From owner-chemistry@ccl.net Fri Mar 27 05:55:01 2009 From: "amine amine m-22()hotmail.fr" To: CCL Subject: CCL:G: resp charge Message-Id: <-38948-090327054034-1786-XpARDww3LCHSxvCrIscM0g-$-server.ccl.net> X-Original-From: "amine amine" Date: Fri, 27 Mar 2009 05:40:26 -0400 Sent to CCL by: "amine amine" [m-22^^^hotmail.fr] Hi, I want to calculate RESP charge: 1-opt=(tight,gdiis) b3lyp/6-31g(d) nosymm geom=connectivity 2-b3lyp/6-31g(d) SCF=Tight Test Pop=MK IOp(6/33=2,6/41=10,6/42=10) 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 file may not complete, exit But when i load molecule.log with Gaussview i can view the ESP charge . 1-What's wrong? 2-Is it correct to reproduce manually ESP-charge from gaussview to put them in molecule.prepi Thanks From owner-chemistry@ccl.net Fri Mar 27 08:05:02 2009 From: "Saurabh Agrawal Saurabh.Agrawal+*+ucdconnect.ie" To: CCL Subject: CCL: VASP "box and lattice vector scale in POSCAR" Message-Id: <-38949-090327075846-25982-JU47sYTc63iuPXMcFSVQEw _ server.ccl.net> X-Original-From: Saurabh Agrawal Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_we8GpwMAXUlEAHDmF4Lh6g)" Date: Fri, 27 Mar 2009 11:58:33 +0000 (GMT) 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_we8GpwMAXUlEAHDmF4Lh6g) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Content-disposition: inline Dear CCL Subscribers, I am trying to simulate rutile crystal. The box size for the crystal has set as given below: O Ti 1.000000000000 16.66900000000 0.00000000000 0.000000000000 0.000000000000 10.50300000000 0.000000000000 0.000000000000 0.000000000000 10.52300000000 48 24 Cartesian 0.189999997616 1.621000051498 -3.956000089645 -0.256999999285 -1.625000000000 1.985999941826 . . . The output I get in OUTCAR shows molecule broken in four small cubes separated with gap even at zero number trajectory. It seems to me that the BOX settings are not correct but it could be some other problem too. I centered the crystal's coordinates and larger box sizes but result were same. Any help to solve this problem would be of great help for me. Regards, Saurabh Saurabh Agrawal, PhD Student, Department of Chemical and Bioprocess Engineering, UCD, Belfield, Dublin-4, Ireland --Boundary_(ID_we8GpwMAXUlEAHDmF4Lh6g) Content-type: text/html; charset=us-ascii Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Dear CCL Subscribers,

I am trying to simulate rutile crystal= . The box size for the crystal has set as given below:
O Ti <= br> 1.000000000000
16.66900000000 0.00000000= 000 0.000000000000
0.000000000000 10.503000= 00000 0.000000000000
0.000000000000 0.00000= 0000000 10.52300000000
48 24
Cartesian
= 0.189999997616 1.621000051498 -3.956000089645
= -0.256999999285 -1.625000000000 1.985999941826
. <= br> .
.
The output I get in OUTCAR shows molecule broken = in four small cubes separated with gap even at zero number trajectory= . It seems to me that the BOX settings are not correct but it could b= e some other problem too. I centered the crystal's coordinates and la= rger box sizes but result were same.

Any help to solve t= his problem would be of great help for me.

