From owner-chemistry@ccl.net Thu Feb 22 05:46:01 2007 From: "Xunlei Ding dingxunlei_._gmail.com" To: CCL Subject: CCL:G: G03-Excessive mixing of frozen core and valence orbitals Message-Id: <-33675-070222044031-9414-MmidQXK+hcnisbdZze8wDg*|*server.ccl.net> X-Original-From: Xunlei Ding Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Feb 2007 10:19:17 +0100 MIME-Version: 1.0 Sent to CCL by: Xunlei Ding [dingxunlei * gmail.com] Dear David, Thank you for your help! Now I found that if it is calculated with "nosymm", everything will be ok. And this is the difference between using key words -Bq and Massage. So I think, for this system, the error is due to symmetry problem. When using symmetry, the calculation is totally wrong. Best regards! Ding Shobe, David David.Shobe*_*sud-chemie.com wrote: >Sent to CCL by: "Shobe, David" [David.Shobe|-|sud-chemie.com] >Ding, > >The Mulliken charges you see on H #7 and F #8 are related to the error message you got earlier. It just means that the basis functions on H #7 and F #8 are being occupied in the calculation. > >What bothers me is the charge of > +7 on F #4. This means that the valence orbitals on F #4 are NOT being used in the wave function!!! You might want to look at the electron density (if you have a suitable visuialization program) to see whether that is strange also. Do you get similar Mulliken charges in a HF calculation? What about other types of charges (NBO, CHELPG, etc.)? > >Regards, >--David Shobe > >-----Original Message----- > > >>From: owner-chemistry_-_ccl.net [mailto:owner-chemistry_-_ccl.net] >> >> >Sent: Tuesday, February 20, 2007 2:59 AM >To: Shobe, David >Subject: CCL:G: G03-Excessive mixing of frozen core and valence orbitals > > >Sent to CCL by: Xunlei Ding [dingxunlei:gmail.com] Dear David, > >Thank you very much for your clear explain and suggestions. > >If this work is done with mp2(fc)/6-311++G**, the error is the same: >" Largest valence mixing into a core orbital is 9.94D-01 Excessive mixing of frozen core and valence orbitals." > >And it finishes successfully with mp2=full, but the energy is very strange, and also the mulliken charge: > > Mulliken atomic charges: > 1 > 1 H -1.463786 > 2 F -0.398420 > 3 H -0.625697 > 4 F 7.487903 > 5 H -1.463786 > 6 F -0.398420 > 7 H -1.625697 > 8 F -1.512097 > >Also mp2(full)/6-311++G** gives strange energy and mulliken charge. > >If the work is done with counterpoise=2 or massage, as suggested by Douglas Fox, everything seems ok (both basis sets, and both mp2-full and mp2-fc). So maybe it is a problem of -bq. > >Best regards! >Ding > >Shobe, David David.Shobe---sud-chemie.com wrote: > > > >>Sent to CCL by: "Shobe, David" [David.Shobe=sud-chemie.com] Because you >>are using ghost atoms, there are empty core orbitals. The HF routine does not distinguish core orbitals from valence orbitals (at least I think this is true), but the MP2 defaults to MP2=FC (frozen core) which of coures does make the distinction. Note that 9.92D-01 = 0.992 = almost full occupancy! >> >>Perhaps using mp2=full would help, but then you'd have to redo any other mp2 calculations (you have to be consistent: either mp2=full everywhere or mp2=fc everywhere). >> >>A larger basis set like 6-311+G* or aug-cc-pVTZ is likely to improve matters. With more valence orbitals to choose from, there is less need to use the core orbital. The 6-31G* basis set is too small for accurate calculations of hydrogen bonding energies anyway, if that's what you're after. Again, you'd have to redo any calculations you've already performed using the smaller basis set. >> >>Regards, >>--David Shobe >> Süd-Chemie, Inc. >> >>Attention to detial is essentail. >> >> >>-----Original Message----- >> >> >> >> >>>From: owner-chemistry=-=ccl.net [mailto:owner-chemistry=-=ccl.net] >>> >>> >>> >>> >>Sent: Sunday, February 18, 2007 8:39 PM >>To: Shobe, David >>Subject: CCL:G: G03-Excessive mixing of frozen core and valence >>orbitals >> >> >>Sent to CCL by: Ding Xunlei [dingxunlei^-^gmail.com] Dear All, >> >>I did a calculation using mp2 and I find an error below. >>Could you give me some suggestion? Thank you! >> >>This input file: >>------------------------------------------------------------ >>#mp2/6-31G* >> >>test >> >>0 1 >> H 0.000000 -0.917747 