From owner-chemistry@ccl.net Sat Jun 20 00:54:01 2009 From: "vadicherla tati reddy tatireddy.vadicherla#gmail.com" To: CCL Subject: CCL: Needed Trial version of any Pharmacophore development tool Message-Id: <-39571-090619225150-22298-TIVAJZF//jQnZ8LlB3uuvQ=server.ccl.net> X-Original-From: vadicherla tati reddy Content-Type: multipart/alternative; boundary=00163628395e980e46046cbe9c34 Date: Sat, 20 Jun 2009 08:13:53 +0530 MIME-Version: 1.0 Sent to CCL by: vadicherla tati reddy [tatireddy.vadicherla(0)gmail.com] --00163628395e980e46046cbe9c34 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All, I am looking for a trial version of pharmacophore development tool (Windows/linux). Your help is much appreciated. Thanks TatiReddy --00163628395e980e46046cbe9c34 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All,
I am looking for a trial version of pharmacophore development tool (Windows/linux).

Your help is much appreciated.



Thanks
TatiReddy
--00163628395e980e46046cbe9c34-- From owner-chemistry@ccl.net Sat Jun 20 04:46:01 2009 From: "Gerard Pujadas gerard.pujadas%a%gmail.com" To: CCL Subject: CCL: Needed Trial version of any Pharmacophore development tool Message-Id: <-39572-090620042007-24414-D8BDHbpVel+OanK1CUvgGg===server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0016e6d27ed181d1b5046cc22349 Date: Sat, 20 Jun 2009 08:56:21 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas###gmail.com] --0016e6d27ed181d1b5046cc22349 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear TatiReddy, I am looking for a trial version of pharmacophore development tool > (Windows/linux). > > Your help is much appreciated. > Sch=F6dinger has Phase that it is a very powerful and flexible pharmacophor= e development tool. Moreover, they have a very nice customer support that giv= e you answer to your questions within 24 hours. You can obtain more information about Phase at http://www.schrodinger.com/ProductDescription.php?mID=3D6&sID=3D16&cID=3D0 One of the lacks of Phase (at least in its current version; a new version will be delivered in the next weeks) is that it is oriented towards obtaining ligand-based pharmacophores and not structure-based pharmacophore= s (*i.e.* obtaining pharmacophores from PDB complexes). We circunvent this by using LigandScout (http://www.inteligand.com/ligandscout/) that it is also an excellent program designed to detect which are the functional groups of = a ligand that are involved in the intermolecular interactions with the protei= n in the PDB complex. Nevertheless, the current version of LigandScout does not allow you to search in a compound library for hits that match the pharmacophore. The company gives you a trial period of the software of one month. In conclusion, I recommend you LigandScout and Phase. Together, they make a= n excellent pharmacophore team Hope this helps Best Gerard --0016e6d27ed181d1b5046cc22349 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear TatiReddy,


I am looking for a trial version of ph= armacophore development tool (Windows/linux).

Your help is much appreciated.

Sch=F6dinger ha= s Phase that it is a very powerful and flexible pharmacophore development t= ool. Moreover, they have a very nice customer support that give you answer = to your questions within 24 hours. You can obtain more information about Ph= ase at http://www.schrodinger.com/ProductDescription.ph= p?mID=3D6&sID=3D16&cID=3D0

One of the lacks of Phase (at least in its current version; a new versi= on will be delivered in the next weeks) is that it is oriented towards obta= ining ligand-based pharmacophores and not structure-based pharmacophores (<= i>i.e. obtaining pharmacophores from PDB complexes). We circunvent this= by using LigandScout (h= ttp://www.inteligand.com/ligandscout/) that it is also an excellent pro= gram designed to detect which are the functional groups of a ligand that ar= e involved in the intermolecular interactions with the protein in the PDB c= omplex. Nevertheless, the current version of LigandScout does not allow you= to search in a compound library for hits that match the pharmacophore. The= company gives you a trial period of the software of one month.

