. 46 (2007) 8503-8506 Hope that helps, Uwe David Marlanov davma7-,-gmail.com schrieb: > Sent to CCL by: "David Marlanov" [davma7]|[gmail.com] > Dear colleagues! > I'm not professional in quantum chemistry. > I did local optimization in g03 and gamess (us) many times. As I understood global geometry optimization (finding the geometry with global energy minimum) was not implemented in these programs ( I mean Monte Carlo methods, genetic algorithm, etc.). Is there any program in quantum chemistry that can do such kind of optimization? > I browsed the net and found many articles about this topic but not implemented algorithm. From owner-chemistry@ccl.net Wed May 13 12:07:01 2009 From: "John McKelvey jmmckel:_:gmail.com" To: CCL Subject: CCL: Symmetry inquiry Message-Id: <-39313-090513112340-6838-pkzWBnxFKWBjKsteaQJt3w*server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001e680f0f882857000469cccb6b Date: Wed, 13 May 2009 11:23:29 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-.-gmail.com] --001e680f0f882857000469cccb6b Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thanks to Denis Gulin, K. Kahn, S. Keinan and Sten Lill who collectively suggested SYMMOL (2), CSM (1), and CHEMCRAFT (1). I was able to download and modify source for SYMMOL slightly and it works beautifully!! Runs on Windows and Linux just fine. Many thanks to all! John McKelvey --001e680f0f882857000469cccb6b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks to Denis Gulin, K. Kahn, S. Keinan and Sten Lill who collectively su= ggested SYMMOL (2), CSM (1), and CHEMCRAFT (1).

I was able to downlo= ad and modify source for SYMMOL slightly=A0 and it works beautifully!!=A0 = Runs on Windows and Linux just fine.

Many thanks to all!

