<= /div>

If you want to optimize the position of H-a= toms only, keeping other atoms intact then one way is to do partial optimiz= ation. you can use

# popt b3ly= p/sto-3g=A0

as your route section. You need to put a -1 after the atom symbol, fo= r the atoms you want to keep frozen and 0 for the atoms which are needed to= optimize. You can search the gaussian manual for details about "popt&= quot; option.

Hope this w= ill help.

Good luck,

Mehboob

On Tue, Apr 24, 2012 at 11:33 AM, Manuel Fer= nandes 0occam]^[gmail.com <owner-ch= emistry++ccl.net> wrote:

Hi everyone,

Silly question. I am cur= rently trying to use G09 to=20 optimize the H positions on a structure of interest without success. I=20 have the following in the input file:

******************************= ********************************
%chk=3Ddi3.chk
%nproc=3D4
# B3LYP/STO-3G Opt=3DReadOpt

Di3 Res= traints Test Calc

0 1
S=A0=A0=A0=A0=A0=A0 4.539427=A0=A0 14.26538= 2=A0=A0=A0 4.065973
S=A0=A0=A0=A0=A0=A0 7.312779=A0=A0 16.132727=A0=A0= =A0 2.561653
.
.
H=A0=A0=A0=A0=A0=A0 5.359781=A0=A0 20.854661=A0= =A0=A0 8.778371
H=A0=A0=A0=A0=A0=A0 4.984391=A0=A0 21.577421=A0=A0=A0 7.214152

atoms= =3DH notatoms=3DC N O S
************************************************= **************

With this I get the following error:

*********= *****************************************************
=A0---------------------------
=A0# B3LYP/STO-3G* Opt=3DReadOpt
=A0--= -------------------------
=A0QPErr --- A syntax error was detected in th= e input line.
=A0# B3LYP/STO-3G* Opt=3DReadOpt
=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 '=
=A0Last state=3D"OPT1"
=A0TCursr=3D45589 LCursr=3D=A0=A0 20=A0Error termination via Lnk1e in /home/gaussian//g09/l1.exe at Tue Apr 24= 09:33:
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 0.1 second= s.
=A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0=A0 5 Int=3D=A0=A0=A0= =A0=A0 0 D2E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 1 Scr=3D
**************************************************************

G09 seems to indicate that the issue is with ReadOpt but I am using the=20 option as advertised in the G09 manual or at least I think so. I've als= o tried ReadFreeze and ReadOptimize. [http://www.gaussian.com/g_tech/g_ur/k= _opt.htm]

Any ideas?

Thanking you in advance,

Manuel Fernandes
<= br>

--f46d042c6b9778d20504be6eea9b-- From owner-chemistry@ccl.net Tue Apr 24 15:39:00 2012 From: "James Prudhomme jprudhomme(0)healthtech.com" To: CCL Subject: CCL: Structure-Based Drug Design: Discount Deadline Week to Register Message-Id: <-46779-120424135117-12314-XdFOh4NsMK6iF+NswXXwKQ###server.ccl.net> X-Original-From: "James Prudhomme" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0111_01CD2221.56980180" Date: Tue, 24 Apr 2012 13:51:13 -0400 MIME-Version: 1.0 Sent to CCL by: "James Prudhomme" [jprudhomme(!)healthtech.com] This is a multipart message in MIME format. ------=_NextPart_000_0111_01CD2221.56980180 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit *** Please distribute this message to your colleagues. Thank you. *** Advanced Registration Discount Ends Friday, April 27 CHI and Bio-IT World Present the Twelfth Annual Structure-Based Drug Design: Predicting Biological and Kinetic Profiles from Structure June 6-8, 2012 Royal Sonesta Hotel Boston, Cambridge, MA http://www.healthtech.com/sbd About the event: Structure-based drug design took nearly two decades of multiple, parallel technological improvements to arrive at its current mainstream position in medicinal chemistry. Developments in computer graphics, high-power radiation sources, computational processing power, refinement protocols, virtual screening and crystallography were all necessary to create the environment for rapid, iterative structure-based drug discovery. Given the crisis facing the pharmaceutical industry in the translation of early stage drug discovery results, a different set of tools, concerned with algorithms and methods for developing best in class drugs that engage biological targets with kinetically optimized potency and selectivity will need to be refined. In this conference, we bring to focus recent advancements in this field from an experienced faculty. Keynote Address: Binding Kinetics in Drug Discovery David Swinney, Ph.D., CEO, Institute for Rare and Neglected Diseases Drug Discovery (iRND3) Themed Sessions: - Structure to Function - Free Energy Calculation and Molecular Dynamics Simulation - GPCR - Fragment-Based Design - Druggability and Kinetics-Based Drug Design - Trends and Advances Download a PDF brochure at http://www.healthtech.com/Conferences_Overview.aspx?ekfrm=111573&libID=11152 8 Advance registration discounts end on April 27. Register at https://chidb.com/register/2012/sbd/reg.asp or call 781-972-5400. To inquire about sponsoring and/or exhibiting, contact Jon Stroup at 781-972-5483, jstroup+*+healthtech.com Please contact me with any questions. James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 jprudhomme+*+healthtech.com ------=_NextPart_000_0111_01CD2221.56980180 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

