From owner-chemistry@ccl.net Mon Mar 30 09:05:01 2009 From: "Chris Thompson chris.thompson(-)sci.monash.edu.au" To: CCL Subject: CCL:G: Troubles with Gaussian03 PCM calculation Message-Id: <-38960-090330032358-16674-KEQd/SIj26adDR6Wr9MtQg * server.ccl.net> X-Original-From: "Chris Thompson" Date: Mon, 30 Mar 2009 03:23:54 -0400 Sent to CCL by: "Chris Thompson" [chris.thompson~!~sci.monash.edu.au] Gday, I've been optimising a reaction pathway and have stumbled over one structure which generates an error during a Gaussian03 calc. Here is the top of the input file (this input is behaving for all other minima and maxima on the pathway); %chk=/short/n29/cdt/int5a_dp2.chk %mem=300MB #b3lyp/6-31+g(d) opt SCRF=(PCM,Read,Solvent=water) The error described at the bottom of the log file looks like this; United Atom Topological Model (UA0 parameters set). UA0: Hydrogen 28 has 2 bonds. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Error termination via Lnk1e in /opt/gaussian/g03e01/g03/l301.exe at Mon Mar 30 10:34 :28 2009. Note: The hydrogen atom in question is on an alcohol with an intermolecular bond to a phosphate ion. Anyone able to explain this to me? Chris From owner-chemistry@ccl.net Mon Mar 30 09:43:01 2009 From: "Stephen.Garrison..srnl.doe.gov" To: CCL Subject: CCL:G: omp_set_num_threads error Message-Id: <-38961-090330092038-23249-MpVT5GWsqZ1k0NgZCcSLdQ]|[server.ccl.net> X-Original-From: Stephen.Garrison%x%srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 0048EA5B85257589_=" Date: Mon, 30 Mar 2009 09:16:23 -0400 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison%a%srnl.doe.gov This is a multipart message in MIME format. --=_alternative 0048EA5B85257589_= Content-Type: text/plain; charset="US-ASCII" Sorry, we are not running a binary-version under Windows. We are running a compiled-from-source version on Redhat. Any other suggestions? Stephen -- Stephen L. Garrison, Ph.D. Senior Engineer Engineering Modeling and Simulation Savannah River National Laboratory Savannah River Site 773-42A, Room 181 Aiken, SC 29808 803-725-2404 Stephen.Garrison[-]SRNL.doe.gov "David Hose Anthrax_brothers!=!hotmail.com" Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov[-]ccl.net 03/26/2009 06:37 PM Please respond to "CCL Subscribers" To "Garrison, Stephen " cc Subject CCL:G: omp_set_num_threads error Sent to CCL by: "David Hose" [Anthrax_brothers(_)hotmail.com] Stephen, I'm guessing that you are using a pre-compiled windows binary? As I understand it, the binary has been compiled to support up to 4 processors. If you want to run a calculation on all 8 cores then you'll have to get the source code and compile it yourself. Regards, Dave. -- Could someone tell me why I am getting the following error when I try to run a "nprocshared=8" Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine? omp_set_num_threads value (8) is invalid FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P ALL' reports 8 CPUs/cores. Thank you. -- Stephen L. Garrison, Ph.D. Senior Engineer Engineering Modeling and Simulation Savannah River National Laboratory Savannah River Site 773-42A, Room 181 Aiken, SC 29808 803-725-2404 Stephen.Garrison],[SRNL.doe.govhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 0048EA5B85257589_= Content-Type: text/html; charset="US-ASCII"
Sorry, we are not running a binary-version under Windows. We are running a compiled-from-source version on Redhat. Any other suggestions?

Stephen

--
Stephen L. Garrison, Ph.D.
Senior Engineer
Engineering Modeling and Simulation
Savannah River National Laboratory
Savannah River Site
773-42A, Room 181
Aiken, SC 29808
803-725-2404
Stephen.Garrison[-]SRNL.doe.gov


"David Hose Anthrax_brothers!=!hotmail.com" <owner-chemistry[-]ccl.net>
Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov[-]ccl.net

03/26/2009 06:37 PM
Please respond to
"CCL Subscribers" <chemistry[-]ccl.net>
To
"Garrison, Stephen " <stephen.garrison[-]srnl.doe.gov>
cc
Subject
CCL:G: omp_set_num_threads error






Sent to CCL by: "David  Hose" [Anthrax_brothers(_)hotmail.com]
Stephen,

I'm guessing that you are using a pre-compiled windows binary?  As I understand it, the binary has
been compiled to support up to 4 processors.  If you want to run a calculation on all 8 cores then
you'll have to get the source code and compile it yourself.

Regards,

Dave.

--


Could someone tell me why I am getting the following error when I try to run a "nprocshared=8"
Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine?

       omp_set_num_threads value (8) is invalid

FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P ALL' reports 8 CPUs/cores.

Thank you.

