From owner-chemistry@ccl.net Mon Mar 7 01:13:00 2011 From: "Tamar Ansbacher tamar.ansbacher/a\mail.huji.ac.il" To: CCL Subject: CCL: external charges calculation and pcm? Message-Id: <-44059-110307011152-2409-cIJXanajna8XTEPZRTYTjQ.:.server.ccl.net> X-Original-From: Tamar Ansbacher Content-Type: multipart/alternative; boundary=001517447d0cc77d96049dde5e0d Date: Mon, 7 Mar 2011 08:11:45 +0200 MIME-Version: 1.0 Sent to CCL by: Tamar Ansbacher [tamar.ansbacher(-)mail.huji.ac.il] --001517447d0cc77d96049dde5e0d Content-Type: text/plain; charset=ISO-8859-1 Dear group. I trying to perform an external charge calculation (using the keyword charge) in a pcm model. I get a warning : Warning! Some of the external charges might be outside the PCM cavity: The PCM calculation in these conditions is not meaningful. also, I see that Error on total polarization charges = 1.18453 I know this error should be much smaller. I wonder if there is a way to enlarge the cavity (not of a certain atom) so it will include the external charges as well? Otherwise- is there any other way to overcome the above problems? Thank you . Tamar --001517447d0cc77d96049dde5e0d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear group.
=A0
I trying to perform an external charge calculation (using the keyword = charge)
in a pcm model.
I=A0get a warning :
=A0
=A0Warning! Some of the external charges might be outside the PCM cavi= ty:
=A0=A0=A0=A0=A0=A0=A0=A0=A0 The PCM calculation in these conditions = is not meaningful.
=A0
also,=A0I see that=A0=A0
=A0
=A0Error on total polarization charges =3D=A0 1.18453
=A0
I=A0know this error should be much smaller.
=A0
I wonder if there is a way to enlarge the cavity (not of a certain ato= m)
so it will include the external charges as well?
=A0
Otherwise- is there any other way to overcome the above problems?
=A0
Thank you .
=A0Tamar

--001517447d0cc77d96049dde5e0d-- From owner-chemistry@ccl.net Mon Mar 7 03:20:00 2011 From: "Tamar Ansbacher tamar.ansbacher(_)mail.huji.ac.il" To: CCL Subject: CCL: external charges calculation and pcm? Message-Id: <-44060-110307031753-2552-a7qgesNppDYIfVI6l9LpTA^server.ccl.net> X-Original-From: Tamar Ansbacher Content-Type: multipart/alternative; boundary=00151747849e68c287049de021d6 Date: Mon, 7 Mar 2011 10:17:45 +0200 MIME-Version: 1.0 Sent to CCL by: Tamar Ansbacher [tamar.ansbacher . mail.huji.ac.il] --00151747849e68c287049de021d6 Content-Type: text/plain; charset=ISO-8859-1 Hi I'm sorry- I forgot to mention I'm using g09! Tamar On Mon, Mar 7, 2011 at 8:11 AM, Tamar Ansbacher tamar.ansbacher/ amail.huji.ac.il wrote: > > Dear group. > > I trying to perform an external charge calculation (using the keyword > charge) > in a pcm model. > I get a warning : > > Warning! Some of the external charges might be outside the PCM cavity: > The PCM calculation in these conditions is not meaningful. > > also, I see that > > Error on total polarization charges = 1.18453 > > I know this error should be much smaller. > > I wonder if there is a way to enlarge the cavity (not of a certain atom) > so it will include the external charges as well? > > Otherwise- is there any other way to overcome the above problems? > > Thank you . > Tamar > > --00151747849e68c287049de021d6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi
I'm sorry- I forgot to mention I'm using g09!
=A0
Tamar

On Mon, Mar 7, 2011 at 8:11 AM, Tamar Ansbacher = tamar.ansbacher/amail.huji.ac.il <owner-chemis= try*ccl.net> wrote:

Dear group.
=A0
I trying to perform an external charge calculation (using the keyword = charge)
in a pcm model.
I=A0get a warning :
=A0
=A0Warning! Some of the external charges might be outside the PCM cavi= ty:
=A0=A0=A0=A0=A0=A0=A0=A0=A0 The PCM calculation in these conditions = is not meaningful.
=A0
also,=A0I see that=A0=A0
=A0
=A0Error on total polarization charges =3D=A0 1.18453
=A0
I=A0know this error should be much smaller.
=A0
I wonder if there is a way to enlarge the cavity (not of a certain ato= m)
so it will include the external charges as well?
=A0
Otherwise- is there any other way to overcome the above problems?
=A0
Thank you .
=A0Tamar