*** Please distribute this message to your colleagues. Thank you. = ***

Advanced Registration Discount Ends Friday, April 27

CHI and Bio-IT World Present the Twelfth Annual
Structure-Based Drug Design: Predicting Biological and Kinetic Profiles = > from Structure

June 6-8, 2012
Royal Sonesta Hotel Boston, Cambridge, MA
http://www.healthtech.com/sbd

About the event:

Structure-based drug design took nearly two decades of multiple, = parallel technological improvements to arrive at its
current mainstream position in medicinal chemistry. Developments in = computer graphics, high-power radiation sources,
computational processing power, refinement protocols, virtual screening = and crystallography were all necessary to
create the environment for rapid, iterative structure-based drug = discovery. Given the crisis facing the pharmaceutical
industry in the translation of early stage drug discovery results, a = different set of tools, concerned with algorithms
and methods for developing best in class drugs that engage biological = targets with kinetically optimized potency
and selectivity will need to be refined. In this conference, we bring to = focus recent advancements in this field from
an experienced faculty.

Keynote Address:

Binding Kinetics in Drug Discovery

David Swinney, Ph.D., CEO, Institute for Rare and Neglected Diseases Drug = Discovery (iRND3)

The= med Sessions:
- Structure to Function
- Free Energy Calculation and Molecular Dynamics Simulation
- GPCR
- Fragment-Based Design
- Druggability and Kinetics-Based Drug Design
- Trends and Advances

Download a PDF brochure at http://www.healthtech.com/Conferences_Overview= .aspx?ekfrm=3D111573&libID=3D111528

Advance registration discounts end on April 27. Register at https://chidb.com/register/2012/sbd/reg.asp

or call 781-972-5400.

To inquire about sponsoring and/or exhibiting, contact Jon Stroup at 781-972-5483, jstroup+*+healthtech.com

Please contact me with any questions.

James Prudhomme
Cambridge Healthtech Institute
250 First Avenue, Suite 300
Needham, MA 02494
jprudhomme+*+healthtech.com

------=_NextPart_000_0111_01CD2221.56980180-- From owner-chemistry@ccl.net Tue Apr 24 18:58:01 2012 From: "John McKelvey jmmckel[]gmail.com" To: CCL Subject: CCL: Effect of using SSD for scratch Message-Id: <-46780-120424174225-8778-SWcFSSR49bWxH1RBl09DYQ++server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Apr 2012 17:42:18 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel#gmail.com] CCLers I am looking to buy a machine sort of specific for running Hartree-Fock and DFT codes. There is always the issue of cpu speed, but for large systems disk-io can be a significant issue, even for the usual scratch file. Has anyone done any direct or reasonable indirect evaluations around this issue? Many thanks, John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel-.-gmail.com From owner-chemistry@ccl.net Tue Apr 24 20:47:00 2012 From: "Joe Leonard jleonard42\a/gmail.com" To: CCL Subject: CCL: Effect of using SSD for scratch Message-Id: <-46781-120424194206-13877-9r1Y+vL3PgZ/UEXvHUivEw.@.server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary="Apple-Mail=_3D5E0A01-143B-457C-A7C9-F1E29D8286D9" Date: Tue, 24 Apr 2012 19:41:41 -0400 Mime-Version: 1.0 (Apple Message framework v1257) Sent to CCL by: Joe Leonard [jleonard42+*+gmail.com] --Apple-Mail=_3D5E0A01-143B-457C-A7C9-F1E29D8286D9 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 John, it's anecdotal, but my wife's Macbook Air boots far faster than a = similarly configured Macbook Pro - the difference is the 4200 rpm laptop = disk in the latter vs. the SSD in the former. We also have a PC at work = with a small/expensive SSD that is noticeably faster with Powerpoint = presentations. This said, I would think that a careful review of read/write/reread = speeds (and seek times) would demonstrate that SSD should outperform = "normal PC/laptop disks". The question is the vendor and cost for such = an SSD... I also wonder whether direct methods would outperform any = external-storage-based method given the staggering speed difference = between chip/cache and I/O pipeline. I would think this especially = important for GPU based codes? But then, I've been wrong before :-). Joe On Apr 24, 2012, at 5:42 PM, John McKelvey jmmckel[]gmail.com wrote: >=20 > Sent to CCL by: John McKelvey [jmmckel#gmail.com] > CCLers >=20 > I am looking to buy a machine sort of specific for running > Hartree-Fock and DFT codes. There is always the issue of cpu speed, > but for large systems disk-io can be a significant issue, even for the > usual scratch file. Has anyone done any direct or reasonable indirect > evaluations around this issue? >=20 > Many thanks, >=20 > John >=20 >=20 >=20 > --=20 > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel^^^gmail.com >=20 >=20 >=20 > -=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>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 -- Apple had just one customer. He passed away last year. --Apple-Mail=_3D5E0A01-143B-457C-A7C9-F1E29D8286D9 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 John, = it's anecdotal, but my wife's Macbook Air boots far faster than a = similarly configured Macbook Pro - the difference is the 4200 rpm laptop = disk in the latter vs. the SSD in the former. We also have a PC at = work with a small/expensive SSD that is noticeably faster with = Powerpoint presentations.