--
Stephen L. Garrison, Ph.D.
Senior Engineer
Engineering Modeling and Simulation
Savannah River National Laboratory
Savannah River Site
773-42A, Room 181
Aiken, SC 29808
803-725-2404
Stephen.Garrison],[SRNL.doe.gov


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--=_alternative 0048EA5B85257589_=-- From owner-chemistry@ccl.net Mon Mar 30 10:12:01 2009 From: "Hemant Srivastava hemantkrsri:-:gmail.com" To: CCL Subject: CCL:G: Troubles with Gaussian03 PCM calculation Message-Id: <-38962-090330100829-32719-nc+F6JSxqm54tP2/2VMurg..server.ccl.net> X-Original-From: Hemant Srivastava Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 30 Mar 2009 19:38:05 +0530 MIME-Version: 1.0 Sent to CCL by: Hemant Srivastava [hemantkrsri^gmail.com] Hi Chris, One option is to add in the SCRF section (Radii=UAHF) it will work but then you need to do all the calculations again with the same keyword because there will difference in between UA0 and UAHF energies. Your keyword will be like follows #b3lyp/6-31+g(d) opt SCRF=(PCM,Read,Solvent=water) The other option is to add SPHEREONH. I prefer to do the first option. Hope it will help, good luck ------------------------------------ Dr. Hemant Kumar Srivastava IICT Hyderabad -------------------------------------------------- On 3/30/09, Chris Thompson chris.thompson(-)sci.monash.edu.au wrote: > > Sent to CCL by: "Chris Thompson" [chris.thompson~!~sci.monash.edu.au] > Gday, > > I've been optimising a reaction pathway and have stumbled over one structure which generates an error during a Gaussian03 calc. Here is the top of the input file (this input is behaving for all other minima and maxima on the pathway); > > %chk=/short/n29/cdt/int5a_dp2.chk > %mem=300MB > #b3lyp/6-31+g(d) opt SCRF=(PCM,Read,Solvent=water) > > The error described at the bottom of the log file looks like this; > > United Atom Topological Model (UA0 parameters set). > UA0: Hydrogen 28 has 2 bonds. Keep it explicit at all point on the > UA0: potential energy surface to get meaningful results. > Error termination via Lnk1e in /opt/gaussian/g03e01/g03/l301.exe at Mon Mar 30 10:34 > :28 2009. > > Note: The hydrogen atom in question is on an alcohol with an intermolecular bond to a phosphate ion. > Anyone able to explain this to me? > Chris> > > From owner-chemistry@ccl.net Mon Mar 30 10:51:00 2009 From: "Saurabh Agrawal Saurabh.Agrawal##ucdconnect.ie" To: CCL Subject: CCL:G: resp charge Message-Id: <-38963-090330101851-11495-E9O266xzYOANkHnwB4ppQg[A]server.ccl.net> X-Original-From: Saurabh Agrawal Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_ThOCfgkXTCSfwz0cBPui7A)" Date: Mon, 30 Mar 2009 15:18:35 +0100 MIME-version: 1.0 Sent to CCL by: Saurabh Agrawal [Saurabh.Agrawal .. ucdconnect.ie] This is a multi-part message in MIME format. --Boundary_(ID_ThOCfgkXTCSfwz0cBPui7A) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Hello, Please read the following readme file. $AMBERHOME/src/resp/0README This could be helpful for you. Cheers, Saurabh ----- Original Message ----- =46rom: "Lukasz Cwiklik cwiklik,,gmail.com" Date: Friday, March 27, 2009 7:57 pm Subject: CCL:G: resp charge To: "Agrawal, Saurabh " >=20 > Sent to CCL by: Lukasz Cwiklik [cwiklik|gmail.com] > On Fri, Mar 27, 2009 at 12:40 PM, amine amine m-22()hotmail.fr > wrote: > > > > Sent to CCL by: "amine =A0amine" [m-22^^^hotmail.fr] > > Hi, > > I want to calculate RESP charge: > > 1-opt=3D(tight,gdiis) b3lyp/6-31g(d) nosymm geom=3Dconnectivity > > 2-b3lyp/6-31g(d) SCF=3DTight Test Pop=3DMK=20 > IOp(6/33=3D2,6/41=3D10,6/42=3D10) Opt > > =A0nosymm > > When i run : > > antechamber -i molecule.log -fi gout -o molecule.prepi -fo=20 > prepi -c resp -s2 > > i get this message error : No atom read in, the gaussian=20 > output file may not complete, exit > > But when i load molecule.log with Gaussview i can view the ESP= =20 > charge . > > 1-What's wrong? > > 2-Is it correct to reproduce =A0manually ESP-charge from=20 > gaussview to put them in molecule.prepi > > Thanks >=20 > Dear Amine, > The procedure for creating resp charges in antechamber can be trick= y, > there are also some situations that can produce strange error > messages. Your problem can be connected with too large number of > fitting points (if your molecules is not very small). Take a=20 > look at > my short tutorial about resp fitting at the Downloads section of my > web page: > http://cwiklik.wordpress.com > Look for "How to prepare residues with RESP charges fitting for > polarizable force fields in Amber8". The way how to change the numb= er > of fitting points is described there. >=20 > Best, > Lukasz >=20 > --=20 > Lukasz Cwiklik > http://cwiklik.wordpress.com >=20 >=20 >=20 > - This is automatically added to each message by the mailing=20 > script - > To recover the email address of the author of the message,=20 > please change>=20> =A0=A0=A0=A0=A0 http://www.ccl.net/cgi- > bin/ccl/send_ccl_message> =A0=A0=A0=A0=A0 http://www.ccl.net/cgi- > bin/ccl/send_ccl_message> =A0=A0=A0=A0=A0=20>=20> Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/>=20> =A0=A0=A0=A0=A0>=20>=20 >=20 Saurabh Agrawal, PhD Student, Department of Chemical and Bioprocess Engineering, UCD, Belfield, Dublin-4, Ireland --Boundary_(ID_ThOCfgkXTCSfwz0cBPui7A) Content-type: text/html; charset=us-ascii Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Hello,

Please read the following readme file.