--00151747849e68c287049de021d6-- From owner-chemistry@ccl.net Mon Mar 7 10:14:00 2011 From: "Mike Towler mdt26|-|cam.ac.uk" To: CCL Subject: CCL: Summer School, Tuscany, Italy Message-Id: <-44061-110307093539-19587-dNE3NGwe0JO6veqr1QVh3A-x-server.ccl.net> X-Original-From: "Mike Towler" Date: Mon, 7 Mar 2011 09:35:36 -0500 Sent to CCL by: "Mike Towler" [mdt26 * cam.ac.uk] SUMMER SCHOOL ANNOUNCEMENT "Quantum Monte Carlo and the CASINO program VI" =============================================== Sat 30th July - Sat 6th August 2011 Apuan Alps Centre for Physics ^_^ TTI, Vallico Sotto, Tuscany, Italy http://www.vallico.net/tti/tti.html A4 POSTER FOR THE SCHOOL AVAILABLE HERE : http://www.tcm.phy.cam.ac.uk/~mdt26/poster.png The sixth international summer school in the series "Quantum Monte Carlo and the CASINO program" will take place during August 2011 at the TTI monastery in the Tuscan Apuan Alps in Italy, organized and hosted by members of Cambridge University physics department's Theory of Condensed Matter Group. The aim of the school is to give students a thorough introduction to quantum Monte Carlo as a method for performing high-quality calculations of the electronic structure of atoms, molecules, and materials. The course is designed for young quantum chemists or theoretical physicists who have no previous experience with this technique, though anyone interested is welcome to take part, including old people. The monastery is a unique venue where the community spirit and magnificent location have inspired memorable workshops in the past. It is a delightful 16th century building incorporating an ancient church, and is situated in the isolated but spectacular setting of the Tuscan mountain village of Vallico Sotto. The church is fully equipped with relevant presentation and computer technology, and all accommodation is on-site. As with all events at the Institute, formal lectures are restricted to the mornings, and participants are given the freedom and space to think and to contemplate and discuss the issues at hand. In addition to hands-on exercises, a programme of healthy recreational activities will be organized in the afternoons, and it is hoped that by following this strict regime, together with breathing clean mountain air and by preparing and sampling fine Tuscan cuisine, the participant will be able to return home mentally and physically refreshed as well as better informed. Describing the complex behaviour of materials at the atomic level requires a sophisticated description of the correlated motion of the electrons. Quantum Monte Carlo (QMC) is an increasingly popular and explicitly many-body method with the unusual capability of yielding highly accurate results whilst also exhibiting a very favourable scaling of computational cost with system size. Over the last eighteen years, the Cambridge group have been researching QMC methods and we have created a powerful, general computer program - CASINO - to carry out the calculations. The school will focus both on the basic theory of QMC and on more advanced practical techniques, and will include a thorough introduction to the CASINO program. A background in density functional theory or similar - though not essential - is normally thought to be useful. Quantum Monte Carlo and the scaling behaviour of CASINO on the fastest computers in the world were the subject of this month's Psi-k "Scientific Highlight of the Month" review article. See "Petascale computing opens new vistas for quantum Monte Carlo" by M.J.Gillan, M.D. Towler and D.Alfe, available for download here: http://www.psi-k.org/newsletters/News_103/Highlight_103.pdf Instructors at the school will include the main authors of the CASINO program (Dr. Mike Towler, Dr. Neil Drummond and Dr. Pablo Lopez Rios) and possibly others. Participants would normally need to book a flight to Pisa airport from where onward transportation will be arranged (though other destinations are possible). Details of previous schools - including photographs - are available under the PUBLIC EVENTS link on the TTI web site. Interested students should email Mike Towler (mdt26 at cam.ac.uk) for registration and further details. From owner-chemistry@ccl.net Mon Mar 7 12:53:00 2011 From: "Aldo HUmberto Romero aromero()qro.cinvestav.mx" To: CCL Subject: CCL: PASI WORKSHOP Electronic Structure Cartagena Colombia Message-Id: <-44062-110307124359-25937-Ii1/JNW9XCKJtAQwiGP20A__server.ccl.net> X-Original-From: "Aldo HUmberto Romero" Date: Mon, 7 Mar 2011 12:43:56 -0500 Sent to CCL by: "Aldo HUmberto Romero" [aromero:qro.cinvestav.mx] Dear Colleague: We would like to invite you to encourage your students, postdoctoral fellows and research scientists to participate in the Pan-American Advanced Study Institute on ELECTRONIC PROPERTIES OF COMPLEX SYSTEMS to be held in the beautiful city of Cartagena, Colombia, between June 6-17 2011. This will have the format of a course/workshop given by leading experts in the field, and attended by a maximum of 65 participants from the