From owner-chemistry@ccl.net Fri Nov 20 06:01:01 2009 From: "Mikael Johansson mikael.johansson:helsinki.fi" To: CCL Subject: CCL: dicopper Message-Id: <-40730-091120045717-5643-g8iCIXxTg7Rsgm+9z/6hTg{:}server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 20 Nov 2009 11:56:54 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson|,|helsinki.fi] Hello Jacopo! On Wed, 11 Nov 2009, Jacopo Sgrignani sgrigna]^[gmail.com wrote: > i would like to perform a simulation (classic MD) of a dicopper > protein (two copper atoms in the same binding site). > Actually i did't find any examples of force fields for dicopper > proteins in the literature, could anybody suggest me any examples? In the following article, charges for the dicopper CuA centre in CcO were parameterized, so perhaps it helps a bit: http://dx.doi.org/10.1002/jcc.20835 The supporting info for the article (now) contains CHARMM topology files, to get you started: http://www.chem.helsinki.fi/Research/supplements/2008-MPJ-VRIK-LL/ I don't have any personal experience for how good the rest of the parameters are, however. And of course, if the system you are looking at is very different from CuA, the charges won't help either. Perhaps someone else on the list can give further advice. Have a good weekend, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Fri Nov 20 08:46:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982-x-yahoo.com" To: CCL Subject: CCL:G: Gaussian 03 + Exceeded Z-Matrix Message-Id: <-40731-091119133035-32571-dR2HXvC7Tru17AJ86AI1rA|-|server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-107456217-1258655423=:48600" Date: Thu, 19 Nov 2009 10:30:23 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982*o*yahoo.com] --0-107456217-1258655423=:48600 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Morad A simple way is to build your system in Cartisian coordinates. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim+/-compchem.net Email: m.ibrahim1982+/-yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Thu, 11/19/09, Morad El-Hendawy m80elhendawy~!~yahoo.com wrote: > From: Morad El-Hendawy m80elhendawy~!~yahoo.com Subject: CCL:G: Gaussian 03 + Exceeded Z-Matrix To: "Ibrahim, Mahmoud A. A. " Date: Thursday, November 19, 2009, 4:24 PM Hey every body, I got the following error when I submit an input file for protien of about = 27000 atoms in order to do AMBER94 calculation using Gaussian 03: "The maximum of 20000 Z-matrix cards has been exceeded Error termination via Lnk1e in C:\G03W\l101.exe" I guess that this error due to exceeding Z-matrix more than 20000 atoms. Is= there a keyword=A0 to solve this problem. Best regards, ***************************************************************************= ***********************Morad M. El-HendawyIreland ***************************************************************************= ***********************=A0If you want a happy life, do four things:=A01- Co= ntemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** =0A=0A=0A=0A =0A=0A=0A --0-107456217-1258655423=:48600 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Morad
A simple way is to build your s= ystem in Cartisian coordinates.
Sincerely;
M. Ibrahim

Mahmoud A. A. Ibrahim
<= /span>
Current Address
=
School of Chemi= stry, University of Manchester,
Oxford Road, Manchester, M13 9PL, Unite= d Kingdom.

Home Address

Contact Infor= mation
Email: m.ibrahim+/-compchem.net
Email: m.ibrahim1982+/-yaho= o.com
Website: www.compchem.net
Fax No.: +20862342601
=


--- On Thu, 11/19/09, Morad El-Hendawy m80e= lhendawy~!~yahoo.com <owner-chemistry+/-ccl.net> wrote:
<= blockquote style=3D"border-left: 2px solid rgb(16, 16, 255); margin-left: 5= px; padding-left: 5px;">
From: Morad El-Hendawy m80elhendawy~!~yahoo.com= <owner-chemistry+/-ccl.net>
Subject: CCL:G: Gaussian 03 + Exceeded = Z-Matrix
To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982+/-yahoo.c= om>
Date: Thursday, November 19, 2009, 4:24 PM

Hey every body,
I got the following error when I submit an= input file for protien of about 27000 atoms in order to do AMBER94 calcula= tion using Gaussian 03:

"The maximum of 20000 Z-matrix cards has been exceeded<= /span>
Error termination = via Lnk1e in C:\G03W\l101.exe"

I guess that this error due to exceeding Z-matr= ix more than 20000 atoms. Is there a keyword  to solve this problem.Best regards,
********************************************************************= ******************************
Morad M. El-Hendawy
Ireland
***= ***************************************************************************= ********************
  
1- Contemplate and be thankful,
2- The past is gone forever,
3- Today all= that you have,
4- Leave the future alone until it come. 
*****************= ***************************************************************************= ***********************
3D""

