From owner-chemistry@ccl.net Tue May 5 00:48:00 2009 From: "Alan Shusterman alan%reed.edu" To: CCL Subject: CCL: NBO interpretation Message-Id: <-39229-090502194343-4109-TKJUA1UeCFFtb7agft0p7g]![server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 02 May 2009 15:59:56 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan%reed.edu] These exponents actually make good sense. The %p character in each hybrid orbital is 100n/(1+n) where n is the exponent on the p orbital. So n = 7.68 implies a hybrid orbital with very high p character. Alan Lydia Rhyman lyd_rhyman#%#hotmail.co.uk wrote: > Sent to CCL by: "Lydia Rhyman" [lyd_rhyman:_:hotmail.co.uk] > Dear CCL Users > > In one of the NBO results, for a P-S bond in a molecule, > I got sigma P-S = 0.612 (sp7.68)P + 0.791 (sp7.29)S > I cannot understand the meaning of p power 7.68 and p power 7.29. > Any help or suitable reference to understand NBO? > > Many thanks. > > L. Rhyman> > > > From owner-chemistry@ccl.net Tue May 5 02:00:01 2009 From: "Ben Roberts roberts%a%qtp.ufl.edu" To: CCL Subject: CCL:G: Gaussian 03 PCM panic Message-Id: <-39230-090504192858-7483-LTWGvo9v0EpuGEdDzMOg9g^-^server.ccl.net> X-Original-From: Ben Roberts Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Mon, 04 May 2009 18:59:00 -0400 Mime-version: 1.0 Sent to CCL by: Ben Roberts [roberts#qtp.ufl.edu] Hi all, I'm hoping someone on this list has seen this and can point me in the right direction... I'm trying to optimise a bimolecular transition state, and I'm modelling water using the Merz-Kollman PCM model (since proton transfer may be involved, I'm keen to model hydrogens using an all-atom approach). It starts off OK, but eventually Gaussian experiences a heart attack. I get a log file that ends like this: -------------------------------------------------------------------------- GePol: Number of tesserae being generated = 1936 GePol: Average area of tesserae = 0.06 Ang**2 GePol: Minimum area of tessera = 0.10D-02 Ang**2 GePol: Maximum area of tessera = 0.30518 Ang**2 GePol: Number of small tesserae = 0 GePol: Fraction of small tesserae (<1% of avg) = 0.00% GePol: Total count of vertices = 8817 GePol: Maximum number of vertices in a tessera = 10 GePol: Cavity surface area = 109.925 Ang**2 GePol: Cavity volume = 72.325 Ang**3 GePol: Maximum number of non-zero 1st derivatives = 990 That is, I get no error message, no nothing. Gaussian just stops. I think it's in link 301 at the time. STDERR and STDOUT also say nothing relevant. (I'm running using a queueing system, but I don't think that should make any real difference.) Can anyone tell me what settings I should try tweaking to get this to work? I suspect the problem may be that my system is breaking up and that the PCM doesn't like that. Does that sound plausible, though, and is there something worth trying to "make it work"? Thanks in advance, Ben -- Benjamin P. Roberts Postdoctoral Research Associate Quantum Theory Project University of Florida 2301 New Physics Building #92 PO Box 118435 Gainesville FL 32611-8435 USA Phone: +1 352 392 6712 Cell: +1 352 222 3677 Member of the Royal Australian Chemical Institute and of the American Chemical Society From owner-chemistry@ccl.net Tue May 5 03:33:00 2009 From: "Pau Farras pfarras+*+icmab.es" To: CCL Subject: CCL: Bond energies Message-Id: <-39231-090505033035-10430-0a0KgP9izcdPkNvSEiDMhg:-:server.ccl.net> X-Original-From: "Pau Farras" Date: Tue, 5 May 2009 03:30:31 -0400 Sent to CCL by: "Pau Farras" [pfarras-.-icmab.es] Hi! I'm doing an NBO analysis and I've found some nice interactions between Co-P and Co-S. Now that I have these values I'd like to compare with the energy of those bonds in orderto have an idea of how strong are the interactions. Does anybody know where I can find the energy of Co-P and Co-S bonds, I mean...just an average value to have an idea. thanks a lot! From owner-chemistry@ccl.net Tue May 5 04:49:00 2009 From: "John Simmie john.simmie .. nuigalway.ie" To: CCL Subject: CCL: Query on Co-P and Co-S bond energies Message-Id: <-39232-090505044356-7948-W/XDt2QhANvMs54im7plXw*_*server.ccl.net> X-Original-From: "John Simmie" Date: Tue, 5 May 2009 04:43:51 -0400 Sent to CCL by: "John Simmie" [john.simmie%%nuigalway.ie] Try "Comprehensive Handbook of Chemical Bond Energies" by Yu-Ran Luo he gives Co-S as 331 kJ/mol based on a 1972 review by Smoes et al. in J Bull Sco Chim Belg 81, 45-56. John Simmie//john.simmie]-[nuigalway.ie//National University of Ireland, Galway From owner-chemistry@ccl.net Tue May 5 07:58:00 2009 From: "Farhan Pasha pashafa^yahoo.co.in" To: CCL Subject: CCL: Boiling temperature data Message-Id: <-39233-090505061628-9353-hTitDK8LdE2528rtmp+xtg/a\server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="0-1353488395-1241518574=:68811" Date: Tue, 5 May 2009 15:46:14 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa . yahoo.co.in] --0-1353488395-1241518574=:68811 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello See this link and additional data you can ask to author or to me Correspondence Address =0ADr. Syed Farhan Ahmad Pasha =0ARoom No. 5202 =0AInstitut de Biologie Structurale =0ALaboratoire de Dynamique Moleculaire =0A41 rue Jules Horowitz =0A38027 Grenoble cedex =0AFrance =0Atel : (+33) (0)4 38 78 99 28 =0Afax : (+33) (0)4 38 78 54 94 =0Afpasha]^[rediffmail.com =0AURL:www.geocities.com/pashafa =0Awww.ibs.fr --- On Mon, 4/5/09, IOANA OPRISIU ioana.oprisiu+/-ulp.u-strasbg.fr wrote: > From: IOANA OPRISIU ioana.oprisiu+/-ulp.u-strasbg.fr Subject: CCL: Boiling temperature data To: "Pasha, Frahan Ahmad " Date: Monday, 4 May, 2009, 9:03 PM Sent to CCL by: "IOANA=A0 OPRISIU" [ioana.oprisiu]=3D[ulp.u-strasbg.fr] Hello, I'm looking for data sets (desirable SDF format or smiles) containing norma= l boiling temperature, in order to develop QSPR models using ISIDA descript= ors. Thank you in advance. IOANA OPRISIU PhD. Student in Chemoinformatics -=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 Now surf faster and smarter ! Check out the new Firefox 3 - = Yahoo! Edition http://downloads.yahoo.com/in/firefox/?fr=3Dom_email_firefox --0-1353488395-1241518574=:68811 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello

See this link and additional dat= a you can ask to author or to me

Correspondence Address
=0ADr. Sy= ed Farhan Ahmad Pasha
=0ARoom No. 5202
=0AInstitut de Biologie Struct= urale
=0ALaboratoire de Dynamique Moleculaire
=0A41 rue Jules Horowit= z
=0A38027 Grenoble cedex
=0AFrance
=0Atel : (+33) (0)4 38 78 99 2= 8
=0Afax : (+33) (0)4 38 78 54 94
=0Afpasha]^[rediffmail.com
=0AURL:= www.geocities.com/pashafa
=0Awww.ibs.fr

--- On Mon, 4/5/09, IO= ANA OPRISIU ioana.oprisiu+/-ulp.u-strasbg.fr <owner-chemistry]^[ccl.net= > wrote:

From: IOANA OPRISIU ioa= na.oprisiu+/-ulp.u-strasbg.fr <owner-chemistry]^[ccl.net>
Subject: C= CL: Boiling temperature data
To: "Pasha, Frahan Ahmad " <pash= afa]^[yahoo.co.in>
Date: Monday, 4 May, 2009, 9:03 PM


Sent to CCL by: "IOANA  OPRISIU" [ioana.oprisiu]=3D= [ulp.u-strasbg.fr]
Hello,

I'm looking for data sets (desirable SD= F format or smiles) containing normal boiling temperature, in order to deve= lop QSPR models using ISIDA descriptors.

Thank you in advance.
IOANA OPRISIU

PhD. Student in Chemoinformatics



-=3D= This is automatically added to each message by the mailing script =3D-
=
the strange characters on the top = line to the ]^[ sign. You can also
look up the X-Original-From: line in th= e mail header.