$AMBERHOM= E/src/resp/0README

This could be helpful for you.

Cheer= s,

Saurabh


----- Original Message -----
From: "L= ukasz Cwiklik cwiklik,,gmail.com" <owner-chemistry===ccl.net>
= Date: Friday, March 27, 2009 7:57 pm
Subject: CCL:G: resp chargeTo: "Agrawal, Saurabh " <Saurabh.Agrawal===ucdconnect.ie&g= t;

>
> Sent to CCL by: Lukasz Cwiklik [cwiklik|gmail= .com]
> On Fri, Mar 27, 2009 at 12:40 PM, amine amine m-22()hot= mail.fr
> <owner-chemistry\a/ccl.net> wrote:
> >=
> > Sent to CCL by: "amine  amine" [m-22^^^hotmail.fr]=
> > Hi,
> > I want to calculate RESP charge:
&g= t; > 1-opt=3D(tight,gdiis) b3lyp/6-31g(d) nosymm geom=3Dconnectivi= ty
> > 2-b3lyp/6-31g(d) SCF=3DTight Test Pop=3DMK
> I= Op(6/33=3D2,6/41=3D10,6/42=3D10) Opt
> >  nosymm
>= ; > When i run :
> > antechamber -i molecule.log -fi gout= -o molecule.prepi -fo
> prepi -c resp -s2
> > i get = this message error : No atom read in, the gaussian
> output fi= le may not complete, exit
> > But when i load molecule.log w= ith Gaussview i can view the ESP
> charge .
> > 1-Wha= t's wrong?
> > 2-Is it correct to reproduce  manually E= SP-charge from
> gaussview to put them in molecule.prepi
&g= t; > Thanks
>
> Dear Amine,
> The procedure for= creating resp charges in antechamber can be tricky,
> there ar= e also some situations that can produce strange error
> message= s. Your problem can be connected with too large number of
> fit= ting points (if your molecules is not very small). Take a
> lo= ok at
> my short tutorial about resp fitting at the Downloads s= ection of my
> web page:
> http://cwiklik.wordpress.com> Look for "How to prepare residues with RESP charges fitting fo= r
> polarizable force fields in Amber8". The way how to change = the number
> of fitting points is described there.
>
= > Best,
> Lukasz
>
> --
> Lukasz Cwiklik=
> http://cwiklik.wordpress.com
>
>
>
&= gt; - This is automatically added to each message by the mailing
= > script -
> To recover the email address of the author of t= he message,
> please change
> the strange characters on = the top line to the === sign. You can also
> look up the X-Origin= al-From: line in the mail header.
>
> E-mail to subscrib= ers: CHEMISTRY===ccl.net or use:
>      = http://www.ccl.net/cgi-
> bin/ccl/send_ccl_message
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>  = ;     http://www.ccl.net/cgi-
> bin/ccl/sen= d_ccl_message
> Subscribe/Unsubscribe:
>   &nbs= p;  
><= br>>
>= ;
> Job: http://www.ccl.net/jobs
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>= http://server.ccl.net/chemistry/announcements/conferences/
> S= earch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml>
>=
>       http://www.ccl.net/spammers.t= xt
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> RTFI: http://www.ccl.net/chemistry/aboutccl/instr= uctions/
>
>

