From owner-chemistry@ccl.net Tue Jul 21 00:28:01 2009 From: "Beatriz C Ramirez bea_ucv__yahoo.com" To: CCL Subject: CCL:G: Error performing ONIOM calculation in MM part Message-Id: <-39829-090721002600-8276-6GyPAtpdVh9KeVurGwhHbw/a\server.ccl.net> X-Original-From: "Beatriz C Ramirez" Date: Tue, 21 Jul 2009 00:25:56 -0400 Sent to CCL by: "Beatriz C Ramirez" [bea_ucv _ yahoo.com] Im trying to perform an ONIOM calculation pm3:amber with a .pdb structure from an enzymatic intermediate. I added the amber atom types and the charges for the MM atoms but I still got this error. Angle bend undefined between atoms 71 74 75 Angle bend undefined between atoms 72 71 74 Angle bend undefined between atoms 73 74 75 Angle bend undefined between atoms 74 75 76 Angle bend undefined between atoms 141 8 144 MM function not complete Error termination via Lnk1e in C:\G03W\l101.exe at Mon Jul 20 19:27:33 2009. Job cpu time: 0 days 0 hours 0 minutes 5.0 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1 Apparently I have to specify some angles, but I dont know how to do it, or how to edit this AMBER parameters, such as impropers or dihedrals for this molecule. I'll appreacite your help because im running out of ideas Beatriz Ramirez From owner-chemistry@ccl.net Tue Jul 21 02:05:00 2009 From: "Bahareh honarparvar bahareh_honarparvar!A!yahoo.com" To: CCL Subject: CCL:G: PCM IO file error on G03 Message-Id: <-39830-090721020329-25610-XvwQ2mQAD8Mtcp9Dhe9uww(!)server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="0-922352345-1248156196=:21440" Date: Mon, 20 Jul 2009 23:03:16 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar^^yahoo.com] --0-922352345-1248156196=:21440 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sarah MOHAMED , you can use volume keyword before performing solvent calculation to obtatai= n the redious of cavity in terms of Angestrom. Good luck Honarparvar --- On Tue, 7/21/09, Sarah MOHAMED mohamedsarah78__yahoo.fr wrote: > From: Sarah MOHAMED mohamedsarah78__yahoo.fr Subject: CCL: PCM IO file error on G03 To: "Honarparvar, Honarparvar " Date: Tuesday, July 21, 2009, 4:08 AM Sent to CCL by: "Sarah=A0 MOHAMED" [mohamedsarah78 ~ yahoo.fr] Dear subscribers, Thank you very much to all persons who help me to resolve my memory's probl= em. Today, I am facing with an other problem of PCM input/output file.=20 Please which commandes are used in the end of the input file to create a ca= vity: (Rmin=3D0.5 and OFac=3D0.8?), or (RADII=3DPAULING, ALPHA=3D1.2,=20 TABS =3D298.158, TSNUM=3D70 and TSARE=3D0.4), or (RADII=3DPAULING)?? The route section of the input file is given below: %chk=3DPCM.chk %mem=3D500MB %nproc=3D1 Will use up to=A0 =A0 1 processors via shared memory. Default route:=A0 MaxDisk=3D2000MB ---------------------------------------------------------------------- # b3lyp/6-31g(d) opt=3D(maxcycle=3D500) scf=3D(qc,tight) scrf=3D(iefpcm,sol= ven t=3Dwater,read) geom=3Dconnectivity Polarizable Continuum Model (PCM) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D Model=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 : PCM. Atomic radii=A0 =A0 =A0 =A0=A0=A0: UA0 (Simple United Atom Topological Mode= l). Polarization charges : Total charges. Charge compensation=A0 : None. Solution method=A0 =A0 =A0 : Matrix inversion. Cavity=A0 =A0 =A0 =A0 =A0 =A0 =A0=A0=A0: GePol (RMin=3D0.500 OFac=3D0.800). =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Default sphere list used, N= SphG=3D=A0=A0=A030. =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Tesserae with average area = of 0.200 Ang**2. 1st derivatives=A0 =A0 =A0 : Analytical V*U(x)*V algorithm (CHGder, D1EAlg= =3D0). =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Cavity 1st derivative terms= included. Solvent=A0 =A0 =A0 =A0 =A0 =A0 =A0 : Water, Eps=3D=A0 78.390000. And the end of the output file is : Error termination in NtrErr: NtrErr Called from FileIO. Please, can anyone kindly help me to identify the error and correct it. Thanks in advance. With best considerations. -=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 --0-922352345-1248156196=:21440 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A --0-922352345-1248156196=:21440-- From owner-chemistry@ccl.net Tue Jul 21 09:19:01 2009 From: "Oellien, F (Frank) frank.oellien .. sp.intervet.com" To: CCL Subject: CCL: 5. German Conference on Chemoinformatics - 2. Call for papers Message-Id: <-39831-090721081454-5716-MnBHrtrGKrx3ioJ2o5B+3Q::server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 21 Jul 2009 14:14:35 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien\a/sp.intervet.com] 2. CALL FOR PAPERS 5th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 8 - 10 November 2009 Dear Colleague, The CIC division of the German Chemical Society wants to inform you = about the upcoming 5. German Conference on Chemoinformatics to be held = in Goslar, Germany, November 8 - 10, 2009 (http://www.gdch.de/gcc2009 = ). We are inviting the submission of abstracts for talks and posters in = the following plenary sessions: * Chemoinformatics and Drug Discovcery * Chemical Information, Patents, and Databases=20 * Molecular Modelling=20 * Computational Material Science and Nanotechnology=20 In addition other highlights in the field of Computational Chemistry are = also welcome.