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From owner-chemistry@ccl.net Mon Jun 22 00:02:01 2009 From: "Kamalakar Jadhav kjadhav^_^vlifesciences.com" To: CCL Subject: CCL: Needed Trial version of any Pharmacophore development tool Message-Id: <-39585-090621235813-5565-SFYChSIiUjPQW0OF3FaRXA++server.ccl.net> X-Original-From: "Kamalakar Jadhav" Date: Sun, 21 Jun 2009 23:58:09 -0400 Sent to CCL by: "Kamalakar Jadhav" [kjadhav]*[vlifesciences.com] Hi You can have a look at MolSign module of VLifeMDS http://www.vlifesciences.com/products/VLifeMDS/mds.htm Best Regards, Kamalakar From owner-chemistry@ccl.net Mon Jun 22 00:36:00 2009 From: "Kamalakar Jadhav kjadhav^^vlifesciences.com" To: CCL Subject: CCL: Needed Trial version of any Pharmacophore development tool Message-Id: <-39586-090622002449-15708-AvL1uvvrFpGm3f0cBUM5GQ-*-server.ccl.net> X-Original-From: Kamalakar Jadhav Content-Type: multipart/alternative; boundary="------------020407050108020109080907" Date: Mon, 22 Jun 2009 09:13:34 +0530 MIME-Version: 1.0 Sent to CCL by: Kamalakar Jadhav [kjadhav~!~vlifesciences.com] This is a multi-part message in MIME format. --------------020407050108020109080907 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi You can have a look at MolSign module of VLifeMDS http://www.vlifesciences.com/products/VLifeMDS/mds.htm Best Regards, Kamalakar vadicherla tati reddy tatireddy.vadicherla#gmail.com wrote: > Hi All, > I am looking for a trial version of pharmacophore development tool > (Windows/linux). > > Your help is much appreciated. > > > > Thanks > TatiReddy > ------------------------------------------------------------------------ > > > Internal Virus Database is out of date. > Checked by AVG - www.avg.com > Version: 8.5.329 / Virus Database: 270.12.20/2100 - Release Date: 05/06/09 06:04:00 > > --------------020407050108020109080907 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi
You can have a look at MolSign module of VLifeMDS
http://www.vlifesciences.com/products/VLifeMDS/mds.htm

Untitled Document

Best Regards,
Kamalakar

vadicherla tati reddy tatireddy.vadicherla#gmail.com wrote:

Hi All,
I am looking for a trial version of pharmacophore development tool (Windows/linux).

Your help is much appreciated.

Thanks
TatiReddy
Internal Virus Database is out of date.
Checked by AVG - www.avg.com 
Version: 8.5.329 / Virus Database: 270.12.20/2100 - Release Date: 05/06/09 06:04:00

  