John McKelvey
--001e680f0f882857000469cccb6b-- From owner-chemistry@ccl.net Wed May 13 12:42:01 2009 From: "Vincent Xianlong Wang xloongw(0)yahoo.com" To: CCL Subject: CCL: Searching for a free software to calculate pK, Stability constant etc Message-Id: <-39314-090513095537-28885-NWTgPPzPKqJwqAcZk7bN3g a server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Type: text/plain; charset=us-ascii Date: Wed, 13 May 2009 06:55:23 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw-x-yahoo.com] Hi Tirtha, I suggest OPIUM which is free and easy to use. Although there is no English manual available, there are many example data sets from its website which should explain enough. Here is the link to download the program. http://www.natur.cuni.cz/~kyvala/opium.html Best regards, Vincent ----- Original Message ---- > From: Tirtha mukherjee mukherjeetirtha===yahoo.co.in To: "Wang, Xianlong " Sent: Wednesday, May 13, 2009 12:36:11 PM Subject: CCL: Searching for a free software to calculate pK, Stability constant etc Sent to CCL by: "Tirtha mukherjee" [mukherjeetirtha _ yahoo.co.in] Respected members I am searching fro a free soft ware to calculate pka and stability constant form potentiometric data. Can any please help?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed May 13 13:17:01 2009 From: "N. Sukumar nagams/a\rpi.edu" To: CCL Subject: CCL: Checking for hydrogen bonding Message-Id: <-39315-090513125156-14978-5c75bLucz3YvDPJO1fT9qA:server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Wed, 13 May 2009 12:51:41 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams * rpi.edu] Try HBPLUS http://www.biochem.ucl.ac.uk/bsm/hbplus/home.html HBPLUS is a hydrogen bond calculation program that inputs a PDB format file and outputs a list of potential hydrogen bonds. It is designed for proteins, but if you can input your coordinates in PDB format, it should work. McDonald and Thornton (1994), "Satisfying Hydrogen Bonding Potential in Proteins", JMB 238:777-793. Dr. N. Sukumar http://www.rpi.edu/research/biotech/researchers/sukumar.html ==============Original message text=============== On Wed, 13 May 2009 4:03:33 EDT "Jerry Chan chanjcc(_)ntu.edu.tw" wrote: Sent to CCL by: Jerry Chan [chanjcc^^^ntu.edu.tw] Dear colleagues, I need to find out if there are any intermolecular hydrogen bondings in an aggregate of peptides. I suppose some NH and CO will form better hydrogen bonding and some do not. Is there any freeware that can analyze such system and has a scoring function for H-bonding? Even pointers to references would be greatly appreciated. Million thanks, Jerry -- Jerry C. C. Chan phone: 886-2-33662994 Chemistry Department fax: 886-2-23636359 National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei, Taiwan http://spin.ch.ntu.edu.twhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Wed May 13 14:14:00 2009 From: "david marlan davma7\a/gmail.com" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39316-090513133648-21855-eVSsykVV6fwoYB7zBlM3Ug_+_server.ccl.net> X-Original-From: david marlan Content-Type: multipart/alternative; boundary=001485f27f5e7968af0469ce39b4 Date: Wed, 13 May 2009 21:35:55 +0430 MIME-Version: 1.0 Sent to CCL by: david marlan [davma7*o*gmail.com] --001485f27f5e7968af0469ce39b4 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Rene, thanks for your reply. Just for clarification - what king of job do your "shell scripts that combine "Taboo Search""? Are they randomize molecule (ok how to do it - is another question) and prepare input file for g03 (or vasp)? After g03 calculates local minimum scripts process new obtained geometry and compare it with geometries obtained at another steps? (saving also E of each geometry). Or these scripts do something else? Thanks a lot! On Mon, May 11, 2009 at 9:02 PM, Rene Fournier renef _ yorku.ca < owner-chemistry]![ccl.net> wrote: > > Sent to CCL by: Rene Fournier [renef=yorku.ca] > >Is there any program in quantum chemistry that can do such > >kind of optimization? > Spartan has had it for many years, but I think it's only > for conformation search, ie "bonds" can't be broken or formed > during optimization. VASP can do simulated annealing in a > general way, I suppose in principle it could work for anything. > We used shell scripts to combine our "Taboo Search" code with > G03 and VASP and do global optimization at DFT level (see PRA 79 (2009) > 043202 and 043203 for recent applications). Ours is a research code still > under development --- not user-friendly, not well supported, and > only works for clusters --- but if you're interested, let me know. > > -- Rene > > Rene Fournier, Chemistry, York University, renef-*-yorku.ca > > > On Mon, 11 May 2009, David Marlanov davma7-,-gmail.com wrote: > > > > > Sent to CCL by: "David Marlanov" [davma7]|[gmail.com] > > Dear colleagues! > > I'm not professional in quantum chemistry. > > I did local optimization in g03 and gamess (us) many times. As I > understood global geometry optimization (finding the geometry with global > energy minimum) was not implemented in these programs ( I mean Monte Carlo > methods, genetic algorithm, etc.). Is there any program in quantum chemistry > that can do such kind of optimization? > > I browsed the net and found many articles about this topic but not > implemented algorithm. > > > > Thanks a lot!> > > --001485f27f5e7968af0469ce39b4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Rene, thanks for your=A0 reply. Just for clarification -
what=A0 king=A0= of job do=A0 your "shell scripts that combine=A0 "Taboo Search&q= uot;"?

Are they=A0 randomize molecule (ok how to do it - is ano= ther question) and prepare
input file for=A0 g03 (or vasp)?=A0 After=A0 g03 calculates local minimum= =A0 scripts
process new obtained geometry and compare it with geometries= obtained
at another steps? (saving also E=A0 of each geometry).
Or= =A0 these scripts do something else?

Thanks a lot!