US and Latin-America (one of the goals of this Institute, mostly funded by the U.S. National Science Foundation, is to strengthen the scientific connections between the US and Latin-America). You will find all information about the workshop in our Web page: www.cursopasi.unal.edu.co The following are the 3 major topics and 15 confirmed lecturers: I - Electronic transport: Latha Venkataraman (Columbia University, USA) Marcel Mayor (University of Basel, Switzerland) Gianluca Stefanucci (University of Rome Tor Vergata, Italy) Jeff Neaton (Lawrence Berkeley National Lab., USA) Caio Lewenkopf (Universidade Federal Fluminense, Brazil) II - Spectroscopy of complex systems: Alex Fainstein (Instituto Balseiro, Argentina) Shaul Mukamel (University of California - Irvine, USA) Weitao Yang (Duke University, USA) Victor Batista (Yale University, USA) III - Laser chemistry and optimal control: E.K.U. Gross (Max Planck Institute - Halle, Germany) Herschel Rabitz (Princeton University, USA) Todd Martinez (Stanford University, USA) Leticia Gonzlez (Friedrich-Schiller Universitt Jena, Germany) Alberto Castro (BIFI-Zaragoza, Spain) Please alert prospective participants that they should present a poster on their ongoing work, and that the deadline to request support is MARCH 15, 2011 (we have a good number of scholarships that include meals and lodging). We would also appreciate if you can circulate this information to any one interested. For inquiries, please e-mail: cursopasi_+_unal.edu.co Thanks, _The Organizing Committee_: Aldo Humberto Romero, CINVESTAV, Mexico Adam Wasserman, Purdue University, USA Todd Martinez, Stanford University, USA Andres Reyes, Universidad Nacional, Colombia -------------------------------------- Prof. Aldo Humberto Romero CINVESTAV-Unidad Queretaro Libramiento Norponiente 2000 CP 76230, Queretaro, QRO, Mexico ph: 442 211 9909 fax: 442 211 9938 email: aromero_+_qro.cinvestav.mx aldorome_+_gmail.com www: qro.cinvestav.mx/~aromero From owner-chemistry@ccl.net Mon Mar 7 15:19:00 2011 From: "Eric Bremond eric-bremond_-_chimie-paristech.fr" To: CCL Subject: CCL: Error code 35072 in Orca Message-Id: <-44063-110307111954-28527-XOYzn2BUDihPoRfydZMTvg+/-server.ccl.net> X-Original-From: "Eric Bremond" Date: Mon, 7 Mar 2011 11:19:52 -0500 Sent to CCL by: "Eric Bremond" [eric-bremond-$-chimie-paristech.fr] Dear everybody, I was using Orca to calculate CCSD(T) energy and I obtained an error code numbered 35072 in MDCI module as described here: ---------------------- RHF TRIPLES CORRECTION (Algorithm 1) ---------------------- Multiplier for the singles contribution ... 1.000000000 3 total processes killed (some possibly by mpirun during cleanup) An error has occured in the MDCI module CALLING COMMAND: mpirun -np 8 /opt/orca/orca_mdci_mpi /tmp/33155.head/dft_opt_rijk_ccsdt.mdciinp.tmp RETURN CODE : 35072 ABORTING THE RUN Does anybody know how can I solve my problem ? Thanks for your help. eric From owner-chemistry@ccl.net Mon Mar 7 15:54:00 2011 From: "Kyle Lutz kyle.r.lutz===gmail.com" To: CCL Subject: CCL: open source software for molecular graph Message-Id: <-44064-110307142912-25589-SgOtoplVBBcb3k/rwMjEJg---server.ccl.net> X-Original-From: Kyle Lutz Content-Type: multipart/alternative; boundary=000e0cd403e031e217049de98204 Date: Mon, 7 Mar 2011 11:29:04 -0800 MIME-Version: 1.0 Sent to CCL by: Kyle Lutz [kyle.r.lutz|,|gmail.com] --000e0cd403e031e217049de98204 Content-Type: text/plain; charset=ISO-8859-1 On Sun, Mar 6, 2011 at 4:04 AM, Jinsong Zhao jszhao!A!yeah.net < owner-chemistry##ccl.net> wrote: > > Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net] > Hi there, > > I hope to convert a molecular structure in XYZ format (or any other format) > to a graph or an adjacency matrix. I have to use a open source software to > do such conversion, however, I find nothing by google. > > Would please to give me a hand? Any suggestions or comments will be really > appreciated. > > Regards, > Jinsong > This can be done rather easily using python and the open source chemkit library (http://www.chemkit.org). Below is a small python script which will read a molecule from a file and print out its adjacency matrix. --- graph.py --------------------------------------------------------------- #!/usr/bin/env python # graph.py - prints adjacency matrix of a molecule # usage: python graph.py import sys import chemkit fileName = sys.argv[1] molecule = chemkit.ChemicalFile.quickRead(fileName) for i in range(molecule.size()): a = molecule.atom(i) for j in range(molecule.size()): b = molecule.atom(j) if(a.isBondedTo(b)): print "1 ", else: print "0 ", print "" --- end graph.py ---------------------------------------------------- And here is a sample output: ./graph.py methanol.sdf 0 1 0 0 0 1 1 0 1 1 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 Hope this helps. Kyle Lutz --000e0cd403e031e217049de98204 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
On Sun, Mar 6, 2011 at 4:04 AM, Jinsong Zhao jsz= hao!A!yeah.net <o= wner-chemistry##ccl.net> wrote:

Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net]
Hi there,

I hope to convert a molecular structure in XYZ format (or any other format)= to a graph or an adjacency matrix. I have to use a open source software to= do such conversion, however, I find nothing by google.

Would please to give me a hand? Any suggestions or comments will be really = appreciated.

Regards,
Jinsong

This can be done rather easily using pyth= on and the open source chemkit library (http://www.chemkit.org).

Below is a small pyth= on script which will read a molecule from a file and print out its adjacenc= y matrix.

--- graph.py ----------------------------------------------------------= -----
#!/usr/bin/env python

# graph.py - prints adjacency matrix = of a molecule
# usage: python graph.py <file>

import sys import chemkit

fileName =3D sys.argv[1]
molecule =3D chemkit.Chem= icalFile.quickRead(fileName)

for i in range(molecule.size()):
=A0= =A0=A0 a =3D molecule.atom(i)

=A0=A0=A0 for j in range(molecule.size= ()):
=A0=A0=A0=A0=A0=A0=A0 b =3D molecule.atom(j)

=A0=A0=A0=A0=A0=A0=A0 if(a.isBondedTo(b)):
=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 print "1 ",
=A0=A0=A0=A0=A0=A0=A0 else:
=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 print "0 ",

=A0=A0=A0 print "= ;"

--- end graph.py -------------------------------------------= ---------

And here is a sample output:

./graph.py methanol.sdf
0=A0 1= =A0 0=A0 0=A0 0=A0 1=A0
1=A0 0=A0 1=A0 1=A0 1=A0 0=A0
0=A0 1=A0 0= =A0 0=A0 0=A0 0=A0
0=A0 1=A0 0=A0 0=A0 0=A0 0=A0
0=A0 1=A0 0=A0 0= =A0 0=A0 0=A0
1=A0 0=A0 0=A0 0=A0 0=A0 0

Hope this helps.