This said, I would think = that a careful review of read/write/reread speeds (and seek times) would = demonstrate that SSD should outperform "normal PC/laptop disks". = The question is the vendor and cost for such an SSD... I = also wonder whether direct methods would outperform any = external-storage-based method given the staggering speed difference = between chip/cache and I/O pipeline. I would think this especially = important for GPU based codes?

But then, I've = been wrong before :-).

Joe

On Apr = 24, 2012, at 5:42 PM, John McKelvey jmmckel[]gmail.com wrote:

Sent to CCL by: John McKelvey = [jmmckel#gmail.com]
CCLers

I am looking to buy a machine sort = of specific for running
Hartree-Fock and DFT codes. There is = always the issue of cpu speed,
but for large systems disk-io can be a = significant issue, even for the
usual scratch file. Has anyone = done any direct or reasonable indirect
evaluations around this = issue?

Many thanks,

John

--
John = McKelvey
10819 Middleford Pl
Ft Wayne, IN = 46818
260-489-2160
jmmckel^^^gmail.com

-=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
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RTFI: http://www.cc= l.net/chemistry/aboutccl/instructions/

<= /div>

Apple had just one customer. He = passed away last = year.

<= /span>

= --Apple-Mail=_3D5E0A01-143B-457C-A7C9-F1E29D8286D9-- From owner-chemistry@ccl.net Tue Apr 24 21:21:00 2012 From: "TJ O Donnell tjo/a\acm.org" To: CCL Subject: CCL: Effect of using SSD for scratch Message-Id: <-46782-120424204805-8360-cJ33iu7WORPfWEq0nbDjDQ{}server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Apr 2012 17:47:59 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo%x%acm.org] I've been using an SSD on my Macbook Pro and see a 5-10 fold speedup on database access for large tables that are not cached. Databases are notoriously dependent on disk i/o. I suppose this would be similar for computations that are heavily dependent on disk i/o. TJ On Tue, Apr 24, 2012 at 2:42 PM, John McKelvey jmmckel[]gmail.com wrote: > > Sent to CCL by: John McKelvey [jmmckel#gmail.com] > CCLers > > I am looking to buy a machine sort of specific for running > Hartree-Fock and DFT codes. �There is always the issue of cpu speed, > but for large systems disk-io can be a significant issue, even for the > usual scratch file. �Has anyone done any direct or reasonable indirect > evaluations around this issue? > > Many thanks, > > John > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel^^^gmail.com> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message> � � �http://www.ccl.net/chemistry/sub_unsub.shtml> � � �http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Tue Apr 24 23:57:01 2012 From: "Andrew Yeung andrew.yeung[-]chem.tamu.edu" To: CCL Subject: CCL: Effect of using SSD for scratch Message-Id: <-46783-120424225232-10395-87QPE2vrXbTND8s4SlXohA.:.server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Apr 2012 21:52:18 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung,+,chem.tamu.edu] Don't a large number of read-write cycles shorten the lifespan of SSDs? Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-04-24 7:47 PM, TJ O Donnell tjo/aacm.org wrote: > Sent to CCL by: "TJ O'Donnell" [tjo%x%acm.org] > I've been using an SSD on my Macbook Pro and see a 5-10 fold speedup > on database access for large tables that are not cached. > Databases are notoriously dependent on disk i/o. > I suppose this would be similar for computations that are heavily > dependent on disk i/o. > > TJ > > On Tue, Apr 24, 2012 at 2:42 PM, John McKelvey jmmckel[]gmail.com > wrote: >> Sent to CCL by: John McKelvey [jmmckel#gmail.com] >> CCLers >> >> I am looking to buy a machine sort of specific for running >> Hartree-Fock and DFT codes. There is always the issue of cpu speed, >> but for large systems disk-io can be a significant issue, even for the >> usual scratch file. Has anyone done any direct or reasonable indirect >> evaluations around this issue? >> >> Many thanks, >> >> John >> >> >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel^^^gmail.com> >