From owner-chemistry@ccl.net Fri Jan 8 02:47:01 2010 From: "Frank Jensen frj ~~ chem.au.dk" To: CCL Subject: CCL:G: SCF converge problem for ROHF calculation in G03 /09 Message-Id: <-41011-100107051836-17509-wYvFjSzW+By7szwHaIgRWg*o*server.ccl.net> X-Original-From: Frank Jensen Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Thu, 07 Jan 2010 10:41:58 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj^_^chem.au.dk] ROHF wave functions are notorious hard to converge, much harder than =20 the corresponding UHF, Let me point out that ROHF is a special case of MCSCF (just one =20 configuration), and many programs have significantly better MCSCF =20 convergence options than for ROHF wave functions, thus you may be able =20 to run it as an MCSCF if you are willing to pay a penalty in terms of =20 computer time. Frank Citat af "Mariusz Radon mariusz.radon|*|gmail.com" = : > > Sent to CCL by: Mariusz Radon [mariusz.radon::gmail.com] > Hello, > > Indeed, (lack of) convergence in ROHF is a problem. I would advice =20 > you to try: > > =C2=A0- different (smaller) basis set - than use converged solution as > guess for the larger basis - as was already suggested; > =C2=A0- play a little bit with level shift (vshift); > =C2=A0- if possible, try also a different software, in particular > Schrodinger's Jaguar, esp. if your system is a transition metal > complex. > > Are your calculations true ROHF or rather RO-DFT? If DFT, you may try > with a different functional. I have heard that it might be easier to > converge RO-DFT with hybrid than with non-hybrid functional (but I > don't know how much it can be helpful in practice). You may also try > the 100% of the exact exchange i.e. true ROHF calculations. If these > calculations converge, you will be able to provide a better guess to > your favorite functional. > > With best regards, > Mariusz Radon > > 2010/1/6 John McKelvey jmmckel%x%gmail.com : >> >> Sent to CCL by: John McKelvey [jmmckel**gmail.com] >> It is not stated what basis was used. =C2=A0On the assumption that as bas= is >> sets get larger convergence difficulties may increase, there is always >> the possibility that starting with smaller basis sets where >> convergence occurs and then slowly increase the size of the basis set >> while using the "guess=3Dread" option, which will pick up the previous >> SCF vectors as a starting guess. >> >> >> John McKelvey >> >> 2010/1/5 xunlei ding dingxunlei###gmail.com : >>> >>> Sent to CCL by: xunlei ding [dingxunlei|a|gmail.com] >>> Dear All, >>> >>> We know that the SCF converge problem for RHF or UHF calculations can >>> be solved by "qc" and many other ways. >>> >>> But the keywords "qc" and "fermi" can not be used in G03/09 for >>> restrict open shell calculations (such as ROHF). >>> >>> In G09, it is said in the manual that "For difficult-to-converge ROHF >>> wavefunctions, where QC cannot be used, add Use=3DL506 to the route >>> section." But it seems not work in my test. >>> >>> Then, how to solve the SCF converge problem for ROHF calculation? >>> >>> Thanks you for your consideration! >>> >>> -- >>> ------------------------------------------------------ >>> Xun-Lei Ding (=E4=B8=81=E8=BF=85=E9=9B=B7) >>> Associate Research Professor of Physical Chemistry, Ph.D >>> State Key Lab for Struct. Chem. of Unstable and Stable Species >>> Institute of Chemistry, Chinese Academy of Sciences >>> Zhongguancun North First Street 2=EF=BC=8C >>> Beijing 100190, P. R. China >>> Phone 86-10-62568330 >>> Fax =C2=A0 86-10-62559373 >>> >>> >>> >>> - This is automatically added to each message by the mailing script -> >>> >>> >> >> >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel.:.gmail.com >> >> >> >> - This is automatically added to each message by the mailing script =20 >> -> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> = =C2=A0 =C2=A0 =20 >> =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =20 >> =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml> =C2=A0 =C2=A0 =20 >> =C2=A0http://www.ccl.net/spammers.txt> >> >> > > > > -- > Mariusz Radon, PhD student > Department of Theoretical Chemistry > Jagiellonian University > http://www.chemia.uj.edu.pl/~mradon > mradon /at/ chemia.uj.edu.pl > (PGP public key available on the website) > > > > -- > Mariusz Radon, PhD student > Department of Theoretical Chemistry > Jagiellonian University > http://www.chemia.uj.edu.pl/~mradon > mradon /at/ chemia.uj.edu.pl > (PGP public key available on the website) > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > http://www.chem.au.dk/~frj From owner-chemistry@ccl.net Fri Jan 8 06:44:00 2010 From: "Gerard Pujadas gerard.pujadas(a)gmail.com" To: CCL Subject: CCL: Criteria for selecting if ligand activities and structures are enough diverse for building a 3D-QSAR model Message-Id: <-41012-100108064133-28986-cNmqH1rn+6RjpxWStremJQ..server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=001636498c5da228d7047ca5aab8 Date: Fri, 8 Jan 2010 12:41:21 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas-,-gmail.com] --001636498c5da228d7047ca5aab8 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL subscribers, I wonder if there is any bibliographic reference (review, book chapter, etc.) where I can find which are the minimum requirements of ligand diversity in activity and structure for building predictive 3D-QSAR models. In other words, before starting to build a 3D-QSAR model (for instance, with Catalyst or Phase) for a set of related molecules (developed during the same SAR study), I would like to know which criteria I have to use to know if I have enough diversity: *(a)* in ligand activities *(b)* in ligand structures to derive predictive 3D-QSAR models. Any help would be highly appreciated With many thanks in advances for your help Yours sincerely Gerard -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 Nutrigenomics Research Group Biochemistry and Biotechnology Department Universitat Rovira i Virgili Tarragona, Catalonia --001636498c5da228d7047ca5aab8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL subscribers,

I wonder if there is any bibliographic referen= ce (review, book chapter, etc.) where I can find which are the minimum requ= irements of ligand diversity in activity and structure for building predict= ive 3D-QSAR models. In other words, before starting to build a 3D-QSAR mode= l (for instance, with Catalyst or Phase) for a set of related molecules (de= veloped during the same SAR study), I would like to know which criteria I h= ave to use to know if I have enough diversity:

(a) in ligand activities
(b) in ligand structures

to derive predictive 3D-QSAR mod= els.

Any help would be highly appreciated

With many thanks in= advances for your help

Yours sincerely

Gerard

--
Gerard Pujada= s
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomic= s Research Group
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia
--001636498c5da228d7047ca5aab8-- From owner-chemistry@ccl.net Fri Jan 8 09:26:01 2010 From: "richard wentworth richardanonanon|*|googlemail.com" To: CCL Subject: CCL:G: partial cartesian freeze in guassian Message-Id: <-41013-100108085920-2848-D4wf5evuzSHrKN9jYUzeHQ===server.ccl.net> X-Original-From: "richard wentworth" Date: Fri, 8 Jan 2010 08:59:16 -0500 Sent to CCL by: "richard wentworth" [richardanonanon^^googlemail.com] Anyone know how to freeze an atom in Gaussian so that it can move along just one or two cartesian axes? I rarely use this program, but I know partial freezing of cartesians is certainly possible in other programs e.g. gamess. Thanks Richard From owner-chemistry@ccl.net Fri Jan 8 14:22:01 2010 From: "Jiabo Li jiaboli(_)yahoo.com" To: CCL Subject: CCL: Criteria for selecting if ligand activities and structures are enough diverse for building a 3D-QSAR model Message-Id: <-41014-100108140455-3172-Kgag8lIxvL3+EqNaX/G/SA^-^server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="0-681553093-1262973883=:26525" Date: Fri, 8 Jan 2010 10:04:43 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli%%yahoo.com] --0-681553093-1262973883=:26525 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Gerhard, =A0 To build a predictive 3D-QSAR model, it is recommended that=A0your training= data set has activity range of more than 3 orders of magnitude. If you do = have such a=A0 set of ligands, it should have enough structure diversity wh= ich allows you to build a good model. See more details in the documentation= s of Catalyst or Discovery Studio.=20 =A0 Jiabo Li --- On Fri, 1/8/10, Gerard Pujadas gerard.pujadas(a)gmail.com wrote: > From: Gerard Pujadas gerard.pujadas(a)gmail.com Subject: CCL: Criteria for selecting if ligand activities and structures ar= e enough diverse for building a 3D-QSAR model To: "Li, Jiabo " Date: Friday, January 8, 2010, 3:41 AM Dear CCL subscribers, I wonder if there is any bibliographic reference (review, book chapter, etc= .) where I can find which are the minimum requirements of ligand diversity = in activity and structure for building predictive 3D-QSAR models. In other = words, before starting to build a 3D-QSAR model (for instance, with Catalys= t or Phase) for a set of related molecules (developed during the same SAR s= tudy), I would like to know which criteria I have to use to know if I have = enough diversity: (a) in ligand activities (b) in ligand structures to derive predictive 3D-QSAR models. Any help would be highly appreciated With many thanks in advances for your help Yours sincerely Gerard --=20 Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22 Nutrigenomics Research Group Biochemistry and Biotechnology Department Universitat Rovira i Virgili Tarragona, Catalonia --0-681553093-1262973883=:26525 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Gerhard,
 