E-mail to subscribers: CHEMISTRY]^[ccl.net= or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl= _message

E-mail to administrators: CHEM= ISTRY-REQUEST]^[ccl.net or use
      http://www.ccl.= net/cgi-bin/ccl/send_ccl_message
&nbs= p;     http://www.ccl.net/chemistry/sub_unsub.shtml

Be= fore posting, check wait time at: http:= //www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://= server.ccl.net/chemistry/announcements/conferences/

Search Messa= ges: http://www.ccl.net/chemistry/searchccl/index.shtml

I= f your mail bounces from CCL with 5.7.1 error, check:
    &nbs= p; http://www= .ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/= aboutccl/instructions/


=
=0A
Bring your gang together. Do your t= hing. Find your favourite Yahoo! Group. --0-1353488395-1241518574=:68811-- From owner-chemistry@ccl.net Tue May 5 08:46:00 2009 From: "V ronique LEGRAND vflegrand++free.fr" To: CCL Subject: CCL: implicit solvent Message-Id: <-39234-090505084231-9130-okD5Yr3S8UJDuB29pcPWNQ(a)server.ccl.net> X-Original-From: "V ronique LEGRAND" Date: Tue, 5 May 2009 08:42:27 -0400 Sent to CCL by: "V ronique LEGRAND" [vflegrand#,#free.fr] Hello every body, I would like only a confirmation. I want to perform an optimization on a radical molecule in an implicit solvent. Is it possible to use an open shell method in this context? I wrote my input as following, but I have a doubt. #P UB3LYP/6-31+G(d,p) GFInput Opt=GDIIS SCF=Tight SCRF=(PCM,Solvent=water) maxdisk=100000000 GFPrint Test Thanks for your opinion, and all precision. Veronique LEGRAND From owner-chemistry@ccl.net Tue May 5 09:21:01 2009 From: "Kunal Roy kroy(0)pharma.jdvu.ac.in" To: CCL Subject: CCL: New Open Access Article on Validation of QSAR Models Message-Id: <-39235-090505033124-10507-zwkDwrlmTdzbO2VyndkGsA**server.ccl.net> X-Original-From: "Kunal Roy" Date: Tue, 5 May 2009 03:31:21 -0400 Sent to CCL by: "Kunal Roy" [kroy-,-pharma.jdvu.ac.in] *****************Apology for multiple posting***************** New Open Access Article on Validation of QSAR Models: Open Access Partha Pratim Roy , Somnath Paul , Indrani Mitra and Kunal Roy * Article: On Two Novel Parameters for Validation of Predictive QSAR Models Molecules 2009, 14(5), 1660-1701; doi:10.3390/molecules14051660 The article is freely downloadable from http://www.mdpi.com/1420-3049/14/5/1660 From owner-chemistry@ccl.net Tue May 5 13:25:00 2009 From: "Gustavo Seabra gustavo.seabra*o*gmail.com" To: CCL Subject: CCL:G: QM/MM and copper Message-Id: <-39236-090505131255-8985-QZj2CAHtZ3QKbWW4Mo7tqQ\a/server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 5 May 2009 13:12:41 -0400 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra~~gmail.com] On Mon, May 4, 2009 at 6:26 PM, Syed Tarique Moin tarisyed^_^yahoo.com wrote: > > Sent to CCL by: "Syed Tarique Moin" [tarisyed-$-yahoo.com] > Dear CCl users, > > I am trying to simulate the copper containing metalloprotein. For the QM/= MM, i am using the hybrid software method incorporating Gaussian as the QM = source and Amber as a MM using pupil package interface. Can anybody tell me= free package other than pupil for interfacing these two programs and the g= ood basis set for the copper (II) coordinated with amino acids. > > Regards Hi Syed, I'm not sure there is another free program to do what you want. Is there a specific reason you can't use PUPIL for it? Gustavo. From owner-chemistry@ccl.net Tue May 5 23:10:00 2009 From: "neeraj misra neerajmisra!=!hotmail.com" To: CCL Subject: CCL: docking Message-Id: <-39237-090505230905-30286-HBLL7+//jZ2YwdhvhA0L0A[#]server.ccl.net> X-Original-From: "neeraj misra" Date: Tue, 5 May 2009 23:09:01 -0400 Sent to CCL by: "neeraj misra" [neerajmisra[-]hotmail.com] PLEASE SUGGEST SOME GOOD PACKAGE FOR DOCKING STUDIES AND MD SIMULATION.