Regards,
=
Saurabh


Saurabh Agrawal,
PhD Student,
Depa= rtment of Chemical and Bioprocess Engineering,
UCD, Belfield,
D= ublin-4, Ireland
--Boundary_(ID_we8GpwMAXUlEAHDmF4Lh6g)-- From owner-chemistry@ccl.net Fri Mar 27 08:51:01 2009 From: "Babak Khalili khalili.babak.:.gmail.com" To: CCL Subject: CCL:G: Gaussian utilization- help Message-Id: <-38950-090327084604-14961-W/BwuGD2N3j0tWThM3hSEg=server.ccl.net> X-Original-From: "Babak Khalili" Date: Fri, 27 Mar 2009 08:46:00 -0400 Sent to CCL by: "Babak Khalili" [khalili.babak],[gmail.com] Dear All In utilization of Gaussian soft ware the L101 error occurs. The main problem is "LP -lone electron pair-" symbol formation in geometry specifications due to energy minimization in Chem3D e.g. (-OH) and /or (-HN2). The Chem 3D makes that but the Gaussian can't recognize it. Surly omitting the lone e-pair makes my results to be invaluable. It will be your great kind if you lead me and say me what can I do. Thanks, Babak Khalili PhD candidate of Biochemistry From owner-chemistry@ccl.net Fri Mar 27 12:37:00 2009 From: "Abu Asaduzzaman a.asaduzzaman|*|gmail.com" To: CCL Subject: CCL: VASP "box and lattice vector scale in POSCAR" Message-Id: <-38951-090327105326-31284-lE52QOoe25jGYsmWvCtSBQ---server.ccl.net> X-Original-From: Abu Asaduzzaman Content-Type: multipart/alternative; boundary=0016364ecc220e29ca04661a3855 Date: Fri, 27 Mar 2009 09:05:02 -0500 MIME-Version: 1.0 Sent to CCL by: Abu Asaduzzaman [a.asaduzzaman:+:gmail.com] --0016364ecc220e29ca04661a3855 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Saurabh I am not sure whether you are trying to calculate the bulk (crystal) or surface. If it is former, it seems there is fewer number of atoms in a big box! Also coordinates of atom have both positive and negative values, which means you are are sharing two simulation box (you know you have periodicity in all three directions). For calculation purpose that should not be a problem. but for visualization purpose, you may see your structure in a broken piece. thanks abu On Fri, Mar 27, 2009 at 6:58 AM, Saurabh Agrawal Saurabh.Agrawal+*+ ucdconnect.ie wrote: > Dear CCL Subscribers, > > I am trying to simulate rutile crystal. The box size for the crystal has > set as given below: > O Ti > 1.000000000000 > 16.66900000000 0.00000000000 0.000000000000 > 0.000000000000 10.50300000000 0.000000000000 > 0.000000000000 0.000000000000 10.52300000000 > 48 24 > Cartesian > 0.189999997616 1.621000051498 -3.956000089645 > -0.256999999285 -1.625000000000 1.985999941826 > . > . > . > The output I get in OUTCAR shows molecule broken in four small cubes > separated with gap even at zero number trajectory. It seems to me that the > BOX settings are not correct but it could be some other problem too. I > centered the crystal's coordinates and larger box sizes but result were > same. > > Any help to solve this problem would be of great help for me. > > Regards, > > Saurabh > > > Saurabh Agrawal, > PhD Student, > Department of Chemical and Bioprocess Engineering, > UCD, Belfield, > Dublin-4, Ireland > --0016364ecc220e29ca04661a3855 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Saurabh
I am not sure whether you are trying to calculate the bulk (c= rystal) or surface. If it is former, it seems there is fewer number of atom= s in a big box! Also coordinates of atom have both positive and negative va= lues, which means you are are sharing two simulation box (you know you have= periodicity in all three directions). For calculation purpose that should = not be a problem. but for visualization purpose, you may see your structure= in a broken piece.

thanks
abu

On Fri, Mar 27, 2009 at= 6:58 AM, Saurabh Agrawal Saurabh.Agrawal+*+ucdconnect.ie <owner-chemistry,ccl.net> wrote:
Dear CCL Subscrib= ers,

I am trying to simulate rutile crystal. The box size for the = crystal has set as given below:
O Ti
1.000000000000
16.66900000000 0.0000= 0000000 0.000000000000
0.000000000000 10.50300000= 000 0.000000000000
0.000000000000 0.000000000000 = 10.52300000000
48 24
Cartesian
0.189999997616 1.621000051498 = -3.956000089645
-0.256999999285 -1.625000000000 1= .985999941826
.
.
.
The output I get in OUTCAR shows= molecule broken in four small cubes separated with gap even at zero number= trajectory. It seems to me that the BOX settings are not correct but it co= uld be some other problem too. I centered the crystal's coordinates and= larger box sizes but result were same.

Any help to solve this problem would be of great help for me.
=
Regards,

Saurabh


Saurabh Agrawal,
PhD = Student,
Department of Chemical and Bioprocess Engineering,
UCD, Belf= ield,
Dublin-4, Ireland

--0016364ecc220e29ca04661a3855-- From owner-chemistry@ccl.net Fri Mar 27 13:23:00 2009 From: "Duy Le ttduyle\a/gmail.com" To: CCL Subject: CCL: VASP "box and lattice vector scale in POSCAR" Message-Id: <-38952-090327132159-16290-lKNveFt+aXAj3qX5meW6pA]^[server.ccl.net> X-Original-From: Duy Le Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 27 Mar 2009 13:21:33 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle,,gmail.com] hi Saurabh, I think you should check the initial coordinates. It seems to me that you don't have reasonable POSCAR. You can check it by using any crystalline structure viewer or check the distance to nearest neighbors of all atoms (those distances for TiO2 rutile are about 1.95 and 2.96 Angstr) D. On Fri, Mar 27, 2009 at 7:58 AM, Saurabh Agrawal Saurabh.Agrawal+*+ucdconnect.ie wrote: > Dear CCL Subscribers, > > I am trying to simulate rutile crystal. The box size for the crystal has set > as given below: > O Ti > 1.000000000000 > 16.66900000000 0.00000000000 0.000000000000 > 0.000000000000 10.50300000000 0.000000000000 > 0.000000000000 0.000000000000 10.52300000000 > 48 24 > Cartesian > 0.189999997616 1.621000051498 -3.956000089645 > -0.256999999285 -1.625000000000 1.985999941826 > . > . > . > The output I get in OUTCAR shows molecule broken in four small cubes > separated with gap even at zero number trajectory. It seems to me that the > BOX settings are not correct but it could be some other problem too. I > centered the crystal's coordinates and larger box sizes but result were > same. > > Any help to solve this problem would be of great help for me. > > Regards, > > Saurabh > > > Saurabh Agrawal, > PhD Student, > Department of Chemical and Bioprocess Engineering, > UCD, Belfield, > Dublin-4, Ireland > -- Men don't need hands to do things! From owner-chemistry@ccl.net Fri Mar 27 15:12:01 2009 From: "Lukasz Cwiklik cwiklik,,gmail.com" To: CCL Subject: CCL:G: resp charge Message-Id: <-38953-090327151031-5278-baChLHvtvLK/L7BS2f6aEw]-[server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 27 Mar 2009 22:10:14 +0300 MIME-Version: 1.0 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 IOp(6/33=3D2,6/41=3D10,6/42=3D= 10) Opt > =A0nosymm > 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 file may = not complete, exit > But when i load molecule.log with Gaussview i can view the ESP charge . > 1-What's wrong? > 2-Is it correct to reproduce =A0manually ESP-charge from gaussview to put= them in molecule.prepi > Thanks Dear Amine, The procedure for creating resp charges in antechamber can be tricky, 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 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 number of fitting points is described there. Best, Lukasz --=20 Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Fri Mar 27 15:47:00 2009 From: "David Mannock dmannock**ualberta.ca" To: CCL Subject: CCL:G: omp_set_num_threads error Message-Id: <-38954-090327013847-30266-zKZ2nq2dlxFPPPP6KIA1rQ|server.ccl.net> X-Original-From: David Mannock Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 26 Mar 2009 23:38:26 -0600 Mime-Version: 1.0 Sent to CCL by: David Mannock [dmannock===ualberta.ca] Greetings Earthlings! I am in the process of setting up an eight core server and this news is a surprise to me! Agghhh! So that means that if I want to run 64 bit anything I need the 64 bit drivers and the source code for each program I want to use and then compile it for the OS! This could take a life time! Are there any sites out there to advise on this issue with major CCL software in a Vista 64 bit application. Is there an idiots guide to compiling stuff for an 8 processors? Yes, I know I should be using Linux, but I don't want too. :-) Dave > Dave At 04:37 PM 3/26/2009, you wrote: >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.govDr David Mannock 339 Med Sci Bldg, Dept of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7 Canada Tel: 1-780-492-2412 FAX: 1-780-492-0886 From owner-chemistry@ccl.net Fri Mar 27 16:24:01 2009 From: "Troy Wymore wymore-*-psc.edu" To: CCL Subject: CCL: PSC/NRBSC Workshop on QC/MM Methods and Applications Message-Id: <-38955-090327155008-24693-mJnfRCF6sIefoWrGDEdrMQ!=!server.ccl.net> X-Original-From: "Troy Wymore" Date: Fri, 27 Mar 2009 15:50:05 -0400 Sent to CCL by: "Troy Wymore" [wymore++psc.edu] The National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center will host a workshop entitled: "Methods and Applications of Hybrid Quantum Chemical/Molecular Mechanical Simulations of Biomolecular Systems" August 11-14, 2009 Pittsburgh, PA Website: http://shannon.psc.edu/mediawiki/index.php/QCMM_Workshop_2009 The workshop will present computational approaches for the simulation of enzymatic reactions. Lectures will be held on the relevant theoretical background including the applicability of Quantum Chemical (QC) methods for large molecules, re-parameterization of Semiempirical Molecular Orbital (SMO) methods for specific reactions, molecular mechanics (MM) force fields, hybrid QC/MM potential energy functions and simulation techniques on high performance computers. In-depth tutorials will be presented primarily with the use of the freely available pDynamo package developed in the lab of Dr. Martin J. Field and will also include developing SMO parameters for quantitatively accurate enzyme reaction simulations, the issues involved in constructing a QC/MM model and the various methods for generating energy profiles of bio-molecular reactions to determine mechanisms and structure-function relationships. Experience with pDynamo is helpful but not a prerequisite for attendance. The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on bio-molecular systems from their own research during the workshop. Space is limited. This workshop is funded by a grant from the NIH National Center for Research Resources. These grants provide tuition and hotel costs, supercomputing time, and workshop materials for US academic participants. All participants are responsible for paying their own travel expenses. Complimentary continental breakfasts and lunches will be provided the days of the workshop. Registration is now open. http://www.nrbsc.org/education/workshops/register.php From owner-chemistry@ccl.net Fri Mar 27 17:23:00 2009 From: "David Santos david[-]fq.uh.cu" To: CCL Subject: CCL: IR spectra of K3Fe(C2O4)3 Message-Id: <-38956-090327172016-23724-aUHecUVBCKmAcWPfI1SXkg]^[server.ccl.net> X-Original-From: "David Santos" Date: Fri, 27 Mar 2009 17:20:13 -0400 Sent to CCL by: "David Santos" [david/a\fq.uh.cu] Dear CCL users, Is there any free spectra database for coordination compounds available on Internet? Actually I need the IR spectra of K3[Fe(C2O4)3]. Thank you any information or the spectra, David Santos Carballal Departamento de Qumica-Fsica Facultad de Qumica-Universidad de la Habana. Zapata s/n entre G y Carlitos Aguirre. Prncipe. Plaza de la Revolucin. Cdigo Postal 10400. Cuba e-mail: david^-^fq.uh.cu phone: 878-0684 url: http://www.fq.uh.cu/investig/gqf/e/dsc.htm