On Mon, May 11,= 2009 at 9:02 PM, Rene Fournier renef _ yorku.c= a <owne= r-chemistry]![ccl.net> wrote:

Sent to CCL by: Rene Fournier [renef=3Dyorku.ca]
>Is there any program in quantum chemistry that can do= such
>kind of =A0optimization?
=A0 =A0Spartan has had it for many years, but I think it's only<= br> for conformation search, ie "bonds" can't be broken or formed=
during optimization. =A0VASP can do simulated annealing in a
general way, I suppose in principle it could work for anything.
We used shell scripts to combine our "Taboo Search" code with
G03 and VASP and do global optimization at DFT level (see PRA 79 (2009)
043202 and 043203 for recent applications). =A0Ours is a research code stil= l
under development --- not user-friendly, not well supported, and
only works for clusters --- but if you're interested, let me know.

-- Rene

Rene Fournier, Chemistry, York University, renef-*-yorku.ca


On Mon, 11 May 2009, David Marlanov davma7-,-gmail.com wrote:

>
> Sent to CCL by: "David =A0Marlanov" [davma7]|[gmail.com]
> Dear colleagues!
> I'm not professional in quantum chemistry.
> I did local optimization =A0in g03 and gamess (us) many times. As I un= derstood global geometry optimization (finding the geometry with global ene= rgy minimum) was not implemented in these programs ( I mean Monte Carlo met= hods, genetic algorithm, etc.). Is there any program in quantum chemistry t= hat can do such kind of =A0optimization?
> I browsed the net and found many articles about this topic but not imp= lemented algorithm.
>
> Thanks a lot!>
>
>



-=3D This is automatically added to each message by the mailing script =3D-=
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--001485f27f5e7968af0469ce39b4-- From owner-chemistry@ccl.net Wed May 13 16:55:00 2009 From: "Esteban Gabriel Vega Hissi egvega(-)gmail.com" To: CCL Subject: CCL: How to add missing residues Message-Id: <-39317-090513125519-17722-cqZwfoLzXGZ0Q01TJPbBNA-x-server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=001485f6c788c9c1640469cd1838 Date: Wed, 13 May 2009 12:45:11 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega[-]gmail.com] --001485f6c788c9c1640469cd1838 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Sangeetha, You can also try WHAT IF Server: http://swift.cmbi.ru.nl/servers/html/corall.html Hope this help too. Compare the methods(SWISS PDBViewer and WHAT IF Server) and share the results! Esteban 2009/5/13 Sangeetha Subramaniam srdshigella|a|gmail.com < owner-chemistry]^[ccl.net> > Thank you all for your kind reply and suggestions. > > Regards > Sangeetha. > > On Mon, May 11, 2009 at 11:08 PM, Deepangi Pandit deepangi.pandita/ > gmail.com > wrote: > >> >> Sent to CCL by: Deepangi Pandit [deepangi.pandit!A!gmail.com] >> Hi Sangeetha: >> Adding missing residues before simulation is an important task and >> people have their own preferences about the methodology. You could try >> the free program SWISS PDBViewer/DeepView program (Link 1) and follow >> the second link which explains the procedure with help of tutorials >> listed on the second link >> >> 1. http://spdbv.vital-it.ch/index.html >> >> >> 2. http://spdbv.vital-it.ch/build.html >> >> Best, >> Deepa >> >> >> >> On Mon, May 11, 2009 at 12:49 PM, Sangeetha Vimal >> srdshigella!A!gmail.com wrote: >> > >> > Sent to CCL by: "Sangeetha Vimal" [srdshigella]^[gmail.com] >> > Hello everyone, >> > >> > Can someone post the tools/methods available for building missing >> residues in the crystal structure. I need the complete structure for >> carrying out simulation studies. >> > >> > thanks >> > sangeetha.> >> > >> > >> >> >> >> - This is automatically added to each message by the mailing script - >> E-mail to subscribers: CHEMISTRY~~ccl.net or >> use:>> >> E-mail to administrators: CHEMISTRY-REQUEST~~ccl.netor use>> >> >> > > > > --001485f6c788c9c1640469cd1838 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Sangeetha,
You can also try WHAT IF Server:

http://swift.cmbi.ru.nl/servers/= html/corall.html
Hope this help too.
Compare the methods(SWISS PD= BViewer and WHAT IF Server) and share the results!