0.000000 >> F 0.000000 0.000000 0.000000 >> H 0.000000 1.956639 0.000000 >> F 0.000000 2.875828 0.000000 >> H 0.000000 -0.917747 -2.250000 >> F 0.000000 0.000000 -2.250000 >> H-bq 0.000000 1.956639 -2.250000 >> F-bq 0.000000 2.875828 -2.250000 >> >>------------------------------------------------------------ >> >>The output file: >>------------------------------------------------------------------- >>SCF Done: E(RHF) = -199.305447100 A.U. after 21 cycles >> Convg = 0.2272D-08 -V/T = 1.9654 >> S**2 = 0.0000 >>ExpMin= 1.61D-01 ExpMax= 7.00D+03 ExpMxC= 1.05D+03 IAcc=1 IRadAn= >> 1 AccDes= 1.00D-06 >>HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 >>ScaDFX= 1.000000 1.000000 1.000000 1.000000 Largest valence mixing into a core orbital is 9.92D-01 Excessive mixing of frozen core and valence orbitals. >>Error termination via Lnk1e in /gaussian/03d02-xlf10/g03/l801.exe at Sat Feb 17 16:37:03 2007. >> >> >>Yours sincerely, >>Ding Xunlei >>2007-02-19 >>______________________________________________http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. >>Thank you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. >> >> >Thank you.> > > > > > From owner-chemistry@ccl.net Thu Feb 22 07:34:00 2007 From: "bala bala(_)igib.res.in" To: CCL Subject: CCL: SDF calculation Message-Id: <-33676-070222034613-6157-bCIx+G3ltLy1bhp6NBoEIA%%server.ccl.net> X-Original-From: "bala" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C75658.A6A08399" Date: Thu, 22 Feb 2007 13:38:35 +0530 MIME-Version: 1.0 Sent to CCL by: "bala" [bala^-^igib.res.in] This is a multi-part message in MIME format. ------_=_NextPart_001_01C75658.A6A08399 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, I have done a simulation in AMBER. I am looking for a program using which i can calculate spatial = distribution function (SDF) of water. I would appreciate if someone could guide me on this. thanks in advance, Bala ------_=_NextPart_001_01C75658.A6A08399 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable SDF calculation

Hello all,

I have done a simulation in AMBER.
I am looking for a program using which i can calculate spatial = distribution function (SDF) of water.

I would appreciate if someone could guide me on this.

thanks in advance,
Bala

------_=_NextPart_001_01C75658.A6A08399-- From owner-chemistry@ccl.net Thu Feb 22 12:50:00 2007 From: "Joseph Han jhh3851.:.yahoo.com" To: CCL Subject: CCL: the cases which B3LYP method or 6-31+G** basis set overestimates Message-Id: <-33677-070221132334-25243-E0q8qCdrFQFobsmUgWleHQ^-^server.ccl.net> X-Original-From: Joseph Han Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 21 Feb 2007 09:23:17 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Joseph Han [jhh3851[-]yahoo.com] If the reaction is not gas-phase, another possibility might be the effect of solvent molecules either through a PCM type effect or else explicitly binding to the complex to stabilize the transition state. Joseph --- "GÜL ALTINBAŞ galtinbas _ gmail.com" wrote: > Hi all, > I have been studying on the mechanism of an organic reaction which occurs > at room temperature. I am using B3LYP/6-31+G** basis set since our > structures are charged. We proposed two plausible mechanisms. I found the > activation barriers of the rate determining steps of these mechanisms as 45 > and 58 kcal/mole. These energy are too high for the reaction at room > temperature. My question is: > "Does anyone know a special case in which B3LYP method or 6-31+G(d,p) basis > set overestimates the activation barrier?" > I am waiting for your answers or any suggestions. > Best regards > Gul > -- > Gül Altinbas Ozpinar > Research Assistant > Marmara University > Arts&Sciences Faculty > Chemistry Department > Göztepe Campus 34722 > Istanbul / Turkey > Phone No: +90 216 347 96 41 - 1167 > Fax No: + 90 216 347 87 83 > From owner-chemistry@ccl.net Thu Feb 22 14:18:00 2007 From: "Reynier Suardiaz reynier.suardiaz#,#gmail.com" To: CCL Subject: CCL: methods to probe light-harvesting capabilities Message-Id: <-33678-070222130238-3451-bFQrZCGGMdMn51hbM5GiaQ.:.server.ccl.net> X-Original-From: "Reynier Suardiaz" Date: Thu, 22 Feb 2007 13:02:35 -0500 Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz^gmail.com] Dear CCl Members I have some