--------------020407050108020109080907-- From owner-chemistry@ccl.net Mon Jun 22 03:14:00 2009 From: "Babak Khalili khalili.babak+/-gmail.com" To: CCL Subject: CCL: Docking free software Message-Id: <-39587-090622030338-8355-cpWdPYH63L+A084ENr3Iow a server.ccl.net> X-Original-From: Babak Khalili Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 22 Jun 2009 10:37:54 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak(-)gmail.com] Dear subscribers, I have to dock 2 peptides together, may you help me to find some free software and a procedure, also. Tank you in advance, Babak Khalili, PhD candidate of biochemistry From owner-chemistry@ccl.net Mon Jun 22 06:55:00 2009 From: "selva raj sengottiyan selvacbm^-^yahoo.co.in" To: CCL Subject: CCL: dear sir Message-Id: <-39588-090622065330-5849-GrLzU+N0/v4gWg7BmapThQ,server.ccl.net> X-Original-From: "selva raj sengottiyan" Date: Mon, 22 Jun 2009 06:53:26 -0400 Sent to CCL by: "selva raj sengottiyan" [selvacbm]_[yahoo.co.in] DEAR SIR HOW DO CALCULATE THE ACCESSIBLE SURFACE AREA OF(ASA)OF PROTEIN AND THE DOCKED COMPLEX USING NACCESS PROGRAM THANKING YOU SELVARAJ From owner-chemistry@ccl.net Mon Jun 22 07:44:01 2009 From: "andrea spitaleri spitaleri.andrea!^!hsr.it" To: CCL Subject: CCL: Docking free software Message-Id: <-39589-090622044920-10317-8A7PWutEn+Q9E29Nn4SLQw,server.ccl.net> X-Original-From: andrea spitaleri content-transfer-encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1" Date: Mon, 22 Jun 2009 10:03:57 +0200 MIME-Version: 1.0 Sent to CCL by: andrea spitaleri [spitaleri.andrea()hsr.it] Hi there, have look to HADDOCK: http://www.nmr.chem.uu.nl/haddock/ Cheers andrea Babak Khalili khalili.babak+/-gmail.com wrote: > Sent to CCL by: Babak Khalili [khalili.babak(-)gmail.com] > Dear subscribers, > > I have to dock 2 peptides together, may you help me to find some free > software and a procedure, also. > > Tank you in advance, > Babak Khalili, > PhD candidate of biochemistry> > > -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ ------------------------------- ----------------------------------------------------------------- La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi "Finanziamento della ricerca sanitaria" il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': 5permille(-)hsr.it o vai sul sito http://www.5xmille.org. From owner-chemistry@ccl.net Mon Jun 22 11:38:00 2009 From: "Anuradha Mittal anuradha.mittal=gmail.com" To: CCL Subject: CCL: Discovery studio - conformation generation Message-Id: <-39590-090622113649-15348-Td697rzBLoPFb8NWq8Kibg|-|server.ccl.net> X-Original-From: Anuradha Mittal Content-Type: multipart/alternative; boundary=0016362835a80c017c046cf1a432 Date: Mon, 22 Jun 2009 10:36:41 -0500 MIME-Version: 1.0 Sent to CCL by: Anuradha Mittal [anuradha.mittal()gmail.com] --0016362835a80c017c046cf1a432 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all, I am new to Discovery Studio. I am trying to generate conformations for a set of input ligands using Diverse Conformation Generation protocol. I am using mdl file as an input. I am running into "catconf failure" error. Any help will be much appreciated. Thanks Anu --0016362835a80c017c046cf1a432 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all,

I am new to Discovery Studio. I am trying to generate conformations for a set of input ligands using Diverse Conformation Generation protocol. I am using mdl file as an input. I am running into "catconf failure" error.

Any help will be much appreciated.

