From owner-chemistry@ccl.net Sun Nov 15 01:10:01 2009 From: "Alan Shusterman alan|a|reed.edu" To: CCL Subject: CCL: Electrostatic potential surface from NBO Message-Id: <-40681-091112191125-4534-0X5ofbA/di9P722Br2ihdw:+:server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 12 Nov 2009 15:39:54 -0800 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan##reed.edu] I'm not familiar with any methods for NBO charges -> electrostatic potential surfaces, but it could be a pointless exercise anyway. The NBO atomic charges are not based on a point-charge (or spherical atom) model. The electron distribution around many atoms is asymmetric, and if you convert that asymmetric distribution into an atomic "charge" and then use this charge to generate an electrostatic potential surface, the original asymmetry will disappear. If your goal is to link electrostatic potentials and charges, it makes more sense to calculate the charges from the potential distribution, and then use these charges to generate surfaces. Alan Shusterman David Eisenberg david.eisen(0)gmail.com wrote: > Sent to CCL by: "David Eisenberg" [david.eisen]![gmail.com] > Dear CCL community, > > Is there a way of displaying an electrostatic potential surface of a molecule, > based on a NBO charge distribution calculation? > > I have Chem3D and Molekel, and NBO 5.0. > > Thanks, > David Eisenberg > Jerusalem> > > > From owner-chemistry@ccl.net Sun Nov 15 03:17:00 2009 From: "Vladimir Chupakhin chupvl]|[gmail.com" To: CCL Subject: CCL: remove salts from compounds Message-Id: <-40682-091112025452-4344-NMxiVRLpZY/HlHUeri0fdw**server.ccl.net> X-Original-From: Vladimir Chupakhin Content-Type: multipart/alternative; boundary="------------010108040403000303010907" Date: Thu, 12 Nov 2009 10:28:19 +0300 MIME-Version: 1.0 Sent to CCL by: Vladimir Chupakhin [chupvl{:}gmail.com] This is a multi-part message in MIME format. --------------010108040403000303010907 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hello, most of the salt stripping software working by removing all except the biggest one fragment. Yes, it's work in the most of the cases but there some that dosen't fit: organometalic, ferracens, etc. I was looking for software that strip "normal" salts but not removing e.g. metals from heme. I can make make my own rules but it's really time consuming for large database where number of "problem" salts is around 2%. Any ideas? Yours, Vladimir Chupakhin, Moscow State University, Moscow, Russia aa aa,+,chemaxon.hu wrote: > HI amit, > > ChemAxon Standardizer will do this. It is not free but is free (as are > all tools) for academic research. See this page > for more info and > how to download. This page > for free academic > package signup. > > Cheers > Alex > > PS - heads up on improvements on Standardizer in JChem 5.3 (due out v > soon), we are introducing checking/fixing/conversion notification > capabilities for structure files. 5.3 will be MarvinSketch only but > will be formally a part of Standardizer soon after. > > > amit dong dongamit123a/gmail.com wrote: >> Hi, >> >> Is there any free tool that can be used for removing ions/salts > >> from a large library of compounds? >> >> Thanks >> AD --------------010108040403000303010907 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello,

most of the salt stripping software working by removing all except the biggest one fragment. Yes, it's work in the most of the cases but there some that dosen't fit: organometalic, ferracens, etc. I was looking for software that strip "normal" salts but not removing e.g. metals from heme. I can make make my own rules but it's really time consuming for large database where number of "problem" salts is around 2%. Any ideas?

Yours,
Vladimir Chupakhin,
Moscow State University,
Moscow, Russia

aa aa,+,chemaxon.hu wrote:

HI amit,

ChemAxon Standardizer will do this. It is not free but is free (as are all tools) for academic research. See this page for more info and how to download. This page for free academic package signup.

Cheers
Alex

PS - heads up on improvements on Standardizer in JChem 5.3 (due out v soon), we are introducing checking/fixing/conversion notification capabilities for structure files. 5.3 will be MarvinSketch only but will be formally a part of Standardizer soon after.

amit dong dongamit123a/gmail.com wrote:

Hi,

Is there any free tool that can be used for removing ions/salts > from a large library of compounds?

Thanks

AD

--------------010108040403000303010907-- From owner-chemistry@ccl.net Sun Nov 15 08:04:01 2009 From: "xunlei ding dingxunlei^gmail.com" To: CCL Subject: CCL: GVIEW Message-Id: <-40683-091114202611-28719-3hQ1sqbLGWEkS64JajNzDQ,server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Sun, 15 Nov 2009 08:00:21 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei^^gmail.com] Hi, Try use the "Results-surfaces-...." Menu to generate the image. 2009/11/12 neeraj misra neerajmisra.:.hotmail.com = : > > Sent to CCL by: "neeraj misra" [neerajmisra|,|hotmail.com] > HOW TO SAVE THE IMAGE OF HOMO-LUMO FROM GAUSSVIEW? > --=20 ------------------------------------------------------ Xun-Lei Ding (=B6=A1=D1=B8=C0=D7) Associate Research Professor of Physical Chemistry, Ph.D State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China Phone 86-10-62568330 Fax 86-10-62559373 From owner-chemistry@ccl.net Sun Nov 15 08:43:00 2009 From: "Morad El-Hendawy M80elhendawy|a|yahoo.com" To: CCL Subject: CCL:G: Mechanical and Electronic Embeddings Message-Id: <-40684-091115084011-15391-PSxqBoH1970LiaAhDeZ3Ng=-=server.ccl.net> X-Original-From: "Morad El-Hendawy" Date: Sun, 15 Nov 2009 08:40:08 -0500 Sent to CCL by: "Morad El-Hendawy" [M80elhendawy##yahoo.com] Hey every body! During my perusal to ONIOM pages on Gaussian website, http://www.gaussian.com/g_tech/g_ur/k_oniom.htm, I found this statement: "For both minima and transition structures, it is usually more efficient to first optimize using mechanical embedding and then perform a second optimization with electronic embedding starting from the resulting structure (rather than trying to use electronic embedding from the beginning)" I wonder if an expertise body tells us why it is preferred to start with mechanical embedding then electronic embedding? Detailed answer with evidences (i.e. published papers)is preferred and more appreciated. Thanks a mil Morad El-Hendawy Ireland From owner-chemistry@ccl.net Sun Nov 15 10:35:00 2009 From: "Mikael Johansson mikael.johansson*o*helsinki.fi" To: CCL Subject: CCL:G: Energy for Gold Atom Message-Id: <-40685-091115102551-26788-K86XYclLLZxzgwf7J45b0Q%server.ccl.net> X-Original-From: Mikael Johansson Content-ID: Content-Type: MULTIPART/MIXED; BOUNDARY="-696237619-1113322278-1258297034=:24918" Date: Sun, 15 Nov 2009 17:25:34 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson-.-helsinki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696237619-1113322278-1258297034=:24918 Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-15; FORMAT=flowed Content-Transfer-Encoding: 8BIT Content-ID: Hello Delwar and All! On Fri, 13 Nov 2009, Delwar Hossain hossaind2004]|[yahoo.com wrote: > I calculated the energy foe Gold atom using TPSS/LanL2DZ and > TPSS/LanL2TZ(f) basis set and G03 programm. The values are -135.3423862 > a.u.(LanL2DZ) and -132.569903 a.u.(LanL2TZ(f)), respectively. I also > check the energy of the other transition metal atoms. It looks to me for > Gold atom, LanL2TZ(f) basis basis set under estimate energy so high > that I am suspious these value. Please send your comments > and suggestions. There's something wrong in your LANL2TZ(f) calculation. With the same ECP, a larger basis set should give you a lower energy, unless the larger basis set is really badly constructed. With Turbomole, I get the following energies (basis sets from EMSL basis set exchange): LANL2DZ: -135.34239 LANL2TZ(f): -135.34791 So check your "TZ" calculation to be sure it hasn't converged to the wrong state (or converged at