Kyle Lutz
--000e0cd403e031e217049de98204-- From owner-chemistry@ccl.net Mon Mar 7 16:29:01 2011 From: "Andrew Orry andy{=}molsoft.com" To: CCL Subject: CCL: Workshop: Protein Structure and Drug Design - April 7-8 Message-Id: <-44065-110307150342-28821-f/1wLbKI6HNCQJSswNteEQ|a|server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 07 Mar 2011 12:01:33 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy,,molsoft.com] "Protein Structure and Drug Discovery" Workshop – April 7-8 2011 San Diego, CA. Please join us at MolSoft's ( www.molsoft.com ) "Protein Structure and Drug Design" Workshop in San Diego, California USA. For more information and a registration form see: www.molsoft.com/training.html This workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan Ph.D. (University of California San Diego) and Dr. Maxim Totrov Ph.D. (MolSoft). Price: $349 (Academics) $749 (Commercial) The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - How To Display Fully Interactive 3D Molecules in PowerPoint and the Web - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking Please see our website at www.molsoft.com for more details or E mail: andy++molsoft.com or call 858-625-2000 ext.108. For the latest MolSoft news see: http://www.molsoft.com/news.html From owner-chemistry@ccl.net Mon Mar 7 17:06:00 2011 From: "Wolf Ihlenfeldt wdi|*|xemistry.com" To: CCL Subject: CCL: open source software for molecular graph Message-Id: <-44066-110307170131-23953-gZpXEmPpgqrQNFY3DBy5tQ- -server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=000e0cd484bcd8957d049deba268 Date: Mon, 7 Mar 2011 23:01:21 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi\a/xemistry.com] --000e0cd484bcd8957d049deba268 Content-Type: text/plain; charset=UTF-8 Here is a script solution for the Cactvs toolkit (not open source, but free for academics, www.xemistry.com/academic): ---snip--- set eh [molfile read [lindex $argv 0]] foreach a1 [ens atoms $eh] { foreach a2 [ens atoms $eh] { puts -nonewline "[expr {$a1==$a2 ? 0 : [bond exists $eh [list $a1 $a2]]}] " } puts "" } ---snip--- Advantages: It works with a lot of chemistry file formats right out of the box (automatic format detection, by looking at the content, not the file name) Automatic bond generation for files without (XYZ) or with incomplete bond information (PDB). This even includes a pretty good resolver for bond *orders*, not just connectivities (ChemKit cannot do that, AFAIK). On Mon, Mar 7, 2011 at 8:29 PM, Kyle Lutz kyle.r.lutz===gmail.com < owner-chemistry:ccl.net> wrote: > On Sun, Mar 6, 2011 at 4:04 AM, Jinsong Zhao jszhao!A!yeah.net < > owner-chemistry|ccl.net> wrote: > >> >> Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net] >> Hi there, >> >> I hope to convert a molecular structure in XYZ format (or any other >> format) to a graph or an adjacency matrix. I have to use a open source >> software to do such conversion, however, I find nothing by google. >> >> Would please to give me a hand? Any suggestions or comments will be really >> appreciated. >> >> Regards, >> Jinsong >> > > This can be done rather easily using python and the open source chemkit > library (http://www.chemkit.org). > > Below is a small python script which will read a molecule from a file and > print out its adjacency matrix. > > --- graph.py > --------------------------------------------------------------- > #!/usr/bin/env python > > # graph.py - prints adjacency matrix of a molecule > # usage: python graph.py > > import sys > import chemkit > > fileName = sys.argv[1] > molecule = chemkit.ChemicalFile.quickRead(fileName) > > for i in range(molecule.size()): > a = molecule.atom(i) > > for j in range(molecule.size()): > b = molecule.atom(j) > > if(a.isBondedTo(b)): > print "1 ", > else: > print "0 ", > > print "" > > --- end graph.py ---------------------------------------------------- > > And here is a sample output: > > ./graph.py methanol.sdf > 0 1 0 0 0 1 > 1 0 1 1 1 0 > 0 1 0 0 0 0 > 0 1 0 0 0 0 > 0 1 0 0 0 0 > 1 0 0 0 0 0 > > Hope this helps. > > Kyle Lutz > -- Wolf-D. Ihlenfeldt, Xemistry GmbH www.xemistry.com --000e0cd484bcd8957d049deba268 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Here is a script solution for the Cactvs toolkit (not open source, but = free for academics, www.xemist= ry.com/academic):

---snip---
set eh [molfile read [lindex $ar= gv 0]]
foreach a1 [ens atoms $eh] {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = foreach a2 [ens atoms $eh] {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 puts -nonewline "[exp= r {$a1=3D=3D$a2 ? 0 : [bond exists $eh [list $a1 $a2]]}] "
=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 puts ""
}
---snip---

Advantages:

It works with a lot of chemistry file= formats right out of the box (automatic format detection, by looking at th= e content, not the file name)

Automatic bond generation for files wi= thout (XYZ) or with incomplete bond information (PDB). This even includes a= pretty good resolver for bond *orders*, not just connectivities (ChemKit c= annot do that, AFAIK).