Thanks
Anu

--0016362835a80c017c046cf1a432-- From owner-chemistry@ccl.net Mon Jun 22 12:13:01 2009 From: "luca bertini luca.bertini-$-unimib.it" To: CCL Subject: CCL: functional for Fe(3+) complexes Message-Id: <-39591-090619141319-30424-YwbSwoNz+p7tZK2GBp8YPw*|*server.ccl.net> X-Original-From: "luca bertini" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1;format="flowed" Date: Fri, 19 Jun 2009 17:46:40 +0200 MIME-Version: 1.0 Sent to CCL by: "luca bertini" [luca.bertini()unimib.it] Dear Kzys, give a look also to these papers. The modificed B3LYP functional presented by Reiher and co-workers works fine. Fouqueau, A.; Mer, S.; Casida, M. E.; Daku, L. M. L.; Hauser, A.; Mineva, T.; Neese, F. J. Chem. Phys. 2004, 120, 9473. Comparison of density functionals for energy and structural differences between the high- [5T2g: (t2g)4(eg)2] and low- [1A1g: (t2g)6(eg)0] spin states of the hexaquoferrous cation [Fe(H2O)6]2+. Fouqueau, A.; Mer, S.; Casida, M. E.; Daku, L. M. L.; Hauser, A.; Neese, F. Comparison of density functionals for energy and structural differences between the high- [5T2g:(t2g)4(eg)2] and low- [1A1g:(t2g)6(eg)0] spin states of iron(II) coordination compounds. II. More functionals and the hexaminoferrous cation, [Fe(NH3)6]2+. J. Chem. Phys. 2005, 122, 044110. Reparameterization of hybrid functionals based on energy differences of states of different multiplicity Reiher, M.; Salomon, O.; Hess, B. A. Theo. Chem. Acc. 2001, 107, 48 Structure and Energetics of Fe2(CO)8 Singlet and Triplet Electronic States Luca Bertini, Maurizio Bruschi, Luca De Gioia, and Piercarlo Fantucci J. Phys. Chem. A, 2007, 111 (48), pp 12152–12162 doi:10.1021/jp075343z -- Luca Bertini Dipartimento di Biotecnologie e Bioscienze Universita' degli Studi di Milano-Bicocca Piazza della Scienza, 2 20126 Milano, Italy Tel: +39 02 64483438 email: luca.bertini ~~ unimib.it On Fri, 19 Jun 2009 12:16:23 +0200 "Marcel Swart marcel.swart%x%icrea.es" wrote: > > Sent to CCL by: Marcel Swart [marcel.swart{:}icrea.es] > > I think you should consider OPBE with STOs (in ADF) or > alternatively a large GTO basis. See e.g. > > M. Swart > "Accurate spin-state energies for iron complexes" > J. Chem. Theor. Comp. 2008, 4, 2057-2066 > http://dx.doi.org/10.1021/ct800277a > > M. Güell, J.M. Luis, M. Solà and M. Swart > "Importance of the basis set for the spin-state >energetics of iron complexes" > J. Phys. Chem. A 2008, 112, 6384-6391 > http://dx.doi.org/10.1021/jp803441m > > M. Güell, M. Solà and M. Swart > "Spin-state splittings of iron(II) complexes with >trispyrazolyl ligands" > Polyhedron, Young Investigator issue, 2009, online > http://dx.doi.org/10.1016/j.poly.2009.06.006 > > Quoting "zborowsk=-=chemia.uj.edu.pl" >: > >> >> Sent to CCL by: zborowsk]![chemia.uj.edu.pl >> Dear all >> >> Could you recommend me the best in your opinion DFT >>functional (also basis >> set)for calculation (mainly geometry, energetical and >>magnetic properties) >> of iron(III) complexes with organic ligands >> >> Thanks in advance >> >> Kzys >> >> >> >> -- >> Krzysztof K. Zborowski >> Faculty of Chemistry >> Jagiellonian University >> 3 Ingardena Street >> 30-060 Krakow >> Poland >> phone: +48(12)632-4888 ext. 2064 or 2067 >> fax: +48(12)634-05-15 >> email: zborowsk{}chemia.uj.edu.pl >> gg 3817259 >> skype kzys70 >> www.chemia.uj.edu.pl/~zborowsk >> >> >> >> -= This is automatically added to each message by the >>mailing script =-> >> >> > > > > > =================================== > dr. Marcel Swart > > ICREA researcher at > Institut de Química Computacional > Universitat de Girona > > Parc Científic i Tecnològic > Edifici Jaume Casademont (despatx A-27) > Pic de Peguera 15 > 17003 Girona > Catalunya (Spain) > > tel > +34-972-183240 > fax > +34-972-183241 > e-mail > marcel.swart{?crea.es > marcel.swart{?dg.edu > web > http://www.icrea.cat/Web/ScientificForm.aspx?key=372 > http://iqc.udg.edu/~marcel > =================================== > > > > -?his is automatically added to each message by the >mailing script ?To recover the email address of the >author of the message, please change > the strange characters on the top line to the ~~ sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST ~~ ccl.net or >useConferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > From owner-chemistry@ccl.net Mon Jun 22 14:30:01 2009 From: "hirdesh kumar hirdeshs8]~[gmail.com" To: CCL Subject: CCL: Needed Trial version of any Pharmacophore development tool Message-Id: <-39592-090620081139-17654-H8zwSEHiorl8bVIFdA2/7Q . server.ccl.net> X-Original-From: hirdesh kumar Content-Type: multipart/alternative; boundary=0016364ef1cc4148f3046cc62fbc Date: Sat, 20 Jun 2009 17:15:58 +0530 MIME-Version: 1.0 Sent to CCL by: hirdesh kumar [hirdeshs8::gmail.com] --0016364ef1cc4148f3046cc62fbc Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Reddy, LigandScout is available for one month trial version and is useful Pharmacophore tool. Enjoy, Regards, Hirdesh Kumar --0016364ef1cc4148f3046cc62fbc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Reddy,
LigandScout is available for one month trial version and is=A0= useful Pharmacophore tool.