Saurabh Agrawal,
PhD Student,Department of Chemical and Bioprocess Engineering,
UCD, Belfield,=
Dublin-4, Ireland
--Boundary_(ID_ThOCfgkXTCSfwz0cBPui7A)-- From owner-chemistry@ccl.net Mon Mar 30 11:23:00 2009 From: "Duy Le ttduyle]^[gmail.com" To: CCL Subject: CCL:G: Troubles with Gaussian03 PCM calculation Message-Id: <-38964-090330102338-17794-vtWbBYciVCbXBg/QELHZqA,server.ccl.net> X-Original-From: Duy Le Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 30 Mar 2009 10:22:55 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle * gmail.com] The error says everything, You can not have 2 bonds at 1 H ion. Try to rearrange the initial structure. Maybe P needs to be linked with O or C of alcohol molecule On Mon, Mar 30, 2009 at 3:23 AM, Chris Thompson chris.thompson(-)sci.monash.edu.au wrote: > > Sent to CCL by: "Chris =A0Thompson" [chris.thompson~!~sci.monash.edu.au] > Gday, > > I've been optimising a reaction pathway and have stumbled over one struct= ure which generates an error during a Gaussian03 calc. Here is the top of t= he input file (this input is behaving for all other minima and maxima on th= e pathway); > > %chk=3D/short/n29/cdt/int5a_dp2.chk > %mem=3D300MB > #b3lyp/6-31+g(d) opt SCRF=3D(PCM,Read,Solvent=3Dwater) > > The error described at the bottom of the log file looks like this; > > United Atom Topological Model (UA0 =A0parameters set). > =A0UA0: Hydrogen =A0 28 has 2 bonds. Keep it explicit at all point on the > =A0UA0: potential energy surface to get meaningful results. > =A0Error termination via Lnk1e in /opt/gaussian/g03e01/g03/l301.exe at Mo= n Mar 30 10:34 > :28 2009. > > Note: The hydrogen atom in question is on an alcohol with an intermolecul= ar bond to a phosphate ion. > Anyone able to explain this to me? > Chris > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Men don't need hands to do things! From owner-chemistry@ccl.net Mon Mar 30 11:58:01 2009 From: "Herbert Fruchtl herbert.fruchtl\a/st-andrews.ac.uk" To: CCL Subject: CCL:G: omp_set_num_threads error Message-Id: <-38965-090330110328-29914-dUCGwPz5JgwMk+ZhzLiDsQ..server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 30 Mar 2009 15:33:10 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl{:}st-andrews.ac.uk] I haven't used or purchased PGI compilers for a while, but a few years ago the standard version was limited to 4 threads with OpenMP. If you don't have the documentation for your installation, it shouldn't take more than 5 minutes to write a program to test that. Herbert Stephen.Garrison..srnl.doe.gov wrote: > Sorry, we are not running a binary-version under Windows. We are running a > compiled-from-source version on Redhat. Any other suggestions? > > Stephen > > -- > Stephen L. Garrison, Ph.D. > Senior Engineer > Engineering Modeling and Simulation > Savannah River National Laboratory > Savannah River Site > 773-42A, Room 181 > Aiken, SC 29808 > 803-725-2404 > Stephen.Garrison~~SRNL.doe.gov > > > > > "David Hose Anthrax_brothers!=!hotmail.com" > Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov~~ccl.net > 03/26/2009 06:37 PM > Please respond to > "CCL Subscribers" > > > To > "Garrison, Stephen " > cc > > Subject > CCL:G: omp_set_num_threads error > > > > > > > > Sent to CCL by: "David Hose" [Anthrax_brothers(_)hotmail.com] > Stephen, > > I'm guessing that you are using a pre-compiled windows binary? As I > understand it, the binary has > been compiled to support up to 4 processors. If you want to run a > calculation on all 8 cores then > you'll have to get the source code and compile it yourself. > > Regards, > > Dave. > > -- > > > Could someone tell me why I am getting the following error when I try to > run a "nprocshared=8" > Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine? > > omp_set_num_threads value (8) is invalid > > FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P ALL' reports > 8 CPUs/cores. > > Thank you. > > -- > Stephen L. Garrison, Ph.D. > Senior Engineer > Engineering Modeling and Simulation > Savannah River National Laboratory > Savannah River Site > 773-42A, Room 181 > Aiken, SC 29808 > 803-725-2404 > Stephen.Garrison],[SRNL.doe.govhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 0048EA5B85257589_= > Content-Type: text/html; charset="US-ASCII" > > >
Sorry, we are not running a binary-version > under Windows. We are running a compiled-from-source version on Redhat. > Any other suggestions? >
>
Stephen >

> --
> Stephen L. Garrison, Ph.D.
> Senior Engineer
> Engineering Modeling and Simulation
> Savannah River National Laboratory
> Savannah River Site
> 773-42A, Room 181
> Aiken, SC 29808
> 803-725-2404
> Stephen.Garrison~~SRNL.doe.gov
> >
>
>
> > >
"David Hose Anthrax_brothers!=!hotmail.com" > <owner-chemistry~~ccl.net> >
Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov~~ccl.net >

03/26/2009 06:37 PM > > >
>
Please respond to
> "CCL Subscribers" <chemistry~~ccl.net>
>
>

> > > > >
>
To
> 		"Garrison, Stephen " > <stephen.garrison~~srnl.doe.gov> >
>
cc
> 		>
>
Subject
> 		CCL:G: omp_set_num_threads error
>
> > >
>
>
>
>
>