=0A=0A=0A=0A

=0A=0A=0A=0A --0-107456217-1258655423=:48600-- From owner-chemistry@ccl.net Fri Nov 20 09:42:00 2009 From: "kamel mansouri kamel_mansouri_+_yahoo.fr" To: CCL Subject: CCL: Looking for a job Message-Id: <-40732-091120093305-1516-0tFPSyCEWmCOfjLiq9O69g ~ server.ccl.net> X-Original-From: "kamel mansouri" Date: Fri, 20 Nov 2009 09:33:02 -0500 Sent to CCL by: "kamel mansouri" [kamel_mansouri(0)yahoo.fr] I hereby wish to state my interest for an engineer place or PhD position in chemistry / computational chemistry. I am convinced that this job corresponds well with my future plans of seeking a career in an international company. It is my dream and ambition to be admitted to use my post-graduate studies in the field of chemical engineering and computer science in order to develop a career that leads to working across the world and I am willing to relocate worldwide. My educational background is quite diverse. I spent three years at the University of Tunis, and have successfully finished my engineering studies in analytical chemistry and instrumentation. And a master degree in chemoinformatics in the university of Louis Pasteur Strasbourg. My choices of majors reflected the diversity of my interests; chemistry and computer sciences. My studies have guided me through systematic researching, analytical thinking and information evaluation and that is what I do best. I am of the opinion that any academic knowledge gained should be applied and utilized through work experience. Therefore I would like to mention that during my undergraduate studies I had the opportunity to practice and complement my knowledge by making internships in different fields such as medical analysis, food industry and petrol production. I did an internship at CEA Saclay to develop a method for generation and virtual screening of conformers of CYP3A4 substrates, I used its successful results to participate by poster in the national meeting of cheminformatics (24-25 june 2009) and submit a paper to an appropriate scientific journal. In addition to my knowledge of analytical chemistry , I acquired new skills of computational chemistry and drug design such as: : Docking, QSAR/QSPR, Data mining, Clustering, Virtual screening, Molecular Modeling, Quantics; Used some softwares: MOE, Sybyl, Fred, AutoDock, Weka, Isida, Spartan, Macromodel, Schrdinger; I have advanced programming skills: : C, C++, HTML, CSS, DHTML, XML/XSL, MySQL, PHP, Java, PHP-MySQL, JavaScript, FORTRAN, Maple, Mathematica I believe that the combination of my past experiences and academic knowledge will qualify me as a good engineer, and furthermore will prepare me to achieve my career goals in the future and I can be sure that this work will equip me with the necessary skills to continue to acquire new knowledge and understanding throughout my entire working life, and I will have the perfect opportunity to excel at it. Thank you for your help. Sincerely yours, Kamel Mansouri From owner-chemistry@ccl.net Fri Nov 20 10:41:00 2009 From: "M. Carmen Ruiz Delgado maycaruiz],[hotmail.com" To: CCL Subject: CCL:G: Two questions about ONIOM calculations: Gaussian03 vs Gaussian09 Message-Id: <-40733-091118221706-16037-vd1t+Wd/C4A0HNs4pt47uA]^[server.ccl.net> X-Original-From: "M. Carmen Ruiz Delgado" Date: Wed, 18 Nov 2009 22:17:02 -0500 Sent to CCL by: "M. Carmen Ruiz Delgado" [maycaruiz+/-hotmail.com] Dear all, I would like to ask you two questions about ONIOM calculations in Gaussian: (1) I would like to use electronic embedding for a three-layer ONIOM calculation. In the gaussian manual it looks like this is possible, however, my calculation crashed with this final message: Rotational constants (GHZ): 0.0067026 0.0043168 0.0027992 Leave Link 202 at Wed Nov 18 11:26:54 2009, MaxMem= 117964800 cpu: 0.1 (Enter /export/apps/g03/l120.exe) Electronic embedding only for two layers Error termination via Lnk1e in /export/apps/g03/l120.exe at Wed Nov 18 11:26:55 2009. Job cpu time: 0 days 0 hours 0 minutes 20.7 seconds. Here, it goes the keywords of my input file (in case someone could give me some advice): #p oniom(b3lyp/6-31+g*:AM1:uff=qeq)=EmbedCharge scf=(maxcyc=500,tight) # pop=chelpg nosym (2) For a two-layer oniom calculation, I have specified a type and a charge for the atoms in the high level region and I want to assign QEq charges for all atoms which have charge zero or were untyped. For that purpose, I have used the UnCharged keyword in the molecule specification input using the EmbedCharged scheme.I got an error when using gaussian09 while exactly the same input finishes successfully in Gaussian03. These are the keywords of my input file: #p oniom(b3lyp/6-31+g*:uff=uncharged)=embed scf=(maxcyc=500,tight) # pop=chelpg nosym This calculation is unsuccessfully completed in Gaussian 09, Revision A.02, although it was successfully finished using Gaussian03 (when using exactly the same input). However, if I do not specified any particular charges for the atoms in the high level region (using just the keyword Qeq), the calculation is completed. This is the error that appears in the oputput: NMagM= 0.0000000 0.0000000 2.7928460 2.7928460 2.7928460 2.7928460 Generating MM parameters. InvSVX failed for QEq1. Error termination via Lnk1e in /opt/g09/l101.exe at Mon Nov 2 16:47:03 2009. Job cpu time: 0 days 0 hours 0 minutes 0.5 seconds. I would really appreciate if someone could help me and give me some advice. Thank you so much in advance! Best regards, MCarmen. M. Carmen Ruiz Delgado, PhD School of Chemistry and Biochemistry Georgia Institute of Technology 901 Atlantic Dr NW MSE Building 2100 C Atlanta, GA 30332-0400 Phone: 404-385-8182 From owner-chemistry@ccl.net Fri Nov 20 11:39:00 2009 From: "rocky walden rocky.walden19/./gmail.com" To: CCL Subject: CCL: Needed help on testing the validation suite present in ccl.net webpages Message-Id: <-40734-091120111412-25169-7/BvtmUMduWwQW4IAfxbQg|a|server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=00151774149c3198ad0478cfc2d8 Date: Fri, 20 Nov 2009 21:43:38 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19[A]gmail.com] --00151774149c3198ad0478cfc2d8 Content-Type: text/plain; charset=ISO-8859-1 Dear All, Thank you very much in advance. I am very new to computational chemistry and also new to ccl.net webpages. I am very much impressed by the way the visitors posting queries and the others replying them. This made me to write a query for you all. In the ccl.net homepage there is a data called force field validation suite posted by Dr.Thomas Halgreen from Schrodinger. I am interested in testing them. As i am new to this field i ask any visitor can help me in the testing process like what are minimum system requirements to run the force fields jobs. what special applications are need . Can any on give me the way how to work on these force fields. Thanks Rocky --00151774149c3198ad0478cfc2d8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear All,
=A0
Thank you very much= in advance.

