From owner-chemistry@ccl.net Tue Dec 15 02:05:00 2009 From: "Tsung-Wen Yen peter308[]gmail.com" To: CCL Subject: CCL: Basis set choices for different components in bimetallic cluster... Message-Id: <-40916-091215015205-11061-uQQQypgINDId3jiHpJLVUw[a]server.ccl.net> X-Original-From: "Tsung-Wen Yen" Date: Tue, 15 Dec 2009 01:52:02 -0500 Sent to CCL by: "Tsung-Wen Yen" [peter308__gmail.com] Dear CCLers: Recently, I am working on bimetallic cluster DFT calculations. However, I am in some confusion lately. Take AgxCu38-x for an example, I compare the dimer results with experimental ones. And found out for Ag2 dimer, The Model Core Potential basis set is closest to experimental datas(bond distances) ;However, for Cu2 dimer, the Relativistic Effective Core Potential(RECP) become closest. If I need to assign basis set in AgxCu38-x alloy cluster. Should I assign MCP for Ag and RECP for Cu? Or should I assign the same basis set for all the components? I am a little bit confused here since I am not sure if assigning different basis set for different components in a alloy cluster will cause me any trouble, such as SCF non-convergence problem or unreasonable simulation datas?I appreciated for your help or suggestions. Many thanks! Best Regards Tsung-Wen Yen From owner-chemistry@ccl.net Tue Dec 15 03:44:00 2009 From: "S. Bill s_bill36^yahoo.co.uk" To: CCL Subject: CCL: An Advice required Message-Id: <-40917-091215034300-9837-HpAarxX1s+5x3Snd3ApjBg..server.ccl.net> X-Original-From: "S. Bill" Date: Tue, 15 Dec 2009 03:42:56 -0500 Sent to CCL by: "S. Bill" [s_bill36(-)yahoo.co.uk] Dear CCL users I hope I can find an advice here. I have two qeustions: 1- For the following reaction: RCH2CH2OH ---> RCH=CH2 + H2O I wanna know which molecule is more stable (RCH2CH2OH or RCH=CH2). Sure, I couldn't compare their energies becuase they have different chemical formula. Also, there is a problem related to the number of molecules ( Reactants =1, Products =2) Could you direct me how I can test this simple reaction? 2- Atomization Energy for a molecule A2B, for example, is given by: A2B ---> 2A + B D(atomization) = 2 E(A) + E(B) - [E(A2B) + ZPE(A2B)] what is should I change if I am going to calcualte it at 298 Kelvin? where there is Thermal correction for atoms in this case Thanks in advance S. Bill From owner-chemistry@ccl.net Tue Dec 15 08:48:00 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim],[compchem.net" To: CCL Subject: CCL:G: zinc parameter for gaff in QM/MM(gaussian) Message-Id: <-40918-091214113452-8076-LTWGvo9v0EpuGEdDzMOg9g%a%server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=000e0cd70618a55b5c047ab2d902 Date: Mon, 14 Dec 2009 16:34:41 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim|,|compchem.net] --000e0cd70618a55b5c047ab2d902 Content-Type: text/plain; charset=ISO-8859-1 Dear Zhijan Here is the Zinc ion parameters; sigma= 1.70 and epsion=0.67 Sorry, due to the copyrights, I couldn't send you the original paper. I am working on Zinc ion, I found the implemented Zinc ion parameters in AMBER gives better results in MM simulation. But, you shouldn't care becuase you are running QM/MM in which Zinc ion will be involved in the QM part. Sincerely; M. Ibrahim On Mon, Dec 14, 2009 at 1:40 PM, Zhi Jian Xu zjxu.[*].mail.shcnc.ac.cn < owner-chemistry[*]ccl.net> wrote: > > Sent to CCL by: "Zhi Jian Xu" [zjxu{:}mail.shcnc.ac.cn] > Dear CCLers, > I need the zinc ion(Zn2+) parameters for gaff(generalized amber force > field) in QM/MM computation using gaussian. I find someone using the > parameters from : Stote, R. H. and M. Karplus (1995). "Zinc binding in > proteins and solution: a simple but accurate nonbonded representation." > Proteins 23(1): 12-31. Howerver, I did not have the permission to download > the full text. So I am very appreciate for who could provide the parameters > or the full txt. > Thanks in advance! > > XU Zhijian> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim[*]compchem.net Website: www.compchem.net Fax No.: +20862342601 --000e0cd70618a55b5c047ab2d902 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Zhijan
Here is the Zinc ion parameters; sigma=3D 1.70 and epsion=3D= 0.67
Sorry, due to the copyrights, I couldn't send you the original = paper.
I am working on Zinc ion, I found the implemented Zinc ion parameters in AMBER gives better results in MM simulation. But, you shouldn't care becuase you are running QM/MM in which Zinc ion will be involved in the QM part.
Sincerely;
M. Ibrahim

On Mon, Dec 14, = 2009 at 1:40 PM, Zhi Jian Xu zjxu.[*].mai= l.shcnc.ac.cn <owner-chemistry[*]ccl.net> wrote:

Sent to CCL by: "Zhi Jian Xu" [zjxu{:}mail.shcnc.ac.cn]
Dear CCLers,
I need the zinc ion(Zn2+) parameters for gaff(generalized amber force field= ) in QM/MM computation using gaussian. I find someone using the parameters = > from : Stote, R. H. and M. Karplus (1995). "Zinc binding in proteins a= nd solution: a simple but accurate nonbonded representation." Proteins= 23(1): 12-31. Howerver, I did not have the permission to download the full= text. So I am very appreciate for who could provide the parameters or the = full txt.
Thanks in advance!

XU Zhijian



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=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
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=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim[*]compche= m.net
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--000e0cd70618a55b5c047ab2d902-- From owner-chemistry@ccl.net Tue Dec 15 10:33:01 2009 From: "brenec-,-rpi.edu" To: CCL Subject: CCL: c++ utility to access pubchem soap interface Message-Id: <-40919-091215080601-28636-LT4yUGJDIkR05ykvq1/dug]![server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Tue, 15 Dec 2009 04:34:18 -0800 (PST) Mime-Version: 1.0 Sent to CCL by: [brenec^-^rpi.edu] Dear Rajarshi, We'll be glad to host it here at RPI on our RECCR website. Cheers, Curt Breneman RPI Chemistry Director, RECCR Center -----Original Message----- > From: "Rajarshi Guha rajarshi.guha**gmail.com" Subj: CCL: c++ utility to access pubchem soap interface Date: Mon Dec 14, 2009 11:01 pm Size: 1K To: "Breneman, Curt " Sent to CCL by: Rajarshi Guha [rajarshi.guha*gmail.com] On Dec 14, 2009, at 3:35 PM, Igor Filippov Contr igorf+*+helix.nih.gov wrote: > > Sent to CCL by: "Igor Filippov [Contr]" [igorf- -helix.nih.gov] > Dear Colleagues, > > I have written a C++ utility to retrieve structures from Pubchem > using > PUG-SOAP interface based on similarity. It can be easily adapted to > access other functions provided by PUG-SOAP. > Is there anybody interested to have this source code and where would > be > the best place to host it? I have contacted Pubchem with the hopes to > have my code included on > http://pubchem.ncbi.nlm.nih.gov/pug_soap/client_help.html > but have not got a reply so far. GitHub (https://github.com/) would be a nice place to host it ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Bus error -- driver executed.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Dec 15 11:08:00 2009 From: "Chunhui Li baotogo2004[*]gmail.com" To: CCL Subject: CCL: help with liquid density prediction Message-Id: <-40920-091215105552-15013-CHX/7O48sygNDgN7PGo5Bg-$-server.ccl.net> X-Original-From: "Chunhui Li" Date: Tue, 15 Dec 2009 10:55:48 -0500 Sent to CCL by: "Chunhui Li" [baotogo2004]-[gmail.com] Dear All, I am trying to predict density for pure organic liquids. I wonder what software (Prefer free) are available for quick and hopefully reliable predictions. Information on review papers are also highly appreciated! Thanks in advance! Lily From owner-chemistry@ccl.net Tue Dec 15 17:08:01 2009 From: "Roy Green powergreen%x%gmail.com" To: CCL Subject: CCL: TopMod Message-Id: <-40921-091215170502-30258-VufT4urpfczE+bnKnxD02w.@.server.ccl.net> X-Original-From: Roy Green Content-Type: multipart/alternative; boundary=00c09f89965f45142f047acb9459 Date: Tue, 15 Dec 2009 17:04:51 -0500 MIME-Version: 1.0 Sent to CCL by: Roy Green [powergreen _ gmail.com] --00c09f89965f45142f047acb9459 Content-Type: text/plain; charset=ISO-8859-1 Hi, Does anyone have experience on TopMod. Using the command "sbf_to_v5d ", I tried to generate v5d files with esyn.sbf files for visualization. But I keep get the following error: ...... vis5d -box 12.000 10.000 12.000 H2O_esyn.v5d do_us: off end of record apparent state: unit 1 named H2O_esyn.sbf lately reading sequential unformatted external IO Aborted Could you help me figure out the problem. Thank you. Roy --00c09f89965f45142f047acb9459 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

Does anyone have experience on TopMod. Using the command "s= bf_to_v5d ",=A0 I tried to generate v5d files with esyn.sbf files for = visualization.=A0 But I keep get the following error:
=A0
......
= =A0 vis5d -box=A0=A0 12.000=A0 10.000=A0 12.000=A0 H2O_esyn.v5d=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0
do_us: off end of record
apparent state: unit 1 named H2O_esyn.sbf
la= tely reading sequential unformatted external IO
Aborted

Could you= help me figure out the problem. Thank you.

Roy

--00c09f89965f45142f047acb9459--