> Sent to CCL by: "David  Hose" [Anthrax_brothers(_)hotmail.com]
> Stephen,
>
> I'm guessing that you are using a pre-compiled windows binary?  As > I understand it, the binary has
> been compiled to support up to 4 processors.  If you want to run a > calculation on all 8 cores then
> you'll have to get the source code and compile it yourself.
>
> Regards,
>
> Dave.
>
> --
>
>
> Could someone tell me why I am getting the following error when I try to > run a "nprocshared=8"
> Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine?
>
>        omp_set_num_threads value (8) is invalid
>
> FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P > ALL' reports 8 CPUs/cores.
>
> Thank you.
>
> --
> Stephen L. Garrison, Ph.D.
> Senior Engineer
> Engineering Modeling and Simulation
> Savannah River National Laboratory
> Savannah River Site
> 773-42A, Room 181
> Aiken, SC 29808
> 803-725-2404
> Stephen.Garrison],[SRNL.doe.gov
>
>
> > >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
> >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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>
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>
> >
-- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Mon Mar 30 12:33:01 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982 * yahoo.com" To: CCL Subject: CCL:G: Troubles with Gaussian03 PCM calculation Message-Id: <-38966-090330115609-19758-i7ceaU76D5Fs4eZDtlP91Q###server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-931215444-1238425252=:18260" Date: Mon, 30 Mar 2009 08:00:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982{=}yahoo.com] --0-931215444-1238425252=:18260 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Chris This problem is generated becuase your hydrogen atom no. 28 is going to for= m 2 bonds, and this gives an error according to UA0 model, in this model, h= ydrogen atoms are treated implicity. So. you should in this case use anothe= r model treated hydrogen atoms explicity to overcome this problem, and this= can be done by using UFF (universal force field model) by specifing in you= r keyword section SCRF=3D(...,read) and at the end of your job description = write: radii =3D UFF and then balnk line. There are other models you may use, have a look on SCRF page on Gaussian (h= ttp://www.gaussian.com/g_ur/k_scrf.htm) under specifing the molecular cavit= y section. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. Mahmoud.Ibrahim-2,postgrad.manchester.ac.uk=20 =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt.=20 M.Ibrahim1982,yahoo.com=20 Mobile Phone No.: +20102554083 =20 Land Phone No.: +20226635916=20 Fax No.: +20862342601 --- On Mon, 3/30/09, Chris Thompson chris.thompson(-)sci.monash.edu.au wrote: > From: Chris Thompson chris.thompson(-)sci.monash.edu.au Subject: CCL:G: Troubles with Gaussian03 PCM calculation To: "Ibrahim, Mahmoud A. A. " Date: Monday, March 30, 2009, 8:23 AM Sent to CCL by: "Chris=A0 Thompson" [chris.thompson~!~sci.monash.edu.au] Gday, I've been optimising a reaction pathway and have stumbled over one structur= e which generates an error during a Gaussian03 calc. Here is the top of the= input file (this input is behaving for all other minima and maxima on the = pathway); %chk=3D/short/n29/cdt/int5a_dp2.chk %mem=3D300MB #b3lyp/6-31+g(d) opt SCRF=3D(PCM,Read,Solvent=3Dwater) The error described at the bottom of the log file looks like this; United Atom Topological Model (UA0=A0 parameters set). UA0: Hydrogen=A0=A0=A028 has 2 bonds. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Error termination via Lnk1e in /opt/gaussian/g03e01/g03/l301.exe at Mon Ma= r 30 10:34 :28 2009. Note: The hydrogen atom in question is on an alcohol with an intermolecular= bond to a phosphate ion. Anyone able to explain this to me? Chris -=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 --0-931215444-1238425252=:18260 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Chris
This problem is generated becua= se your hydrogen atom no. 28 is going to form 2 bonds, and this gives an er= ror according to UA0 model, in this model, hydrogen atoms are treated impli= city. So. you should in this case use another model treated hydrogen atoms = explicity to overcome this problem, and this can be done by using UFF (univ= ersal force field model) by specifing in your keyword section SCRF=3D(...,r= ead) and at the end of your job description write:
radii =3D UFF
and = then balnk line.
There are other models you may use, have a look on SCRF= page on Gaussian (http://www.gaussian.com/g_ur/k_scrf.htm) under specifing= the molecular cavity section.
Sincerely;
M. Ibrahim

Mahmoud A. A. Ibrahim

Current Address
School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.
Mahmoud.Ibrahim-2,pos= tgrad.manchester.ac.uk

Home Address =
Chemistry Department, Faculty of Science,
= Minia University,
Minia 61519,Egypt.
M.Ib= rahim1982,yahoo.com
Mobile Phone No.: +20102554083
Land Phone No.: +20226635916
= Fax No.: +20862342601


--- On Mon, 3/30/09, Ch= ris Thompson chris.thompson(-)sci.monash.edu.au <owner-chemistry,ccl.net> wrote:

From: Chris Thompson chris.thompson(-)sci.monash.edu.au <owner-c= hemistry,ccl.net>
Subject: CCL:G: Troubles with Gaussian03 PCM calcul= ation
To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982,yahoo.com&= gt;
Date: Monday, March 30, 2009, 8:23 AM


Sent to CCL by: "Chris  Thompson" [chris.thompson~!~sci.monash.e= du.au]
Gday,

I've been optimising a reaction pathway and have stu= mbled over one structure which generates an error during a Gaussian03 calc.= Here is the top of the input file (this input is behaving for all other mi= nima and maxima on the pathway);

%chk=3D/short/n29/cdt/int5a_dp2.chk=
%mem=3D300MB
#b3lyp/6-31+g(d) opt SCRF=3D(PCM,Read,Solvent=3Dwater)<= br>
The error described at the bottom of the log file looks like this;

United Atom Topological Model (UA0  parameters set).
= UA0: Hydrogen   28 has 2 bonds. Keep it explicit at all poi= nt on the
UA0: potential energy surface to get meaningful results.
= Error termination via Lnk1e in /opt/gaussian/g03e01/g03/l301.exe at Mon Mar= 30 10:34
:28 2009.

Note: The hydrogen atom in question is on an = alcohol with an intermolecular bond to a phosphate ion.
Anyone able to e= xplain this to me?
Chris



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=0A=0A --0-931215444-1238425252=:18260-- From owner-chemistry@ccl.net Mon Mar 30 13:07:01 2009 From: "noreya bestaoui noreya.bestaoui#gmail.com" To: CCL Subject: CCL:G: Calculations methods Message-Id: <-38967-090330085951-8994-eIHOxR2X4oPLGLCCW9UTNw++server.ccl.net> X-Original-From: noreya bestaoui Content-Type: multipart/alternative; boundary=001636b431b4d2b4520466553622 Date: Mon, 30 Mar 2009 14:28:04 +0200 MIME-Version: 1.0 Sent to CCL by: noreya bestaoui [noreya.bestaoui~!~gmail.com] --001636b431b4d2b4520466553622 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Please, Can anyone tell me how to use the counterpoise keyword and other options in z-matrix of water and dimer (charge=0), to calculate BSSE correction in G03 ? It will be greatly appreciated if someone could provide me with the z-matrix of the input file for this. I want to calculate using counterpoise keyword in G03. Thanks in advance. --001636b431b4d2b4520466553622 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Please,
=A0Can anyone tell me how to use the counterpoise keyword a= nd other options in
=A0z-matrix of water and dimer (charge=3D0), to calc= ulate BSSE correction in
G03 ? It will be greatly appreciated if someone= could provide me with the z-matrix of the input file for this.
=A0I want to calculate using counterpoise keyword in G03.