In conclusion, I recommend you LigandScout and Phase. Together, they ma= ke an excellent pharmacophore team

Hope this helps

Best
Gerard

--0016e6d27ed181d1b5046cc22349-- From owner-chemistry@ccl.net Sat Jun 20 06:56:00 2009 From: "Ba Tai Truong Truong.BaTai+/-chem.kuleuven.be" To: CCL Subject: CCL:G: Gaussian error Message-Id: <-39573-090619220314-18570-SDvZVsytDiydtjwew10+SA!^!server.ccl.net> X-Original-From: Ba Tai Truong Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sat, 20 Jun 2009 03:30:23 +0200 MIME-Version: 1.0 Sent to CCL by: Ba Tai Truong [Truong.BaTai _ chem.kuleuven.be] Quoting "Naser Eltaher Eltayeb nasertaha90/./yahoo.co.uk" =20 : There are some problems in this cases. You can do few change: - Increasing scfcyc=3D500 or st. Default scfcyc=3D128. - Put keyword: scf=3Dxqc - Change basic set to lower basic, increasing them step by step. I =20 mean, b3lyp/sto-3g, then b3lyp/6-31g*, 6-311+G*,.... - Change initial geometry. Perfect symmetry is good for some cases, =20 but sometime it will lead not converg. You can decrease symmetry to =20 lower. For example, you structure is D6h, you can run it with D2h, or =20 something. Hope this help Good luck > > Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90]![yahoo.co.uk] > Dear All > > I am trying to optmize Fe(OH)3 using hf/6-31+g but always I get this messa= ge: > >>>>>>>>>>> Convergence criterion not met. > SCF Done: E(UHF) =3D -1488.40938041 A.U. after 129 cycles > Convg =3D 0.3874D-02 -V/T =3D 2.0007 > S**2 =3D 0.9208 > Annihilation of the first spin contaminant: > S**2 before annihilation 0.9208, after 0.7543 > Convergence failure -- run terminated. > Error termination via Lnk1e in C:\G03W\l502.exe at Fri Jun 19 03:08:29 20= 09. > Job cpu time: 0 days 0 hours 0 minutes 34.0 seconds. > File lengths (MBytes): RWF=3D 16 Int=3D 0 D2E=3D 0 Chk=3D = =20 > 1 Scr=3D 1 > > Could anyone give me suggesion How to overcome this error. > > Thank you > > Naser > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > Truong Ba Tai Afdeling Kwantumchemie en Fysicochemie Celestijnenlaan 200F - bus 2404 3001 Heverlee, Belgium From owner-chemistry@ccl.net Sat Jun 20 07:30:02 2009 From: "Sangeetha Subramaniam srdshigella]=[gmail.com" To: CCL Subject: CCL: Needed Trial version of any Pharmacophore development tool Message-Id: <-39574-090620023138-12624-TLelH+xv4CTQ1FzsQAYAGQ-#-server.ccl.net> X-Original-From: Sangeetha Subramaniam Content-Type: multipart/alternative; boundary=0016364ef3c8bf6915046cc0e429 Date: Fri, 19 Jun 2009 22:26:54 -0700 MIME-Version: 1.0 Sent to CCL by: Sangeetha Subramaniam [srdshigella=gmail.com] --0016364ef3c8bf6915046cc0e429 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, You can have a look at LigandScout. http://www.inteligand.com/ligandscout/ Regards Sangeetha. On Fri, Jun 19, 2009 at 7:43 PM, 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 > --0016364ef3c8bf6915046cc0e429 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

You can have a look at LigandScout.

http://www.inteligand.com/l= igandscout/


Regards
Sangeetha.

On Fri, Jun 19, 2009 at 7:43 PM, vadicherla tati reddy tatireddy.vadicherla= #gmail.com <owner= -chemistry]![ccl.net> wrote:
Hi All,
I am l= ooking for a trial version of pharmacophore development tool (Windows/linux= ).

Your help is much appreciated.