recently obtained compounds, i would like to explore theoretically its capabilities as light-harvesting structures. Does anybody knows how to study this fenomenum using the most standar methods in quantum chemistry? For instance, demonstration of posSibility of charge tranSfer (ct) directionality of this ct, spectroscopy evidence of it... Is there any review or general literature about the posible methodology? I will appreciate any comment or suggestion thanks in advance reynier From owner-chemistry@ccl.net Thu Feb 22 17:56:01 2007 From: "Victor Rosas-Garcia quimico69,yahoo.com" To: CCL Subject: CCL: cavity determination Message-Id: <-33679-070222174812-8252-vM3/tXIrCgSWsd3ROYoPGA*|*server.ccl.net> X-Original-From: "Victor Rosas-Garcia" Date: Thu, 22 Feb 2007 17:48:08 -0500 Sent to CCL by: "Victor Rosas-Garcia" [quimico69 _ yahoo.com] Hello everybody, I am trying to calculate the size of the molecular cavity for a series of macrocycles, and someone suggested the use of alpha shapes. I am not very familiar with these. I have located some (highly mathematical) literature and web pages about alpha shapes. In addition, I am trying to get a copy of Edelbrunner's papers on its application to chemical species (don't have them yet). So my questions are: a) How widely used are alpha shapes in working with molecular cavities? (my library search has turned up very little) b) Can anyone recommend software to calculate alpha shapes of molecules? So far I have found Hull by Ken Clarkson, and Alpha Shapes at Duke, but I'm still trying to get them to compile with gcc. thank you for you attention Victor M. Rosas Garca, PhD Facultad de Ciencias Quimicas, UANL e-mail: quimico69|-|yahoo.com From owner-chemistry@ccl.net Thu Feb 22 19:36:00 2007 From: "Elaine C Meng meng-,-cgl.ucsf.edu" To: CCL Subject: CCL: cavity determination Message-Id: <-33680-070222193413-9994-TSV2hu6xlMayg7/XHIT1vQ,+,server.ccl.net> X-Original-From: "Elaine C Meng" Date: Thu, 22 Feb 2007 19:34:10 -0500 Sent to CCL by: "Elaine C Meng" [meng[#]cgl.ucsf.edu] Hi Victor, Take a look at CASTp - this page links to a server and a publications list. http://sts.bioengr.uic.edu/castp/ It definitely works for proteins. It may not work "as is" on your macrocycles, but the publications may help to get you started. Best, Elaine ----- Elaine C. Meng, Ph.D. meng a cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Thu Feb 22 21:19:00 2007 From: "Ronald L Cook cookrl===tda.com" To: CCL Subject: CCL: Docking programs Message-Id: <-33681-070222184947-3224-0nYNsKKITqbIeMhN4jwGhQ^_^server.ccl.net> X-Original-From: "Ronald L Cook" Date: Thu, 22 Feb 2007 18:49:44 -0500 Sent to CCL by: "Ronald L Cook" [cookrl###tda.com] Dear CCLers Many of the docking programs available calculate a fit between a host (e.g. an enzyme, etc) and a small molecule to look for small molecule drugs. My interest/need lies in the opposite direction. Does anyone know of a program that takes a guest and (using for example a genetic algorithm or other equivalent stochastic optimization method) builds a small peptide (or other molecular backbone) chain that provides a good fit to the small molecule? Thanks Ronald Cook Principal Scientist TDA Research, Inc. From owner-chemistry@ccl.net Thu Feb 22 21:53:00 2007 From: "N. Sukumar nagams++rpi.edu" To: CCL Subject: CCL: cavity determination Message-Id: <-33682-070222212737-16548-DhvkCYMZPYuc+pChcLNVDw-.-server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 22 Feb 2007 20:25:25 -0500 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams+/-rpi.edu] MOE's Site Finder (from Chemical Computing Group, Inc.) is an implementation based on alpha spheres, used for locating binding sites in proteins; see this document by Paul Labute and Martin Santavy: http://www.chemcomp.com/journal/sitefind.htm Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Thu, 22 Feb 2007 17:48:08 EST "Victor Rosas-Garcia quimico69,yahoo.com" wrote: Sent to CCL by: "Victor Rosas-Garcia" [quimico69 _ yahoo.com] Hello everybody, I am trying to calculate the size of the molecular cavity for a series of macrocycles, and someone suggested the use of alpha shapes. I am not very familiar with these. I have located some (highly mathematical) literature and web pages about alpha shapes. In addition, I am trying to get a copy of Edelbrunner's papers on its application to chemical species (don't have them yet). So my questions are: a) How widely used are alpha shapes in working with molecular cavities? (my library search has turned up very little) b) Can anyone recommend software to calculate alpha shapes of molecules? So far I have found Hull by Ken Clarkson, and Alpha Shapes at Duke, but I'm still trying to get them to compile with gcc. thank you for you attention Victor M. Rosas Garca, PhD Facultad de Ciencias Quimicas, UANL e-mail: quimico69.:.yahoo.