=A0Thanks in advance.

--001636b431b4d2b4520466553622-- From owner-chemistry@ccl.net Mon Mar 30 13:43:00 2009 From: "Rafal Korlacki rkorlacki2(-)unl.edu" To: CCL Subject: CCL:G: omp_set_num_threads error Message-Id: <-38968-090330132842-26635-0/zvI31llJ7P3B287VHDUA%server.ccl.net> X-Original-From: "Rafal Korlacki" Content-language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Mar 2009 11:34:32 -0500 MIME-Version: 1.0 Sent to CCL by: "Rafal Korlacki" [rkorlacki2[]unl.edu] There was a note to be found somewhere: "currently it is not possible to run Gaussian's released binaries on more than 4 CPUs (or cores) using OpenMP on Opteron based systems. The reason is that the rev C.02 binaries distributed by Gaussian, Inc. have been built with the WorkStation version of the PGI compilers. The Server version of these compilers moves the limitation from 4 to 16 processes." It is why everybody assumed you are using the binary distribution. But maybe you only used the same version of compilers? BTW, what will happen if you set OMP_NUM_THREADS=1 ? It should turn off the OpenMP part of the code (and is often worth doing anyway). Rafal > -----Original Message----- > From: owner-chemistry+korlacki==unlserve.unl.edu\a/ccl.net [mailto:owner- > chemistry+korlacki==unlserve.unl.edu\a/ccl.net] On Behalf Of > Stephen.Garrison..srnl.doe.gov > Sent: Monday, March 30, 2009 8:16 AM > To: Korlacki, Rafal > Subject: CCL:G: omp_set_num_threads error > > Sorry, we are not running a binary-version under Windows. We are > running a > compiled-from-source version on Redhat. Any other suggestions? > > Stephen > > -- > Stephen L. Garrison, Ph.D. > Senior Engineer > Engineering Modeling and Simulation > Savannah River National Laboratory > Savannah River Site > 773-42A, Room 181 > Aiken, SC 29808 > 803-725-2404 > Stephen.Garrison~~SRNL.doe.gov > > > > > "David Hose Anthrax_brothers!=!hotmail.com" > Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov~~ccl.net > 03/26/2009 06:37 PM > Please respond to > "CCL Subscribers" > > > To > "Garrison, Stephen " > cc > > Subject > CCL:G: omp_set_num_threads error > > > > > > > > Sent to CCL by: "David Hose" [Anthrax_brothers(_)hotmail.com] > Stephen, > > I'm guessing that you are using a pre-compiled windows binary? As I > understand it, the binary has > been compiled to support up to 4 processors. If you want to run a > calculation on all 8 cores then > you'll have to get the source code and compile it yourself. > > Regards, > > Dave. > > -- > > > Could someone tell me why I am getting the following error when I try > to > run a "nprocshared=8" > Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine? > > omp_set_num_threads value (8) is invalid > > FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P ALL' > reports > 8 CPUs/cores. > > Thank you. > > -- > Stephen L. Garrison, Ph.D. > Senior Engineer > Engineering Modeling and Simulation > Savannah River National Laboratory > Savannah River Site > 773-42A, Room 181 > Aiken, SC 29808 > 803-725-2404 > Stephen.Garrison],[SRNL.doe.govhttp://www.ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhtt > p://www.ccl.net/spammers.txt--=_alternative 0048EA5B85257589_= > Content-Type: text/html; charset="US-ASCII" > > >
Sorry, we are not running a binary- > version > under Windows. We are running a compiled-from-source version on Redhat. > Any other suggestions? >
>
Stephen >

> --
> Stephen L. Garrison, Ph.D.
> Senior Engineer
> Engineering Modeling and Simulation
> Savannah River National Laboratory
> Savannah River Site
> 773-42A, Room 181
> Aiken, SC 29808
> 803-725-2404
> Stephen.Garrison~~SRNL.doe.gov
> >
>
>
> > >
"David Hose > Anthrax_brothers!=!hotmail.com" > <owner-chemistry~~ccl.net> >
Sent by: owner- > chemistry+stephen.garrison==srnl.doe.gov~~ccl.net >

03/26/2009 06:37 PM > > >
>
Please respond to
> "CCL Subscribers" > <chemistry~~ccl.net>
>
>

> > > > >
>
To
> 		"Garrison, Stephen " > <stephen.garrison~~srnl.doe.gov> >
>
cc
> 		>
>
Subject
> 		CCL:G: omp_set_num_threads > error
>
> > >
>
>
>
>
>