Enjoy,

Regards,

Hirdesh K= umar
--0016364ef1cc4148f3046cc62fbc-- From owner-chemistry@ccl.net Mon Jun 22 15:04:01 2009 From: "Francisco Hernandez-Guzman fhernand^^^accelrys.com" To: CCL Subject: CCL: Discovery studio - conformation generation Message-Id: <-39593-090622141202-16918-AVIXLLfmBQqoYybXziKeGA__server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_E05DB3B9FDB9D846B6C9E1875CD41A332E16F32Eexch1hiaccelrys_" Date: Mon, 22 Jun 2009 13:11:48 -0400 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [fhernand..accelrys.com] --_000_E05DB3B9FDB9D846B6C9E1875CD41A332E16F32Eexch1hiaccelrys_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Anu, I encourage you to call our support group for any type of help using Discov= ery Studio. There are dedicated scientists ready to help. Accelrys Support: 1-800-756-4674 (US) email: support-*-accelrys.com If you're outside the US, then email is best and a regional office will tak= e your case. Kind regards, Francisco Francisco Hernandez-Guzman, Ph.D. Lead Solutions Scientist, Protein Modeling, Simulations and X-ray - USA Accelrys, Inc. (http://www.accelrys.com) San Diego, CA 92121 Office: (858) 799 - 5606 Fax: (858) 799 - 5100 Mobile: (858) 361 - 3020 E-mail: fhernandez-*-accelrys.com ---------------------------------------------------------------------------= ----------- Accelrys Support: 1-800-756-4674 E-mail: support-*-accelrys.com > From: owner-chemistry+fhernandez=3D=3Daccelrys.com-*-ccl.net [mailto:owner-ch= emistry+fhernandez=3D=3Daccelrys.com-*-ccl.net] On Behalf Of Anuradha Mittal = anuradha.mittal=3Dgmail.com Sent: Monday, June 22, 2009 8:37 AM To: Francisco Hernandez-Guzman Subject: CCL: Discovery studio - conformation generation Hi all, I am new to Discovery Studio. I am trying to generate conformations for a s= et of input ligands using Diverse Conformation Generation protocol. I am us= ing mdl file as an input. I am running into "catconf failure" error. Any help will be much appreciated. Thanks Anu --_000_E05DB3B9FDB9D846B6C9E1875CD41A332E16F32Eexch1hiaccelrys_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Anu,

I encourage you to call our support group for any type of he= lp using Discovery Studio. There are dedicated scientists ready to help. =

Accelrys Support: 1-800-756-4674 (US)

email: support-*-accelrys.com

If you're outside the US, then email is best and a regional office will take your case.

Kind regards,

Francisco

Francisco Hernandez-Guzman, Ph.D.

Lead Solutions Scientist, Protein Modeling, Simulations and X-ray - USA

Accelrys, Inc. (http://w= ww.accelrys.com)

San Diego, CA 92121

Office: (858) 799 - 5606

Fax: (858) 799 - 5100

Mobile: (858) 361 - 3020

E-mail: fhernandez-*-accelrys.com

------------------------------------------------------------= --------------------------

Accelrys Support: 1-800-756-4674

E-mail: support-*-accelrys.com

From: owner-chemistry+fhernandez=3D=3Daccelrys.com-*-ccl.net [mailto:owner-chemistr= y+fhernandez=3D=3Daccelrys.com-*-ccl.net] On Behalf Of Anuradha Mittal anuradha.mittal=3Dgmail.com
Sent: Monday, June 22, 2009 8:37 AM
To: Francisco Hernandez-Guzman
Subject: CCL: Discovery studio - conformation generation<= /span>

Hi all,

I am new to Discovery Studio. I am trying to generate conformations for a s= et of input ligands using Diverse Conformation Generation protocol. I am using= mdl file as an input. I am running into "catconf failure" error.

Any help will be much appreciated.

Thanks
Anu

--_000_E05DB3B9FDB9D846B6C9E1875CD41A332E16F32Eexch1hiaccelrys_-- From owner-chemistry@ccl.net Mon Jun 22 17:09:00 2009 From: "Jiabo Li jiaboli---yahoo.com" To: CCL Subject: CCL: Discovery studio - conformation generation Message-Id: <-39594-090622164824-20795-Rpi1pL1CBkMw8PLcA2/HJw*|*server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="0-630626625-1245700095=:30331" Date: Mon, 22 Jun 2009 12:48:15 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli\a/yahoo.com] --0-630626625-1245700095=:30331 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Anu, =A0 Please provide the input file, and also let me know which version of DS you= are using. The error message can be generated by any thing like wrong data= , license issue etc.=20 =A0 Jiabo --- On Mon, 6/22/09, Anuradha Mittal anuradha.mittal=3Dgmail.com wrote: > From: Anuradha Mittal anuradha.mittal=3Dgmail.com Subject: CCL: Discovery studio - conformation generation To: "Li, Jiabo " Date: Monday, June 22, 2009, 8:36 AM Hi all, I am new to Discovery Studio. I am trying to generate conformations for a s= et of input ligands using Diverse Conformation Generation protocol. I am us= ing mdl file as an input. I am running into "catconf failure" error. Any help will be much appreciated. Thanks Anu --0-630626625-1245700095=:30331 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Hi Anu,

Please provide the input file, and also let me know which version of D= S you are using. The error message can be generated by any thing like wrong= data, license issue etc.