On Mon, Mar 7, 2011 at 8:29 PM, Kyle= Lutz kyle.r.lutz=3D=3D=3Dgmail.com <owner-chemistry:= ccl.net> wrote:
On Sun, Mar 6, 2011 at 4:04 AM, Jinsong Zhao jszhao!A!yeah.net <owner-chemistry|c= cl.net> wrote:

Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net]
Hi there,

I hope to convert a molecular structure in XYZ format (or any other format)= to a graph or an adjacency matrix. I have to use a open source software to= do such conversion, however, I find nothing by google.

Would please to give me a hand? Any suggestions or comments will be really = appreciated.

Regards,
Jinsong

This can be done rather easily using pyth= on and the open source chemkit library (http://www.chemkit.org).

Below is a small pyth= on script which will read a molecule from a file and print out its adjacenc= y matrix.

--- graph.py ----------------------------------------------------------= -----
#!/usr/bin/env python

# graph.py - prints adjacency matrix = of a molecule
# usage: python graph.py <file>

import sys import chemkit

fileName =3D sys.argv[1]
molecule =3D chemkit.Chem= icalFile.quickRead(fileName)

for i in range(molecule.size()):
=C2= =A0=C2=A0=C2=A0 a =3D molecule.atom(i)

=C2=A0=C2=A0=C2=A0 for j in r= ange(molecule.size()):
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 b =3D = molecule.atom(j)

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 if(a.isBondedTo(b)):
=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 print "= ;1 ",
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 else:
=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 print "0 &qu= ot;,

=C2=A0=C2=A0=C2=A0 print ""

--- end graph.py -= ---------------------------------------------------

And here is a sample output:

./graph.py methanol.sdf
0=C2=A0= 1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 1=C2=A0
1=C2=A0 0=C2=A0 1=C2=A0 1=C2= =A0 1=C2=A0 0=C2=A0
0=C2=A0 1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0
0=C2=A0 1=C2=A0 0=C2= =A0 0=C2=A0 0=C2=A0 0=C2=A0
1=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0=C2=A0 0
Hope this helps.