Esteban

2009/5/13 Sangeetha Subramani= am srdshigella|a|gmail.com <owner-chemistry]^[ccl.net>
Thank you all for= your kind reply and suggestions.

Regards
Sangeetha.

On Mon, May 11, 2009 at 11:08 PM, Deepangi Pandit deepangi.pandita/gmail.com <= ;owner-ch= emistry~~ccl.net> wrote:

Sent to CCL by: Deepangi Pandit [deepangi.pandit!A!gmail.com]
Hi Sangeetha:
Adding missing residues before simulation is an important task and
people have their own preferences about the methodology. You could try
the free program SWISS PDBViewer/DeepView program (Link 1) and follow
the second link which explains the procedure with help of tutorials
listed on the second link

1. http:/= /spdbv.vital-it.ch/index.html


2. http:/= /spdbv.vital-it.ch/build.html

Best,
Deepa



On Mon, May 11, 2009 at 12:49 PM, Sangeetha Vimal
srdshigella!A!gmail.com = <owner-chemistry^ccl.net> wrote:
>
> Sent to CCL by: "Sangeetha =A0Vimal" [srdshigella]^[gmail.com]
> Hello everyone,
>
> Can someone post the tools/methods available for building missing resi= dues in the crystal structure. I need the complete structure =A0for carryin= g out simulation studies.
>
> thanks
> sangeetha.
>
>
>
> -=3D This is automatically added to each message by the mailing script= =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message= > =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> = =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 = =A0http://www= .ccl.net/spammers.txt>
>
>



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--001485f6c788c9c1640469cd1838-- From owner-chemistry@ccl.net Wed May 13 17:30:01 2009 From: "Greg Warren greg===eyesopen.com" To: CCL Subject: CCL: problem with FRED -refine lig_mmff Message-Id: <-39318-090513163940-17540-er1nFeQgxQ3KBxsq40Lppg|,|server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_BB3CCF2D3D6B094D96588383620C5F3E38F9455E48EXVMBX01811ex_" Date: Wed, 13 May 2009 13:08:57 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg .. eyesopen.com] --_000_BB3CCF2D3D6B094D96588383620C5F3E38F9455E48EXVMBX01811ex_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Rezauddin, The -refine option with Zap does not always work. To be able to provide he= lp it is important that you supply version number of the program you are us= ing. However, this method is very unlikely to give you better results than= if you used one of Fred's scoring functions. The reason is that the liga= nd placement is optimized on the receptor grid so Zap scores are very unlik= ely to be good because of grid artifacts. You will be more successful, if = you need to optimize the ligand position post docking and to score using a = ZAP interaction energy, using the OpenEye application Szybki. Regards, Greg > From: owner-chemistry+greg=3D=3Deyesopen.com(-)ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com(-)ccl.net] On Behalf Of Reaz Uddin riaasuddin|,|yaho= o.com Sent: Wednesday, May 13, 2009 2:39 AM To: Greg Warren Subject: CCL: problem with FRED -refine lig_mmff Hello ccls,. You know I have a little problem with FRED. Whenever I use option -refine l= ig_mmff with Zap job, it doesn't work. It shows all docking failed. I am us= ing ~8000 compounds for docking. But no single compound is docked successfu= lly. Without -refine option the job runs well and no trouble. Does anybody have any idea.?? I appreciate for your time. Thanks FRED Parameter file looks like: # -exhaustive_scoring chemgauss3 -opt chemgauss3 -assign_protein_charges true -refine lig_mmff # -pose_select_weight_shapegauss 1 -pose_select_weight_plp 1 -pose_select_weight_chemgauss3 1 -pose_select_weight_oechemscore 1 -pose_select_weight_chemscore 1 -pose_select_weight_screenscore 1 # -pose_select_weight_chemgauss2 1 #-pose_select_weight_cgo 0 #-pose_select_weight_cgt 0 # -shapegauss true -plp true -chemgauss3 true -oechemscore true # -screenscore true -zapbind true -consensus true -chemgauss2 true #-cgo false #-cgt false # -shapegauss_masc true -plp_masc true -chemgauss3_masc true -chemscore_masc true -oechemscore_masc true -screenscore_masc true -zapbind_masc true -consensus_masc true # -chemgauss2_masc true #-cgo-masc false #-cgt-masc false #-report_masc_failures true -pvmconf hosts -prefix ZAP-withAll-MASC- REAZUDDIN Research Scholar HEJ Research Institute of Chemistry University of Karachi Karachi, Pakistan Email: riaasuddin++yahoo.com, mriazuddin++iccs.edu --_000_BB3CCF2D3D6B094D96588383620C5F3E38F9455E48EXVMBX01811ex_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Rezauddin,