all). On a more general note, I'd like to point out that LANL2DZ is much too small a basis set for gold interactions (like almost any other DZ basis is). The LANL2TZ(f) isn't much better, it's just a decontracted LANL2DZ basis with one f-function added. For DFT calculations on the heavy metals, like Au, I recommend the Karlsruhe "def2" basis sets (the older "def" basis sets are not that good!) As an example, a small table on the geometry of SeAu2, computed at TPSS level with different basis sets. It's from (the supporting info of) PRA 77 (2008) 053202, http://dx.doi.org/10.1103/PhysRevA.77.053202 r(Au--Au) r(Au--Se) angle(Au-Se-Au) LANL2DZ 324.2 235.7 86.9 LANL2TZ(f) 327.5 234.7 88.5 def2-SVP 325.1 236.2 87.0 def2-TZVPP 311.9 235.6 82.9 7s5p3d1f 303.6 236.2 80.0 def2-QZVPP 305.2 235.4 80.8 aug-cc-pVQZ 301.5 235.1 79.8 ---- MP2 282.8 231.8 75.2 CCSD 312.5 235.1 83.3 CCSD(T) 299.4 235.2 79.1 Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ ---696237619-1113322278-1258297034=:24918-- From owner-chemistry@ccl.net Sun Nov 15 12:34:00 2009 From: "Jacopo Sgrignani sgrigna]^[gmail.com" To: CCL Subject: CCL: dicopper Message-Id: <-40686-091111053531-9649-nI48yTErbUYtcbcbbuPJcQ..server.ccl.net> X-Original-From: Jacopo Sgrignani Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 11 Nov 2009 11:03:53 +0100 MIME-Version: 1.0 Sent to CCL by: Jacopo Sgrignani [sgrigna.:.gmail.com] Hi 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? Thanks a lot Jacopo From owner-chemistry@ccl.net Sun Nov 15 16:07:00 2009 From: "Basma Ghazal basmaghazal::ymail.com" To: CCL Subject: CCL: Autodock Message-Id: <-40687-091115160511-19194-iuhTQn2FpfQCL0g+OMqxjw^_^server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-1881779462-1258319094=:88815" Date: Sun, 15 Nov 2009 13:04:54 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal^ymail.com] --0-1881779462-1258319094=:88815 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi,=0AI work on enzyme has a known active site structure, The docking proce= ss take place by a 2 step mechanism First, the ligand will optimized on the= active site then on a second step it make a covalent bond with the hydroxy= l group of one of the amino acid.=0AI will use autodock for docking and I h= ave some things need explanation:=0AOn Running AutoGrid:=0AGrid=E2=86=92Gri= dBox.=0AI need to know the meaning of the Options in the (Center) menu =0AA= nd What is the most suitable option for my case?=0ADoes the Option Grid=E2= =86=92SetMapType=E2=86=92SetUp CovalentMap is suitable for the formation of= a covalent bond?=0AI would appreciate your suggestions, =0A=0A=0A --0-1881779462-1258319094=:88815 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

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=0A=0A --0-1881779462-1258319094=:88815-- From owner-chemistry@ccl.net Sun Nov 15 21:04:00 2009 From: "fatsi k. fatsouk fatsi.fatso,+,gmail.com" To: CCL Subject: CCL: durand-Barthelat large-core ECP for Ti Message-Id: <-40688-091115142502-12218-mfwVfr0dZyhgCH49h2xAQA,+,server.ccl.net> X-Original-From: "fatsi k. fatsouk" Date: Sun, 15 Nov 2009 14:24:58 -0500 Sent to CCL by: "fatsi k. fatsouk" [fatsi.fatso~~gmail.com] Hi, Can anyone please give me the Durand-Barthelat large-core ECP for the titanium atom? I want to do some calculations on a large cluster. The aim is to the large-core ECP for Ti atoms far away from the adsorbate and all-electron basis sets for the Ti and O atoms near the adsorption site. I do not have access to the original papers and google isn't helping. Thanks.