Thanks
TatiReddy

--0016364ef3c8bf6915046cc0e429-- From owner-chemistry@ccl.net Sat Jun 20 10:10:00 2009 From: "Andrzej Szyczewski aszy _ amu.edu.pl" To: CCL Subject: CCL: Gd basis sets Message-Id: <-39575-090619112356-13241-jShlJeYtnjKXGtLCg6zBpQ]*[server.ccl.net> X-Original-From: "Andrzej Szyczewski" Date: Fri, 19 Jun 2009 11:23:52 -0400 Sent to CCL by: "Andrzej Szyczewski" [aszy : amu.edu.pl] Dear CCL Netters, Could you recommend me the best in your opinion DFT functional (also basis set)for calculation (mainly geometry, energetical and magnetic properties) of gadolinium(III) complexes with organic ligands Best regards Andrzej ============================================================== Dr.hab. Andrzej Szyczewski | | Institute of Physics, | e-mail: aszy^-^amu.edu.pl | A.Mickiewicz University | | Umultowska 85, | | 61-614 Poznan/Poland | fax: (4861) 825-77-58 | ============================================================== From owner-chemistry@ccl.net Sat Jun 20 10:45:00 2009 From: "Andrzej Szyczewski aszy-#-amu.edu.pl" To: CCL Subject: CCL: Gd basis sets Message-Id: <-39576-090620074307-27659-71PbPOnRvbArXKVTXhle1w()server.ccl.net> X-Original-From: "Andrzej Szyczewski" Date: Sat, 20 Jun 2009 07:43:03 -0400 Sent to CCL by: "Andrzej Szyczewski" [aszy##amu.edu.pl] Dear CCL Netters, Could you recommend me the best in your opinion DFT functional (also basis set)for calculation (mainly geometry, energetical and magnetic properties) of gadolinium(III) complexes with organic ligands Best regards Andrzej From owner-chemistry@ccl.net Sat Jun 20 15:23:01 2009 From: "Bahareh honarparvar bahareh_honarparvar#yahoo.com" To: CCL Subject: CCL: Gd basis sets Message-Id: <-39577-090620152146-13844-XxtGrG9GFALF4lDiHRxmcg::server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="0-759105104-1245525693=:1977" Date: Sat, 20 Jun 2009 12:21:33 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar**yahoo.com] --0-759105104-1245525693=:1977 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello B3LYP/LANL2DZ is proper theoretical model for your case. Regards B.H --- On Sat, 6/20/09, Andrzej Szyczewski aszy-#-amu.edu.pl wrote: > From: Andrzej Szyczewski aszy-#-amu.edu.pl Subject: CCL: Gd basis sets To: "Honarparvar, Honarparvar " Date: Saturday, June 20, 2009, 4:13 PM Sent to CCL by: "Andrzej=A0 Szyczewski" [aszy##amu.edu.pl] Dear CCL Netters, Could you recommend me the best in your opinion DFT functional (also basis set)for calculation (mainly geometry, energetical and magnetic properties) = of gadolinium(III) complexes with organic ligands Best regards Andrzej -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-759105104-1245525693=:1977 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello
B3LYP/LANL2DZ is proper theoretical = model for your case.
Regards
B.H

--- On Sat, 6/20/09, Andrz= ej Szyczewski aszy-#-amu.edu.pl <owner-chemistry : ccl.net> = wrote:

From: Andrzej Szyczewski aszy-#-amu.= edu.pl <owner-chemistry : ccl.net>
Subject: CCL: Gd basis sets
To= : "Honarparvar, Honarparvar " <bahareh_honarparvar : yahoo.com>=
Date: Saturday, June 20, 2009, 4:13 PM

=
Sent to CCL by: "Andrzej  Szyczewski" [aszy##amu.edu.pl]
Dear C= CL Netters,

Could you recommend me the best in your opinion DFT func= tional (also basis
set)for calculation (mainly geometry, energetical and= magnetic properties) of gadolinium(III) complexes with organic ligands