 =

The –refine option= with Zap does not always work.  To be able to provide help it is important that= you supply version number of the program you are using.  However, this met= hod is very unlikely to give you better results than if you used  one of F= red’s scoring functions.  The reason is that the ligand placement is optimiz= ed on the receptor grid so Zap scores are very unlikely to be good because of gri= d artifacts.  You will be more successful, if you need to optimize the ligand position post docking and to score using a ZAP interaction energy, u= sing the OpenEye application Szybki.

 =

Regards,

Greg

 

From: owner-chemistry+greg=3D=3Deyesopen.com(-)ccl.net [mailto:owner-chemistry+greg=3D=3Deyesopen.com(-)ccl.net] On Behalf Of Reaz Uddin riaasuddin|,|yahoo.com
Sent: Wednesday, May 13, 2009 2:39 AM
To: Greg Warren
Subject: CCL: problem with FRED -refine lig_mmff

 

Hello ccls,.

You know I have a litt= le problem with FRED. Whenever I use option -refine lig_mmff with Zap j= ob, it doesn't work. It shows all docking failed. I am using ~8000 compo= unds for docking. But no single compound is docked successfully. <= o:p>

Without -refine option= the job runs well and no trouble.

Does anybody have any = idea.??

I appreciate for your = time.

Thanks

 

FRED Parameter file lo= oks like:

#
-exhaustive_scoring chemgauss3
-opt chemgauss3
-assign_protein_charges true
-refine lig_mmff
#
-pose_select_weight_shapegauss 1
-pose_select_weight_plp 1
-pose_select_weight_chemgauss3 1
-pose_select_weight_oechemscore 1
-pose_select_weight_chemscore 1
-pose_select_weight_screenscore 1
#
-pose_select_weight_chemgauss2 1
#-pose_select_weight_cgo 0
#-pose_select_weight_cgt 0
#
-shapegauss true
-plp true
-chemgauss3 true
-oechemscore true
#
-screenscore true
-zapbind true
-consensus true

-chemgauss2 true
#-cgo false
#-cgt false
#
-shapegauss_masc true
-plp_masc true
-chemgauss3_masc true
-chemscore_masc true
-oechemscore_masc true
-screenscore_masc true
-zapbind_masc true
-consensus_masc true
#
-chemgauss2_masc true
#-cgo-masc false
#-cgt-masc false
#-report_masc_failures true
-pvmconf hosts
-prefix ZAP-withAll-MASC-



REAZUDDIN
Research Scholar
HEJ Research Institute of Chemistry
University of Karachi
Karachi, Pakistan
Email: riaasuddin++yahoo.com, mri= azuddin++iccs.edu

 

--_000_BB3CCF2D3D6B094D96588383620C5F3E38F9455E48EXVMBX01811ex_--