Jiabo

--- On Mon, 6/22/09, Anuradha Mittal anuradha.mittal= =3Dgmail.com <owner-chemistry+/-ccl.net> wrote:

From: Anuradha Mittal anuradha.mittal=3Dgmail.com= <owner-chemistry+/-ccl.net>
Subject: CCL: Discovery studio - confor= mation generation
To: "Li, Jiabo " <jiaboli+/-yahoo.com>
= Date: Monday, June 22, 2009, 8:36 AM

Hi all,

I am new to Discovery Studio. I am t= rying to generate conformations for a set of input ligands using Diverse Co= nformation Generation protocol. I am using mdl file as an input. I am runni= ng into "catconf failure" error.

Any help will be much appreciated.<= BR>
Thanks
Anu

--0-630626625-1245700095=:30331-- From owner-chemistry@ccl.net Mon Jun 22 18:06:00 2009 From: "veronica ferraresi veroferraresi#gmail.com" To: CCL Subject: CCL:G: help on restart optimization Message-Id: <-39595-090622170148-21902-HUxe212LcWIrK3mOVXVbIA(_)server.ccl.net> X-Original-From: veronica ferraresi Content-Type: multipart/alternative; boundary=001485f19a042d0552046cf49a00 Date: Mon, 22 Jun 2009 16:08:41 -0300 MIME-Version: 1.0 Sent to CCL by: veronica ferraresi [veroferraresi:-:gmail.com] --001485f19a042d0552046cf49a00 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Try extracting the last geometry of the output (the one that ran out of time), make a new input, and run it as it was a new one. Vero. 2009/6/20 nadia boutabba eleuch n_boutabba _ yahoo.fr < owner-chemistry * ccl.net> > > Sent to CCL by: "nadia boutabba eleuch" [n_boutabba,,yahoo.fr] > Dear ccl memberes, > i am doing a Gaussian calculation which is terminated prematurely due to > running out of time. To restart the optimization i use opt=restart but i get > the following error > NBasis= 190 RedAO= T NBF= 190 > NBsUse= 190 1.00D-06 NBFU= 190 > Initial guess read from the read-write file: > Error in GetGes, MD**2= 36100 but NWrd= 26569. > Error termination via Lnk1e in > /cineca/prod/gaussian/03d02-xlf10/g03/l401.exe at Sat Jun 20 10:00:45 2009. > Job cpu time: 0 days 0 hours 0 minutes 1.2 seconds. > File lengths (MBytes): RWF= 68 Int= 0 D2E= 0 Chk= 16 > Scr= 2 > > > > would you help me please > > nadia boutabba > phone:9794027688 > adress 3902 college main str 77801 bryan texas> > > --001485f19a042d0552046cf49a00 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Try extracting the last geometry of the output (the one that ran out of tim= e), make a new input, and run it as it was a new one.
Vero.

2009/6/20 nadia boutabba eleuch n_boutabba _ yahoo.fr <owner-chemistry * ccl.net>

Sent to CCL by: "nadia boutabba eleuch" [n_boutabba,,yahoo.fr]
Dear ccl memberes,
i am doing a Gaussian calculation which is =A0terminated prematurely due to= running out of time. To restart the optimization i use opt=3Drestart but i= get the following error
=A0NBasis=3D =A0 190 RedAO=3D T =A0NBF=3D =A0 190
=A0NBsUse=3D =A0 190 1.00D-06 NBFU=3D =A0 190
=A0Initial guess read from the read-write file:
=A0Error in GetGes, MD**2=3D =A0 =A0 36100 but NWrd=3D =A0 =A0 26569.
=A0Error termination via Lnk1e in /cineca/prod/gaussian/03d02-xlf10/g03/l40= 1.exe at Sat Jun 20 10:00:45 2009.
=A0Job cpu time: =A00 days =A00 hours =A00 minutes =A01.2 seconds.
=A0File lengths (MBytes): =A0RWF=3D =A0 =A0 68 Int=3D =A0 =A0 =A00 D2E=3D = =A0 =A0 =A00 Chk=3D =A0 =A0 16 Scr=3D =A0 =A0 =A02

would you help me please

nadia boutabba
phone:9794027688
adress 3902 college main str 77801 bryan =A0texas

-=3D This is automatically added to each message by the mailing script =3D-=
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--001485f19a042d0552046cf49a00--