I am very new to computational chemistry and also new t= o ccl.net webpages. I am v= ery much impressed by the way the visitors posting queries and the others r= eplying them.
This made me to write a query for you all.

In the ccl.net homepage there is a data called forc= e field validation suite posted by Dr.Thomas Halgreen from Schrodinger.
I am interested in testing them. As i am new to this field i ask any visito= r can help me in the testing process like what are minimum system requireme= nts to run the force fields jobs. what special applications are need .
Can any on give me the way how to work on these force fields.


Th= anks
Rocky

--00151774149c3198ad0478cfc2d8-- From owner-chemistry@ccl.net Fri Nov 20 14:18:01 2009 From: "Mariusz Radon mariusz.radon(0)gmail.com" To: CCL Subject: CCL: Which program to optimize the crystal structure of transition metal complex? Message-Id: <-40735-091120141657-31960-rJ6uWjhxiWd+5G17dcRIog/a\server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=UTF-8 Date: Fri, 20 Nov 2009 19:25:01 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon]-[gmail.com] Dear Colleagues, I am looking for a program being able to optimize the crystal structure of transition metal complex (molecular structure and unit cell parameters) at DFT level. An important point is that I must be able to control the spin state of the complex, because I would like to perform such optimizations for different spin states in order to capture the influence of the spin state on the molecular structure and packing in the crystal. Could you recommend me any program capable to achieve this goal (preferably, but not necessarily free software)? Thank you in advance very much. Best regards, Mariusz Radon -- Mariusz Radon, PhD student Department of Theoretical Chemistry Jagiellonian University http://www.chemia.uj.edu.pl/~mradon mradon /at/ chemia.uj.edu.pl (PGP public key available on the website) From owner-chemistry@ccl.net Fri Nov 20 17:04:00 2009 From: "Michel Petitjean petitjean.chiral : gmail.com" To: CCL Subject: CCL: chemoinformatics / a nomenclature challenge Message-Id: <-40736-091120154107-2411-zFSMSXi5lueLT8kpUE89Cw]-[server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 20 Nov 2009 20:26:23 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral%x%gmail.com] Dear CCLers, Here is my challenge: assign a name to the [6.6]chiralane, C27H28. The connection table is available from http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html#CHIR If somebody has a programme running successfully on this small molecule, please tell me and send me the name: until now, nomenclature assignment programmes failed ! Furthermore, I would be delighted to know what name is generated from CAS or IUPAC rules. Many thanks. All my best, Michel Petitjean, CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean{=}cea.fr, petitjean.chiral{=}gmail.com (preferred) http://petitjeanmichel.free.fr/itoweb.petitjean.html