=20 Invited Speakers this year are:=20 * Karl-Heinz Baringhaus, Sanofi-Aventis, Frankfurt am Main/D=20 * Knut Baumann, University Braunschweig, Braunschweig/D=20 * G=FCnter von Kiedrowski, University of Bochum, Bochum/D=20 * Ekaterina Ryjkina, Henkel, D=FCsseldorf/D=20 * Christoph Sotriffer, University of W=FCrzburg, W=FCrzburg/D=20 * Eberhard Voit, Georgia Institute of Technology, Atlanta/USA=20 * Antony Williams, ChemSpider, Wake Forest/USA Visit the conference website at www.gdch.de/gcc2009 for more information = or access directly the Call-for-Paper PDF = http://www.gdch.de/vas/tagungen/tg/einlad5358.pdf The deadline for the submission of abstracts is 30 July 2009.=20 Again we limit the number of participants to max 200. So please register = early. In addition we will introduce a limit of 60 posters. I hope to see you in Goslar again.=20 Frank Oellien=20 GDCh CIC Division Chair=20 Mit freundlichen Gr=FC=DFen / With kind regards=20 Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien-#-sp.intervet.com Phone: +49 (6130) 948 365 =09 Fax: +49 (6130) 948 517 =09 =20 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 = Gesch=E4ftsf=FChrer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From owner-chemistry@ccl.net Tue Jul 21 10:51:00 2009 From: "Harry Stern hstern16 _ mac.com" To: CCL Subject: CCL: Particle-mesh method Message-Id: <-39832-090720173925-28422-giWUCTk6E8jPt53X4PjtiQ++server.ccl.net> X-Original-From: Harry Stern Content-type: multipart/alternative; boundary="Boundary_(ID_tDu807kBkSUyRqzMV9Jibw)" Date: Mon, 20 Jul 2009 16:38:49 -0400 MIME-version: 1.0 Sent to CCL by: Harry Stern [hstern16[]mac.com] --Boundary_(ID_tDu807kBkSUyRqzMV9Jibw) Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-transfer-encoding: 7BIT hi all, free (GPL) standalone C code for the reciprocal-space part of the PPPM Ewald method is available from http://hstern.chem.rochester.edu/group/downloads.html this code uses the FFTW3 library http://www.fftw.org/ Harry - - - - Harry A. Stern Assistant Professor, Department of Chemistry University of Rochester RC Box 270216 Rochester, NY 14627-0216 (585) 275-8804 On Jun 18, 2009, at 3:06 AM, Brunsteiner, Michael micb|-|uic.edu wrote: > > Sent to CCL by: "Brunsteiner, Michael" [micb%a%uic.edu] > On Wed, June 17, 2009 23:11, Leila Ram lram5228 : usyd.edu.au wrote: >> >> Sent to CCL by: "Leila Ram" [lram5228]^[usyd.edu.au] >> Hi, >> >> for the charge calculation in lubricant system under friction, which >> method is preffered, Ewald summation or Particle-mesh method(PPPM) >> and >> why? > > There is number of methods (EW, PME, FMA, PPPM) out there > and a lot of studies have been published discussing the merits > of one or the other, but if properly implemented and > parameterized the performance in terms of accuracy/speed > is probably similar for all of them, unless you have an > exceptionally large system, in which case PPPM or FMA might > be more efficient than an Ewald based method (some people > have claimed). This being said, I assume the system you are > dealing with is anisotropic (i.e. periodic in less than 3 > dimensions), and in such a case PPPM might be the better > choice, as accounting for anisotropy with any other method > is comparatively cumbersome IIRC. > > Unfortunately there's not much out there in terms of open source > PPPM. The only open source package that I am aware of which > has PPPM implemented is Gromcas, but be warned, the Gromacs > source code is rather involved and complex. If you are not > good at C-programming understanding this code might turn out > to be more time consuming than writing something from scratch. > > implementation of any serious method to account for electrostatic > long range interactions is generally a rather non-trivial task. > If your lubricants have a low enough dielectric permittivity you > might get away with some variation of a cut-off based method > which is considerably easier to code (and parallelize). > > good luck! > mic > > >> also, Can you please give me some source code(Fortran preffered) >> for PPPM calculation? >> Your advise would be highly appriciated. >> >> Leila > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > --Boundary_(ID_tDu807kBkSUyRqzMV9Jibw) Content-type: text/html; charset=US-ASCII Content-transfer-encoding: quoted-printable
hi all, free (GPL) = standalone C code for the reciprocal-space part of the PPPM Ewald = method is available from
this code uses = the FFTW3 library    http://www.fftw.org/

Harry
- - - -
Harry A. Stern
Assistant Professor, = Department of Chemistry
University of Rochester
RC Box = 270216
(585) = 275-8804

On Jun 18, = 2009, at 3:06 AM, Brunsteiner, Michael micb|-|uic.edu wrote:


Sent to CCL by: "Brunsteiner, Michael" = [micb%a%uic.edu]
On Wed, June 17, 2009 23:11, Leila Ram lram5228 : = usyd.edu.au wrote:

Sent to CCL by: = "Leila  Ram" [lram5228]^[usyd.edu.au]
Hi,

for the charge = calculation in lubricant system under friction, = which
method is preffered, = Ewald summation or Particle-mesh method(PPPM) = and
why?

There is number of methods (EW, = PME, FMA, PPPM) out there
and a lot of studies have been published = discussing the merits
of one or the other, but if properly = implemented and
parameterized the performance in terms of = accuracy/speed
is probably similar for all of them, unless you have = an
exceptionally large system, in which case PPPM or FMA might
be = more efficient than an Ewald based method (some people
have claimed). = This being said, I assume the system you are
dealing with is = anisotropic (i.e. periodic in less than 3
dimensions), and in such a = case PPPM might be the better
choice, as accounting for anisotropy = with any other method
is comparatively cumbersome = IIRC.

Unfortunately there's not much out there in terms of open = source
PPPM. The only open source package that I am aware of = which
has PPPM implemented is Gromcas, but be warned, the = Gromacs
source code is rather involved and complex. If you are = not
good at C-programming understanding this code might turn = out
to be more time consuming than writing something from = scratch.

implementation of any serious method to account for = electrostatic
long range interactions is generally a rather = non-trivial task.
If your lubricants have a low enough dielectric = permittivity you
might get away with some variation of a cut-off = based method
which is considerably easier to code (and = parallelize).

good luck!
mic


also, Can you please give me some source code(Fortran = preffered)
for PPPM = calculation?
Your advise would = be highly appriciated.

Leila



-=3D This is = automatically added to each message by the mailing script =3D-
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
look up the X-Original-From: line in the mail = header.

E-mail to subscribers: CHEMISTRY|*|ccl.net or use:
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<= /div>


= --Boundary_(ID_tDu807kBkSUyRqzMV9Jibw)-- From owner-chemistry@ccl.net Tue Jul 21 12:29:01 2009 From: "Sahan Thanthiriwatte sahanchem(a)gmail.com" To: CCL Subject: CCL:G: Package for CCSD(T) Message-Id: <-39833-090721122754-13362-r0WtUc0cu3KQJ0sCan23UQ..server.ccl.net> X-Original-From: Sahan Thanthiriwatte Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 21 Jul 2009 11:28:42 -0400 MIME-Version: 1.0 Sent to CCL by: Sahan Thanthiriwatte [sahanchem|*|gmail.com] There are several free QC programs availble for CCSD & CCSD(T). 1) ACES II & ACES III http://www.qtp.ufl.edu/ACES/index.shtml CCSD(T) energy and gradients 2) PSI3 http://www.psicode.org/ RHF/UHF/ROHF CCSD(T) energy and gradients 3) GAMESS http://www.msg.chem.iastate.edu/gamess/ CCSD(T) energy only 4) DALTON http://www.kjemi.uio.no/software/dalton/dalton.html CCSD(T) energy only Regards, -Sahan- Neha Awasthi neha.awasthi%%gmail.com wrote: > Sent to CCL by: "Neha Awasthi" [neha.awasthi-#-gmail.com] > Hello CCL community, > > I wanted to ask for advise for a reliable program for performing CCSD and CCSD(T) calculations using (aug)-cc-pVxZ (where x = D, T, Q...) basis sets. > I have tried Gaussian, G03, and it turns out to be very inefficient (save large scratch files, and slow) for small molecules upto ~5 atoms. > > Please let me know which package/program is considered reliable as well as has good performance. > > It would be ideal to have one with a free license or free to download :) > I will compile all responses and post them. > > Thank you, > Neha> > From owner-chemistry@ccl.net Tue Jul 21 13:18:01 2009 From: "steve heller steve##hellers.com" To: CCL Subject: CCL: InChI Trust launched Message-Id: <-39834-090721131057-16366-g1+awv9xGYHVSQVScouMSA[A]server.ccl.net> X-Original-From: "steve heller" Date: Tue, 21 Jul 2009 13:10:53 -0400 Sent to CCL by: "steve heller" [steve=hellers.com] Launch of the InChI Trust DISTRIBUTED BY NATURE PUBLISHING GROUP ON BEHALF OF THE INCHI TRUST 21 July 2009 Contact: Grace Baynes Corporate Public Relations, Nature Publishing Group T:+44 (0)20 7014 4063 g.baynes_-_nature.com The InChI Trust, a not-for-profit organisation to expand and develop the InChI Open Source chemical structure representation algorithm, is formally launched this week. Originally developed by the International Union of Pure and Applied Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is an alpha-numeric character string generated by an algorithm. The InChI was developed as a new, non-proprietary, international standard to represent chemical structures. The Trust aims to develop and improve on the current InChI standard, further enabling the interlinking of chemistry and chemical structures on the web. The connection with IUPAC is maintained through IUPAC's InChI Subcommittee. The InChI algorithm turns chemical structures into machine-readable strings of information. InChIs are unique to the compound they describe and can encode absolute stereochemistry Machine-readable, the InChI allows chemistry and chemical structures to be navigable and discoverable. A simple analogy is that InChI is the bar-code for chemistry and chemical structures. The InChI format and algorithm are non-proprietary and the software is open source, with ongoing development done by the community. "The goal of the InChI Trust", says Project Director Stephen Heller "is to continue to develop the InChI and InChIKey, the condensed machine-searchable version, as a tool to enable widescale linking of chemical information." The InChI Trust was formally incorporated in the UK in May 2009, and now has 6 charter members: The Royal Society of Chemistry, Nature Publishing Group, FIZ-Chemie Berlin, Symyx Technologies, Taylor & Francis and OpenEye. Further organizations and publishers are in the process of joining the InChI Trust. "Nature Publishing Group is delighted to be a charter member of the InChI Trust", says Jason Wilde, Publisher for the Physical Sciences, Nature Publishing Group. "We view the ongoing maintenance of the InChI algorithm, and the resulting adoption of InChI, as important for the development of chemistry communication. The interlinking that the InChI offers between journal content and databases ensures that chemistry is the first truly web-enabled scientific discipline." "The InChI has already gained a wide user base," says Richard Kidd, Informatics Manager at the Royal Society of Chemistry, "and the Trust will ensure continuing development and support for this key standard, helping to link together chemical resources across the internet. The RSC is proud to support the InChI Trust." Since the introduction of the InChI in 2005, there has been widespread take-up of InChI standards by public databases and journals. Today, there are more than 100 million InChIs in scientific literature and products. To date, numerous databases, journals, and chemical structure drawing programs have incorporated the InChI algorithm. These include the NIST WebBook and mass spectral databases, the NIH/NCBI PubChem database, the NIH/NCI database, the EBI chemistry database, ChemSpider, Symyx Draw and many others. The initiative serves chemists, publishers, chemical software companies, chemical structure drawing vendors, librarians, and intermediaries by creating an international standard to represent defined chemical structures. This provides a consistent, credible and compatible way for databases of chemical structures to be linked together for the benefit of users of chemical information around the world. -ENDS- For further information, please contact: Project Director, Dr. Stephen Heller at steve_-_inchi-trust.org Background notes: The InChI project was initially undertaken by IUPAC with the cooperation of National Institute for Standards and Technology (NIST). In 2009, a standard version of InChI and the InChIKey were released. Members of the InChI Trust will pay annual dues to support the continued development of InChI, and maintainance of the InChI algorithm. This income will be used exclusively for InChI algorithm development, maintenance, outreach, and educational activities associated with the project Details of the up-take by many chemical database providers, software developers, and journal publishers are available at www.iupac.org/inchi/adopters.html From owner-chemistry@ccl.net Tue Jul 21 15:19:01 2009 From: "John McKelvey jmmckel[A]gmail.com" To: CCL Subject: CCL:G: Package for CCSD(T) Message-Id: <-39835-090721151542-30716-nrUZlgP0Ja1ajWeUVJqFVA_+_server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001485f94ea2ce98fb046f3c1304 Date: Tue, 21 Jul 2009 15:15:27 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel+*+gmail.com] --001485f94ea2ce98fb046f3c1304 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit ORCA should be added to the free program list. John McKelvey On Tue, Jul 21, 2009 at 11:28 AM, Sahan Thanthiriwatte sahanchem(a)gmail.com wrote: > > Sent to CCL by: Sahan Thanthiriwatte [sahanchem|*|gmail.com] > There are several free QC programs availble for CCSD & CCSD(T). > > 1) ACES II & ACES III > http://www.qtp.ufl.edu/ACES/index.shtml > CCSD(T) energy and gradients > > > 2) PSI3 http://www.psicode.org/ > RHF/UHF/ROHF CCSD(T) energy and gradients > > 3) GAMESS http://www.msg.chem.iastate.edu/gamess/ > CCSD(T) energy only > > 4) DALTON http://www.kjemi.uio.no/software/dalton/dalton.html > CCSD(T) energy only > > Regards, > -Sahan- > > > Neha Awasthi neha.awasthi%%gmail.com wrote: > >> Sent to CCL by: "Neha Awasthi" [neha.awasthi-#-gmail.com] >> Hello CCL community, >> >> I wanted to ask for advise for a reliable program for performing CCSD and >> CCSD(T) calculations using (aug)-cc-pVxZ (where x = D, T, Q...) basis sets. >> I have tried Gaussian, G03, and it turns out to be very inefficient (save >> large scratch files, and slow) for small molecules upto ~5 atoms. >> >> Please let me know which package/program is considered reliable as well as >> has good performance. >> It would be ideal to have one with a free license or free to download :) >> I will compile all responses and post them. >> >> Thank you, >> Nehahttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --001485f94ea2ce98fb046f3c1304 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable ORCA should be added to the free program list.

John McKelvey

=
On Tue, Jul 21, 2009 at 11:28 AM, Sahan Thanthir= iwatte sahanchem(a)gmail.com <owner-chemistry**ccl.net= > wrote:

Sent to CCL by: Sahan Thanthiriwatte [sahanchem|*|gmail.com]
There are several free QC programs availble for CCSD & CCSD(T).

1) ACES II & ACES III
=A0 = http://www.qtp.ufl.edu/ACES/index.shtml
=A0 CCSD(T) energy and gradients


2) PSI3 http://www.ps= icode.org/
=A0 RHF/UHF/ROHF CCSD(T) energy and gradients

3) GAMESS http://www.msg.chem.iastate.edu/gamess/
=A0 CCSD(T) energy only

4) DALTON http://www.kjemi.uio.no/software/dalton/dalton.html =A0 CCSD(T) energy only

Regards,
-Sahan-


Neha Awasthi neha.awasthi%%g= mail.com wrote:
Sent to CCL by: "Neha =A0Awasthi" [neha.awasthi-#-gmail.com]
Hello CCL community,

I wanted to ask for advise for a reliable program for performing CCSD and C= CSD(T) calculations using (aug)-cc-pVxZ (where x =3D D, T, Q...) basis sets= .
I have tried Gaussian, G03, and it turns out to be very inefficient (save l= arge scratch files, and slow) for small molecules upto ~5 atoms.

Please let me know which package/program is considered reliable as well as = has good performance.
It would be ideal to have one with a free license or free to download :) I will compile all responses and post them.

Thank you,
Neha>



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY**ccl.net or use:
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--001485f94ea2ce98fb046f3c1304--
Dear Sarah MOHAMED ,
you can use volume keyword before performing solvent calculati= on to obtatain the redious of cavity in terms of Angestrom.
Good luck
Honarparvar

--- On Tue, 7/21/09, Sarah MOHA= MED mohamedsarah78__yahoo.fr <owner-chemistry*_*ccl.net> wro= te:

From: Sarah MOHAMED mohamedsarah78__yahoo.fr <= owner-chemistry*_*ccl.net>
Subject: CCL: PCM IO file error on G03
To= : "Honarparvar, Honarparvar " <bahareh_honarparvar*_*yahoo.com>=
Date: Tuesday, July 21, 2009, 4:08 AM


Sent to CCL by: "Sarah  MOHAMED" [mohamedsa= rah78 ~ yahoo.fr]
Dear subscribers,

Thank you very much to all pe= rsons who help me to resolve my memory's problem.

Today, I am facing= with an other problem of PCM input/output file.
Please which commandes= are used in the end of the input file to create a cavity: (Rmin=3D0.5 and = OFac=3D0.8?), or (RADII=3DPAULING, ALPHA=3D1.2,
TABS =3D298.158, TSNUM= =3D70 and TSARE=3D0.4), or (RADII=3DPAULING)??

The route section of = the input file is given below:

%chk=3DPCM.chk
%mem=3D500MB
%np= roc=3D1
Will use up to    1 processors via shared memory.
D= efault route:  MaxDisk=3D2000MB
-----------------------------------= -----------------------------------
# b3lyp/6-31g(d) opt=3D(maxcycle=3D5= 00) scf=3D(qc,tight) scrf=3D(iefpcm,solven
t=3Dwater,read) geom=3Dconnec= tivity

Polarizable Continuum Model (PCM)
=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
Model                : PCM.
Atomic radii  &nb= sp;      : UA0 (Simple United Atom Topological Model).<= BR>Polarization charges : Total charges.
Charge compensation  : Non= e.
Solution method      : Matrix inversion.
Cavity&nbs= p;              : GePol (RMin=3D0.5= 00 OFac=3D0.800).
               = ;         Default sphere list used, NSphG=3D  = ; 30.
                 = ;       Tesserae with average area of 0.200 Ang**2.
1st d= erivatives      : Analytical V*U(x)*V algorithm (CHGder, D1E= Alg=3D0).
                 =       Cavity 1st derivative terms included.
Solvent = ;             : Water, Eps=3D  78.390000.

And the end of the output file is :

Error termina= tion in NtrErr:
NtrErr Called from FileIO.


Please, can anyone= kindly help me to identify the error and correct it.

Thanks in adva= nce.
With best considerations.



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