To build a predictive 3D-QSAR model, it is recommended that your = training data set has activity range of more than 3 orders of magnitude. If= you do have such a  set of ligands, it should have enough structure d= iversity which allows you to build a good model. See more details in the do= cumentations of Catalyst or Discovery Studio.
 
Jiabo Li

--- On Fri, 1/8/10, Gerard Pujadas gerard.pujadas(a)gmail.com <= I><owner-chemistry##ccl.net> wrote:

From: Gerard Pujadas gerard.pujadas(a)gmail.com &= lt;owner-chemistry##ccl.net>
Subject: CCL: Criteria for selecting if l= igand activities and structures are enough diverse for building a 3D-QSAR m= odel
To: "Li, Jiabo " <jiaboli##yahoo.com>
Date: Friday,= January 8, 2010, 3:41 AM

Dear CCL subscribers,

I wonder if there is a= ny bibliographic reference (review, book chapter, etc.) where I can find wh= ich are the minimum requirements of ligand diversity in activity and struct= ure for building predictive 3D-QSAR models. In other words, before starting= to build a 3D-QSAR model (for instance, with Catalyst or Phase) for a set = of related molecules (developed during the same SAR study), I would like to= know which criteria I have to use to know if I have enough diversity:
<= BR>
(a) in ligand activities
(b)<= /B> in ligand structures

to derive predictive 3D-QSAR models.<= BR>
Any help would be highly appreciated

With many thanks in adva= nces for your help

Yours sincerely

Gerard

= --
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitx= a.jsp?id=3D22
Nutrigenomics Research Group
Biochemistry and Biote= chnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia=
--0-681553093-1262973883=:26525-- From owner-chemistry@ccl.net Fri Jan 8 22:32:00 2010 From: "rocky walden rocky.walden19:-:gmail.com" To: CCL Subject: CCL: Books or Links where i can concepts of Homology modeling and Threading Message-Id: <-41015-100108121149-27922-vS6wvg2lmmd8TdzBoFhOgw_-_server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=001636c5971bd4c202047caa47b7 Date: Fri, 8 Jan 2010 22:41:38 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19 : gmail.com] --001636c5971bd4c202047caa47b7 Content-Type: text/plain; charset=ISO-8859-1 Dear People, I am interested in learning Homology modeling techniques, how to predict secondary structure,loop prediction,energy minimizations of proteins, Blast search techniques,HHMM models etc., I request all users please you can suggest me some really good books if posible form beginners to advanced. Your help is invaluable. Thanks Rocky --001636c5971bd4c202047caa47b7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear People,
=A0 I am interested in learning Homology modeling technique= s, how to predict secondary structure,loop prediction,energy minimizations = of proteins, Blast search techniques,HHMM models etc.,
I request all use= rs please you can suggest me some really good books if posible form beginne= rs to advanced.

Your help is invaluable.

Thanks
Rocky
--001636c5971bd4c202047caa47b7--