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Thu Feb 22 22:28:00 2007 From: "Vincent Xianlong Wang xloongw%%yahoo.com" To: CCL Subject: CCL:G: an error in terms of frequency calculation in Gaussian 03. Message-Id: <-33683-070222215233-28294-DMaBY7VuaJZ0VAMhiq/Tog~!~server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 22 Feb 2007 17:52:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw*o*yahoo.com] Dear Dr. Hori, I am not exactly sure what happened with your calculation. But the symbol "NaN" appears when the number is too big, i.e. outflow. If you send your input file, we may tell more. Best regards, Vincent --- "Takumi Hori thori3jp*_*mac.com" wrote: > > Sent to CCL by: Takumi Hori [thori3jp!=!mac.com] > Dear CCL users, > > I got a following error in terms of frequency > calculation in Gaussian03. > > > (Enter /opt/g03nscco64/g03/l716.exe) > > Dipole =-5.74843628D-01-5.82225009D-01 > 2.70383092D-01 > > Polarizability= 6.07153970D+02-3.92605031D+01 > 5.30253486D+02 > > -6.00698286D+01-1.82463985D+01 > 2.60811735D+02 > > Full mass-weighted force constant matrix: > > Low frequencies --- Infinity NaN NaN > NaN > > NaN NaN > > Low frequencies --- NaN NaN NaN > > Molecule is non-linear but NTrRo=0. > > Error termination via Lnk1e in > /opt/g03nscco64/g03/l716.exe at Fri > > Feb 16 13:04:48 2007. > > Job cpu time: 3 days 15 hours 28 minutes 16.0 > seconds. > > File lengths (MBytes): RWF= 4756 Int= 0 > D2E= 0 > > Chk= 21 Scr= 1 > > > > Could you please tell me possible reasons why > gaussian gave such an > error? > Could anyone tell me how to fix this problem? > > Any suggestions are appreciated. > > Thank you very much in advance for your advice. > > Best regards, > Takumi > > -- > > Dr. Takumi Hori > > Research & Development Laboratories > Nippon Steel Chemical Co., Lid. > 46-80 Nakabaru Sakinohama > Tobata-ku, Kitakyushu, Fukuoka 804-8503 > Japan > Tel: +81-93-884-1621 > Fax: +81-93-884-1923 > E-mail: horitk---nscc.co.jp > thori3jp---mac.com > http://www.nscc.co.jp/english/index.html > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the [] > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST[]ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL From owner-chemistry@ccl.net Thu Feb 22 23:27:01 2007 From: "N. Sukumar nagams-x-rpi.edu" To: CCL Subject: CCL: Docking programs Message-Id: <-33684-070222231537-19630-bWBoTAynOXOHqv1kOwkGxg-x-server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 22 Feb 2007 23:15:27 -0500 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams[A]rpi.edu] Perhaps not exactly what you have in mind, but the CoLiBRI method [Oloff, et al, J. Chem. Inf. Model. 46 (2), 844-851, 2006] is based on a representation of both receptor binding sites and their complimentary ligands in a space of universal chemical descriptors, therby enabling one to identify possible complementary receptor cavities starting from a ligand chemical structure. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Thu, 22 Feb 2007 18:49:44 EST "Ronald L Cook cookrl===tda.com" wrote: Sent to CCL by: "Ronald L Cook" [cookrl###tda.com] Dear CCLers Many of the docking programs available calculate a fit between a host (e.g. an enzyme, etc) and a small molecule to look for small molecule drugs. My interest/need lies in the opposite direction. Does anyone know of a program that takes a guest and (using for example a genetic algorithm or other equivalent stochastic optimization method) builds a small peptide (or other molecular backbone) chain that provides a good fit to the small molecule? Thanks Ronald Cook Principal Scientist TDA Research, Inc.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========