> Sent to CCL by: "David  Hose" > [Anthrax_brothers(_)hotmail.com]
> Stephen,
>
> I'm guessing that you are using a pre-compiled windows binary?  As > I understand it, the binary has
> been compiled to support up to 4 processors.  If you want to run a > calculation on all 8 cores then
> you'll have to get the source code and compile it yourself.
>
> Regards,
>
> Dave.
>
> --
>
>
> Could someone tell me why I am getting the following error when I try > to > run a "nprocshared=8"
> Gaussian/G03 job on a dual-CPU quad-core (8 cores total) machine?
>
>        omp_set_num_threads value (8) is invalid >
>
> FYI: An "nprocshared=4" job runs just fine. Also, 'mpstat -P > ALL' reports 8 CPUs/cores.
>
> Thank you.
>
> --
> Stephen L. Garrison, Ph.D.
> Senior Engineer
> Engineering Modeling and Simulation
> Savannah River National Laboratory
> Savannah River Site
> 773-42A, Room 181
> Aiken, SC 29808
> 803-725-2404
> Stephen.Garrison],[SRNL.doe.gov
>
>
> > >      http://www.ccl.net/cgi- > bin/ccl/send_ccl_message
> >      http://www.ccl.net/cgi- > bin/ccl/send_ccl_message
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From owner-chemistry@ccl.net Mon Mar 30 14:20:01 2009 From: "David Eisenberg david.eisen,gmail.com" To: CCL Subject: CCL: NBO viewer evaluation Message-Id: <-38969-090330141855-895-6FSp5qT5fshJ0OD9khptIQ()server.ccl.net> X-Original-From: "David Eisenberg" Date: Mon, 30 Mar 2009 14:18:51 -0400 Sent to CCL by: "David Eisenberg" [david.eisen*|*gmail.com] Dear CCL members, Can the NBO viewer software be downloaded for evaluation, prior to purchase? Are there any demo/shareware/academic license versions of it anywhere around? I wrote to the program developers on their site, but they didn't answer. Thank you, David Eisenberg Hebrew University of Jerusalem, Israel From owner-chemistry@ccl.net Mon Mar 30 15:56:01 2009 From: "Thomas Patko tpatko^gmail.com" To: CCL Subject: CCL: NBO viewer evaluation Message-Id: <-38970-090330145700-31723-c0A+02B88kAoo0HagHVThg * server.ccl.net> X-Original-From: Thomas Patko Content-Type: multipart/alternative; boundary=000e0cd22de69b8c8e04665aa492 Date: Mon, 30 Mar 2009 11:56:41 -0700 MIME-Version: 1.0 Sent to CCL by: Thomas Patko [tpatko~!~gmail.com] --000e0cd22de69b8c8e04665aa492 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello David: If you are looking for an evaluation version of a visualization tool for NBO jobs, you could look at Chemcraft. It has a 150 day evaluation period. The windows version can look at NBO jobs from a variety of QC programs. http://www.chemcraftprog.com/ Cheers, Thomas On Mon, Mar 30, 2009 at 11:18 AM, David Eisenberg david.eisen,gmail.com < owner-chemistry:-:ccl.net> wrote: > > Sent to CCL by: "David Eisenberg" [david.eisen*|*gmail.com] > Dear CCL members, > > Can the NBO viewer software be downloaded for evaluation, prior to > purchase? > Are there any demo/shareware/academic license versions of it anywhere > around? > > I wrote to the program developers on their site, but they didn't answer. > > Thank you, > David Eisenberg > Hebrew University of Jerusalem, Israel> > > --000e0cd22de69b8c8e04665aa492 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello David:

If you are looking for an evaluation version of a visua= lization tool for NBO jobs, you could look at Chemcraft.=A0 It has a 150 da= y evaluation period.=A0 The windows version can look at NBO jobs from a var= iety of QC programs.

http://www.chemcraftprog.com/=

Cheers,

Thomas

On Mon,= Mar 30, 2009 at 11:18 AM, David Eisenberg david.eisen,gmail.com <owner-chemistry:-:ccl.net> wrote:

Sent to CCL by: "David =A0Eisenberg" [david.eisen*|*gmail.com]
Dear CCL members,

Can the NBO viewer software be downloaded for evaluation, prior to purchase= ?
Are there any demo/shareware/academic license versions of it anywhere
around?

I wrote to the program developers on their site, but they didn't answer= .