Best regards

Andrzej



-=3D This is aut= omatically added to each message by the mailing script =3D-
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=0A=0A --0-759105104-1245525693=:1977-- From owner-chemistry@ccl.net Sat Jun 20 15:58:01 2009 From: "Jose Alberto Fernandes jafernandes(-)ua.pt" To: CCL Subject: CCL: Gd basis sets Message-Id: <-39578-090620152519-14852-jD7o1Y8CvgcWISP6NXIMiw]![server.ccl.net> X-Original-From: "Jose Alberto Fernandes" Date: Sat, 20 Jun 2009 15:25:15 -0400 Sent to CCL by: "Jose Alberto Fernandes" [jafernandes:-:ua.pt] hi Andrzej I have already worked with europium and I used Lanl2DZ, but my work was only related with geometry and energy. If you can avoid the magnetism you can simplify and start using Lanthanum instead of gadolinium. You get a good starting geometry and no problems with unpaired spins. Then, if you wish to go further you can switch to gadolinium. I really do not know if Lanl2dz produces good magnetic properties. Jose > "Andrzej Szyczewski aszy _ amu.edu.pl" wrote: > > Sent to CCL by: "Andrzej Szyczewski" [aszy : amu.edu.pl] > > Dear CCL Netters, > > Could you recommend me the best in your opinion DFT functional (also basis > set)for calculation (mainly geometry, energetical and magnetic properties) of > gadolinium(III) complexes with organic ligands > > Best regards > > Andrzej > > > ============================================================== > Dr.hab. Andrzej Szyczewski | | > Institute of Physics, | e-mail: aszy^-^amu.edu.pl | > A.Mickiewicz University | | > Umultowska 85, | | > 61-614 Poznan/Poland | fax: (4861) 825-77-58 | > ============================================================== > > From owner-chemistry@ccl.net Sat Jun 20 16:32:00 2009 From: "Jerome Kieffer jerome.Kieffer,+,terre-adelie.org" To: CCL Subject: CCL:G: NMR coupling constant and radicals Message-Id: <-39579-090620152743-15825-+WSWHe8948LaxGxHYwkEqg*server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Sat, 20 Jun 2009 21:27:29 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer|terre-adelie.org] Dear CCLers, I wonder if there is any special issue in calculating the NMR spectrum and especially the nuclear spin coupling constants with a radical (electronic unpaired spin) ? (with Gaussian, NMR=3DSpinSpin) Thank you for your help. --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Sat Jun 20 17:08:00 2009 From: "Bahareh honarparvar bahareh_honarparvar a yahoo.com" To: CCL Subject: CCL:G: =?utf-8?B?IM6xMSBzdWJ1bml0IG9mIEdBQkFBIHJlY2VwdG9yIHdpdGggR2F1c3NpYW4=?= Message-Id: <-39580-090620153127-17394-/5skQuMtzqQRhsvn7AvhcQ(a)server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="0-1253713399-1245526276=:82333" Date: Sat, 20 Jun 2009 12:31:16 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar^^yahoo.com] --0-1253713399-1245526276=:82333 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable =0A=0ADear All.=C2=A0 , =0A =0A=0A=0A .I want to investigate the interaction=0Aof benzodiazepine=0Awith= GABAA=0Areceptor.=0A=0AI=0Aunderstood that the =CE=B11 subunit of GABAA re= ceptor contributes to make=0Aup the binding to benzodiazepine to modulate G= ABAA activity.=0A=0ANow=0AI have pdb of GABAA receptor and I am enthusiasti= c about the possibility of extracting=0Ajust the =CE=B11=0Asubunit from pdb= of=C2=A0=0A=C2=A0GABAA receptor and study the =CE=B11 subunit section sepa= rately with=0AGaussian program. I would be much obliged if you kindly help = me in=0Athis case .how is it possible?any comment is appriciatable.Bahareh =0A=0A=0A=0A=0A --0-1253713399-1245526276=:82333 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A=0A

Dear All.=   ,
=0A
=0A

=0A=0A

= .I want to investigate the interaction=0Aof benzodi= azepine=0Awith GABAA=0Areceptor.<= /p>=0A=0A

I=0Aunderstood that the =CE=B11 subunit of GABAA receptor contrib= utes to make=0Aup the binding to benzodiazepine to modulate GABAA activity.

=0A=0A

Now=0AI have pdb of GABAA recepto= r and I am enthusiastic about the possibility of ex= tracting=0Ajust the =CE=B11=0Asubunit from pdb of =0A GABAA receptor and = study the =CE=B11 subunit section separa= tely with=0AGaussian program. I would be much oblig= ed if you kindly help me in=0Athis case .how is it possible?

any comment is appriciatable.

Bahareh

=0A=0A

=0A=0A --0-1253713399-1245526276=:82333-- From owner-chemistry@ccl.net Sat Jun 20 19:07:01 2009 From: "nadia boutabba eleuch n_boutabba _ yahoo.fr" To: CCL Subject: CCL:G: help on restart optimization Message-Id: <-39581-090620190432-2422-TmeIFw7c5XdPzSXVZhdWPw- -server.ccl.net> X-Original-From: "nadia boutabba eleuch" Date: Sat, 20 Jun 2009 19:04:29 -0400 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