Kyle Lutz



--
Wolf-D. Ihlenfel= dt, Xemistry GmbH
= www.xemistry.com

--000e0cd484bcd8957d049deba268-- From owner-chemistry@ccl.net Mon Mar 7 17:40:00 2011 From: "Jim Kress ccl_nospam||kressworks.com" To: CCL Subject: CCL: Error code 35072 in Orca Message-Id: <-44067-110307173556-24257-vDRx32rTofxfz+xZIS8+lQ^^^server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 7 Mar 2011 17:35:37 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam/a\kressworks.com] Did you try asking your question at the Orca Forum? http://www.thch.uni-bonn.de/tc/orca/index.php?option=com_joobb&view=board&la yout=joobb&Itemid=44 Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com_-_ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com_-_ccl.net] On Behalf Of Eric Bremond > eric-bremond_-_chimie-paristech.fr > Sent: Monday, March 07, 2011 11:20 AM > To: Kress, Jim > Subject: CCL: Error code 35072 in Orca > > > Sent to CCL by: "Eric Bremond" [eric-bremond-$-chimie-paristech.fr] > Dear everybody, > > I was using Orca to calculate CCSD(T) energy and I obtained an error > code numbered 35072 in MDCI > module as described here: > > ---------------------- > RHF TRIPLES CORRECTION (Algorithm 1) > ---------------------- > > Multiplier for the singles contribution ... 1.000000000 > 3 total processes killed (some possibly by mpirun during cleanup) > > An error has occured in the MDCI module > CALLING COMMAND: mpirun -np 8 /opt/orca/orca_mdci_mpi > /tmp/33155.head/dft_opt_rijk_ccsdt.mdciinp.tmp > RETURN CODE : 35072 > ABORTING THE RUN > > Does anybody know how can I solve my problem ? > > Thanks for your help. > eric> To recover the email address of the author of the message, please > change From owner-chemistry@ccl.net Mon Mar 7 19:06:00 2011 From: "Zijun Yu zjyu-*-lamar.colostate.edu" To: CCL Subject: CCL: scan problem Message-Id: <-44068-110307190424-16977-n6CUgJbOmCBfxrr94YZDNA*server.ccl.net> X-Original-From: "Zijun Yu" Date: Mon, 7 Mar 2011 19:04:22 -0500 Sent to CCL by: "Zijun Yu" [zjyu.:.lamar.colostate.edu] Dear All, I try to do a scan calculation on PETN. Molecular structure is C(CH2O-NO2)4. I want to scan bond O-N to get NO2 elimination reaction path. But after 29 steps, the oxygen atom from NO2 forms hydrogen bond with the hydrogen atom of CH2, and then totally changs the structure to have HONO elinination. How to scan get the NO2 elimination reaction path? thanks! My input file is below: %chk=ONIOMscan1.chk %mem=4000MB %nprocshared=4 #p oniom(b3lyp/6-31g(d):uff) opt=(modredundant,QuadMacro,maxcycle=300) scf=(maxcycle=300) nosymm scan O26-N27 bond 0 1 0 1 0 1 C-C_3 0 1.42009700 0.53656500 0.25153200 L H-H_ 23 C-C_3 0 2.07396300 -0.84802900 0.37737100 L H-H_ 0 1.36956600 -1.56242000 0.80781700 L H-H_ 0 2.96774300 -0.80139000 1.00252200 L O-O_R 0 2.42565100 -1.25162100 -0.95419100 L N-N_R 0 3.01180200 -2.54467800 -1.03268600 L O-O_R 0 3.15309300 -3.13954200 -0.00064200 L O-O_R 0 3.28399500 -2.85195300 -2.15091700 L C-C_3 0 2.44552900 1.51059000 -0.34865100 L H-H_ 0 3.33484800 1.56157000 0.28248100 L H-H_ 0 2.73450400 1.20072700 -1.35478600 L O-O_R 0 1.80541100 2.79425600 -0.39424600 L N-N_R 0 2.63361700 3.83820100 -0.89022900 L O-O_R 0 2.07531400 4.89031300 -0.90775200 L O-O_R 0 3.74807700 3.53753400 -1.21659400 L C-C_3 0 0.96947700 0.99493300 1.64698200 L H-H_ 0 0.26948800 0.28048400 2.08450200 L H-H_ 0 0.49433000 1.97609000 1.58884300 L O-O_R 0 2.15671100 1.07457400 2.44933100 L N-N_R 0 1.93014300 1.53029000 3.77701500 L O-O_R 0 2.93555800 1.59242600 4.41280300 L O-O_R 0 0.79684600 1.78423000 4.07716600 L C-C_3 0 0.19136700 0.48882200 -0.66957300 H H-H_ 0 0.48166000 0.17218300 -1.67320600 H H-H_ 0 -0.29178400 1.46621100 -0.72530700 H O-O_R 0 -0.70713000 -0.47190700 -0.09568100 H N-N_R 0 -1.89509300 -0.67769500 -0.84941300 H O-O_R 0 -2.01768400 -0.03471500 -1.85464300 H O-O_R 0 -2.61438000 -1.48554500 -0.35045700 H B 26 27 1.42187 S 70 0.05 From owner-chemistry@ccl.net Mon Mar 7 19:40:01 2011 From: "Cory Pye cpye++ap.smu.ca" To: CCL Subject: CCL: open source software for molecular graph Message-Id: <-44069-110306145858-15778-eBGWrtWFfCnIZ4g0r6TYDA.:.server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 6 Mar 2011 16:03:53 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye###ap.smu.ca] Hi, This code is easy to write. I did it as part of my Ph. D. project some years ago. See Equation 1 in C. C. Pye and R. A. Poirier, J. Comput. Chem., 19, 504 (1998). All you need are - the distance matrix d_ij - the atomic radii R_i^BS (we used Bragg-Slater radii) - scale factor lambda (we set this to 1.2). Basically, if the distance between the atoms is less than the sum of the Bragg-Slater radii times the scale factor, we assume the atoms are bonded and the adjacency matrix is 1, otherwise it is 0. Note that this will not tell you if you have a single, double, or triple bond. -Cory On Sun, 6 Mar 2011, Jinsong Zhao jszhao!A!yeah.net wrote: > > Sent to CCL by: Jinsong Zhao [jszhao^^^yeah.net] > Hi there, > > I hope to convert a molecular structure in XYZ format (or any other > format) to a graph or an adjacency matrix. I have to use a open source > software to do such conversion, however, I find nothing by google. > > Would please to give me a hand? Any suggestions or comments will be > really appreciated. > > Regards, > Jinsong > > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye[A]crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans)