From owner-chemistry@ccl.net Fri Mar 27 05:55:01 2009
From: "amine amine m-22()hotmail.fr" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL:G: resp charge
Message-Id: <-38948-090327054034-1786-XpARDww3LCHSxvCrIscM0g-$-server.ccl.net>
X-Original-From: "amine amine" <m-22]|[hotmail.fr>
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" <owner-chemistry _ server.ccl.net>
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 <Saurabh.Agrawal%x%ucdconnect.ie>
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,<br><br> I am trying to simulate rutile crystal=
. The box size for the crystal has set as given below: <br> O Ti <=
br> 1.000000000000 <br> 16.66900000000 0.00000000=
000 0.000000000000 <br> 0.000000000000 10.503000=
00000 0.000000000000 <br> 0.000000000000 0.00000=
0000000 10.52300000000 <br> 48 24 <br> Cartesian <br> =
0.189999997616 1.621000051498 -3.956000089645 <br> =
-0.256999999285 -1.625000000000 1.985999941826 <br> . <=
br> . <br> . <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. <br> <br> Any help to solve t=
his problem would be of great help for me. <br> <br> Regards, <br>=
<br> Saurabh <br><br><br>Saurabh Agrawal,<br>PhD Student,<br>Depa=
rtment of Chemical and Bioprocess Engineering,<br>UCD, Belfield,<br>D=
ublin-4, Ireland<br>
--Boundary_(ID_we8GpwMAXUlEAHDmF4Lh6g)--
From owner-chemistry@ccl.net Fri Mar 27 08:51:01 2009
From: "Babak Khalili khalili.babak.:.gmail.com" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian utilization- help
Message-Id: <-38950-090327084604-14961-W/BwuGD2N3j0tWThM3hSEg=server.ccl.net>
X-Original-From: "Babak Khalili" <khalili.babak~!~gmail.com>
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" <owner-chemistry---server.ccl.net>
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 <a.asaduzzaman]-[gmail.com>
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 <owner-chemistry,ccl.net> 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<br>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. <br>
<br>thanks<br>abu<br><br><div class=3D"gmail_quote">On Fri, Mar 27, 2009 at=
6:58 AM, Saurabh Agrawal Saurabh.Agrawal+*+<a href=3D"http://ucdconnect.ie=
">ucdconnect.ie</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry=
,ccl.net">owner-chemistry,ccl.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear CCL Subscrib=
ers,<br><br> I am trying to simulate rutile crystal. The box size for the =
crystal has set as given below: <br>
O Ti <br> 1.000000000000 <br> 16.66900000000 0.0000=
0000000 0.000000000000 <br> 0.000000000000 10.50300000=
000 0.000000000000 <br> 0.000000000000 0.000000000000 =
10.52300000000 <br>
48 24 <br> Cartesian <br> 0.189999997616 1.621000051498 =
-3.956000089645 <br> -0.256999999285 -1.625000000000 1=
.985999941826 <br> . <br> . <br> . <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 co=
uld be some other problem too. I centered the crystal's coordinates and=
larger box sizes but result were same. <br>
<br> Any help to solve this problem would be of great help for me. <br>=
<br> Regards, <br> <br> Saurabh <br><br><br>Saurabh Agrawal,<br>PhD =
Student,<br>Department of Chemical and Bioprocess Engineering,<br>UCD, Belf=
ield,<br>
Dublin-4, Ireland<br>
</blockquote></div><br>
--0016364ecc220e29ca04661a3855--
From owner-chemistry@ccl.net Fri Mar 27 13:23:00 2009
From: "Duy Le ttduyle\a/gmail.com" <owner-chemistry]^[server.ccl.net>
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 <ttduyle++gmail.com>
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 <owner-chemistry*|*ccl.net> 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" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL:G: resp charge
Message-Id: <-38953-090327151031-5278-baChLHvtvLK/L7BS2f6aEw]-[server.ccl.net>
X-Original-From: Lukasz Cwiklik <cwiklik*o*gmail.com>
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
<owner-chemistry##ccl.net> 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" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL:G: omp_set_num_threads error
Message-Id: <-38954-090327013847-30266-zKZ2nq2dlxFPPPP6KIA1rQ|server.ccl.net>
X-Original-From: David Mannock <dmannock:+:ualberta.ca>
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" <owner-chemistry!=!server.ccl.net>
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" <wymore- -psc.edu>
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" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: IR spectra of K3Fe(C2O4)3
Message-Id: <-38956-090327172016-23724-aUHecUVBCKmAcWPfI1SXkg]^[server.ccl.net>
X-Original-From: "David Santos" <david]![fq.uh.cu>
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