Thank you,
David Eisenberg
Hebrew University of Jerusalem, Israel



-=3D This is automatically added to each message by the mailing script =3D-=
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--000e0cd22de69b8c8e04665aa492-- From owner-chemistry@ccl.net Mon Mar 30 16:32:00 2009 From: "Peter Burger burger()chemie.uni-hamburg.de" To: CCL Subject: CCL: NBO viewer evaluation Message-Id: <-38971-090330161822-11225-GEcRoDcxk3esp/mdQRMMMQ=-=server.ccl.net> X-Original-From: Peter Burger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 30 Mar 2009 21:27:19 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Burger [burger~!~chemie.uni-hamburg.de] I would suggest to use Chemcraft as an alternative. http://www.chemcraftprog.com/ They have a trial versian afaik Cheers Peter David Eisenberg david.eisen,gmail.com schrieb: > Sent to CCL by: "David Eisenberg" [david.eisen*|*gmail.com] > Dear CCL members, > > Can the NBO viewer software be downloaded for evaluation, prior to purchase? > Are there any demo/shareware/academic license versions of it anywhere > around? > > I wrote to the program developers on their site, but they didn't answer. > > Thank you, > David Eisenberg > Hebrew University of Jerusalem, Israel> > > > -- Prof. Dr. Peter Burger Institut fuer Anorganische und Angewandte Chemie Universitaet Hamburg Martin-Luther-King-Platz 6 D-20146 Hamburg Tel.:+49 040 42838 3662 FAX 6097 email: burger=chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/ac/AKs/Burger From owner-chemistry@ccl.net Mon Mar 30 18:31:01 2009 From: "Rick Venable venabler-*-nhlbi.nih.gov" To: CCL Subject: CCL: Cartesian symmetry operations Message-Id: <-38972-090330182624-1420-CdhhrkCwzeqZgrFqLyiwUQ!^!server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Mon, 30 Mar 2009 17:54:24 -0400 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler~!~nhlbi.nih.gov] I'm looking for the Cartesian symmetry operations for the P21212 space group; for the P21 space group the coordinate tranformation is (-X,Y+1/2,-Z) but I need to know the 3 transforms for P21212, a less common space group. Pointers to online sources or the transformations would be greatly appreciated. Regards, -- Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov From owner-chemistry@ccl.net Mon Mar 30 19:05:01 2009 From: "ysubboti__ucalgary.ca" To: CCL Subject: CCL: NBO viewer evaluation Message-Id: <-38973-090330185323-12610-VkVgULrYi8DiPPf+RZ0e8A===server.ccl.net> X-Original-From: ysubboti|ucalgary.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 30 Mar 2009 16:53:03 -0600 (MDT) MIME-Version: 1.0 Sent to CCL by: ysubboti*|*ucalgary.ca Hi, David! There is number of other options. Following orbital viewers are completely freely available (well, you have to cite them, but that's it): http://www.bioinformatics.org/molekel/wiki/pmwiki.php http://www.csc.fi/english/pages/g0penMol Both are very useful. Julia Subbotina Postdoctoral Associate, Institute for Biocomplexity and Informatics, University of Calgary > Sent to CCL by: "David Eisenberg" [david.eisen*|*gmail.com] > Dear CCL members, > > Can the NBO viewer software be downloaded for evaluation, prior to > purchase? > Are there any demo/shareware/academic license versions of it anywhere > around? > > I wrote to the program developers on their site, but they didn't answer. > > Thank you, > David Eisenberg > Hebrew University of Jerusalem, Israel> > > > From owner-chemistry@ccl.net Mon Mar 30 20:20:00 2009 From: "Francisco Hernandez-Guzman fhernand\a/accelrys.com" To: CCL Subject: CCL: Cartesian symmetry operations Message-Id: <-38974-090330201820-29202-RqaXVAH7qzpJaWbBFc/Wrg * server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Mar 2009 19:15:55 -0400 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [fhernand%x%accelrys.com] Hi Rick, The transforms for P212121 (space group 19) are: (x,y,z) (-x+1/2,-y,z+1/2) (-x,y+1/2,-z+1/2) (x+1/2,-y+1/2,-z) These are found in the 'International Tables for Crystallography - Volume A= '. Cheers, Francisco Francisco Hernandez-Guzman, Ph.D. Lead Solutions Scientist, Protein Modeling, Simulations and X-ray - USA Accelrys, Inc. (http://www.accelrys.com) 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 -----Original Message----- > From: owner-chemistry+fhernandez=3D=3Daccelrys.com-#-ccl.net [mailto:owner-ch= emistry+fhernandez=3D=3Daccelrys.com-#-ccl.net] On Behalf Of Rick Venable ven= abler-*-nhlbi.nih.gov Sent: Monday, March 30, 2009 2:54 PM To: Francisco Hernandez-Guzman Subject: CCL: Cartesian symmetry operations Sent to CCL by: Rick Venable [venabler~!~nhlbi.nih.gov] I'm looking for the Cartesian symmetry operations for the P21212 space group; for the P21 space group the coordinate tranformation is (-X,Y+1/2,-Z) but I need to know the 3 transforms for P21212, a less common space group. Pointers to online sources or the transformations would be greatly appreciated. Regards, =20 --=20 Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Mar 30 21:24:00 2009 From: "Vincent Xianlong Wang xloongw*o*yahoo.com" To: CCL Subject: CCL: Cartesian symmetry operations Message-Id: <-38975-090330212225-27163-NqlLObDbIs3EQwL/8R3y5Q a server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Type: text/plain; charset=us-ascii Date: Mon, 30 Mar 2009 18:22:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw---yahoo.com] Hi Rick, Bilbao Crystallographic Server may be your best destination for online information on crystallographic space group. http://www.cryst.ehu.es/ Vincent ----- Original Message ---- > From: Rick Venable venabler-*-nhlbi.nih.gov To: "Wang, Xianlong " Sent: Tuesday, March 31, 2009 5:54:24 AM Subject: CCL: Cartesian symmetry operations Sent to CCL by: Rick Venable [venabler~!~nhlbi.nih.gov] I'm looking for the Cartesian symmetry operations for the P21212 space group; for the P21 space group the coordinate tranformation is (-X,Y+1/2,-Z) but I need to know the 3 transforms for P21212, a less common space group. Pointers to online sources or the transformations would be greatly appreciated. Regards, -- Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*govhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt