From owner-chemistry@ccl.net Mon Apr 10 03:05:00 2006 From: "James Kirkpatrick james.kirkpatrick- -imperial.ac.uk" To: CCL Subject: CCL:G: single proton calculation with DFT Message-Id: <-31463-060410025833-10960-nHCzSi2HiWVWoDdFG5ufgA,+,server.ccl.net> X-Original-From: James Kirkpatrick Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 10 Apr 2006 07:56:20 +0100 MIME-Version: 1.0 Sent to CCL by: James Kirkpatrick [james.kirkpatrick_+_imperial.ac.uk] Hi Gonzalo, What is the sense of this calculation? If the system has no interacting particles, only a stationary proton, then whatever level of theory you use should yeald 0 energy! The fact that the DFT program crashes indicates that it is simply not capable of dealing with a situation with 0 electrons: the error message is one i do nto know but it seems to be complaining about a lack of Molecular orbitals: so I suppose what the program is trying to do is calculate the charge density, but that - due to the lack of electrons - it cannot do so! Hope this helps a little James Gonzalo Jimenez Oses gonzalo.jimenez]*[dq.unirioja.es wrote: > Sent to CCL by: "Gonzalo Jimenez Oses" [ ] > Dear CLL'ers, > > Maybe my question is somewhat naive, but I have encountered some unexpected errors when evaluating one single proton energy using DFT methods, particularly with b3lyp, whereas Hartree-Fock method gives no errors. Here is the last part of my G03 output after the l502 link crashes: > ------------------------- > The electronic state of the initial guess is 1-A1G. > Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > No special actions if energy rises. > Keep R1 integrals in memory in canonical form, NReq= 426535. > Integral accuracy reduced to 1.0D-05 until final iterations. > MOs to be used but not provided to CalDFT. > Error termination via Lnk1e in C:\G03W\l502.exe at Sun Apr 09 22:58:41 2006. > Job cpu time: 0 days 0 hours 0 minutes 12.0 seconds. > File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 4 Scr= 1 > ------------------------- > > Could you please shed some light into this question, please?. > > On the oher hand, I wish to gratefully thank Prof. Chris Cramer for his quick and valuable answer regarding multipole moments and PCM solvation energy. > > Thank you all, > > Gonzalo> > > > > From owner-chemistry@ccl.net Mon Apr 10 05:56:00 2006 From: "Gonzalo Jimenez Oses gonzalo.jimenez[*]dq.unirioja.es" To: CCL Subject: CCL: single proton calculation with DFT - more info - Message-Id: <-31464-060410055537-19258-QQFa5sCvBUKYVunZphKTMA,+,server.ccl.net> X-Original-From: "Gonzalo Jimenez Oses" Date: Mon, 10 Apr 2006 05:55:36 -0400 Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez++dq.unirioja.es] Dear CCL'ers, Thank you all for the interest shown in my last post. It seems that my question has a little sense, doesn`t it?. Well, I want to calculate a single proton energy in order to stablish a reasonable comparison between a protonated specie and a deprotonated one (like a carbanion). Once I have optimized the carbanionic structure, I wonder if I could evaluate the infinitely-separated proton energy in some way, only with comparative purposes. I hope this clarify a little more. Thanks again. Regards, Gonzalo From owner-chemistry@ccl.net Mon Apr 10 07:54:00 2006 From: "Serguey Alekseevich Pozdneev pozdneev[*]sci.lebedev.ru" To: CCL Subject: CCL: Gamess Source code for PC WINDOWS Message-Id: <-31465-060410043221-9457-srbtU9tcrPhrCfIzvNuN/w++server.ccl.net> X-Original-From: "Serguey Alekseevich Pozdneev" Date: Mon, 10 Apr 2006 04:32:19 -0400 Sent to CCL by: "Serguey Alekseevich Pozdneev" [pozdneev++sci.lebedev.ru] Dear Cllegs, If it is possible I schould like to have Gamess Source code for PC WINDOWS Sincerely yours S.Pozdneev From owner-chemistry@ccl.net Mon Apr 10 08:28:01 2006 From: "William F. Polik polik!=!hope.edu" To: CCL Subject: CCL:G: NBO visualization Message-Id: <-31466-060409170326-19857-dlUWOntrNyhi1zOgk0PMDg{=}server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Sun, 09 Apr 2006 16:20:32 -0400 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik*_*hope.edu] WebMO Pro allows for computation and visualization of NBO's by Gaussian03 (and other programs). Try it out at: www.webmo.net/demo Since WebMO is a web-based interface, there is no need to install any software on your PC. Just login, build a molecule, submit your calculation, and view the results, all from within your Windows, Mac OS X, or Linux web-browser. Will Polik At 01:36 AM 4/8/2006, you wrote: >I was wondering if anyone knew how to visualize the NBO 3.1 orbitals >produced by Gaussian 03. I don't have access to NBO 5.0. I've tried >using some functions in Molekel to do it, but to no avail. If >someone has a method, complete with instructions, it would be >greatly appreciated! ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik-*-hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ From owner-chemistry@ccl.net Mon Apr 10 09:04:00 2006 From: "Robinson, James James.Robinson*evotec.com" To: CCL Subject: CCL: Total charge of whole protein Message-Id: <-31467-060410082808-13671-iuYvfo5ze51znWLxP1Ojqw- -server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 10 Apr 2006 13:28:28 +0100 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson(~)evotec.com] One important aspect is to ensure that the FAD510 residue has the correct charge, I think the FAD510 must be -4 charge as the two phosphate groups are probably deprotonated. I have often found in the past that cofactors such as NADP, heme rings etc.., often have aromatic rings that get protonated when simply adding hydrogens. Metals such as Ni or Fe have caused me many problems in the past. Hope this helps. James, UK. -----Original Message----- > From: owner-chemistry\a/ccl.net [mailto:owner-chemistry\a/ccl.net] Sent: 08 April 2006 14:41 To: Robinson, James Subject: CCL: Total charge of whole protein Sent to CCL by: "Hajime Ohno" [h_ohno{}cheng.es.osaka-u.ac.jp] Hello. I am a student of Osaka university in Japan and studying a redox reaction in a protein (PDB: 1B4V) by the QM/MM approach to compute free energy change. It can be easily expected that the total charge of the protein affects seriously the redox potential. My question is how I can get the proper value of the total charge of the whole protein. In other words, how can we know the protnation states of the constituent amino acids in the protein? At present, we fully rely on the web tool MOLPROBITY to add hydrogen atoms on the PDB data. If it cant be known at all, how do researchers who study protein deal with the problem? Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531, Japan Hajime Ohno e-mail: h_ohno=cheng.es.osaka-u.ac.jphttp://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 Mon Apr 10 09:57:00 2006 From: "Shobe, David dshobe]~[sud-chemieinc.com" To: CCL Subject: CCL: single proton calculation with DFT - more info - Message-Id: <-31468-060410094411-24711-evSruPNsywUXhpMfYYkt0w---server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 10 Apr 2006 15:43:59 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe-.-sud-chemieinc.com] Perhaps the functional (or the algorithm used to implement the functional) "blows up" at zero e- density! Anyway, I agree with James Kirkpatrick that you can take the energy of H+ as being = 0 for in your proton affinity calculation. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] Sent: Monday, April 10, 2006 6:08 AM To: Shobe, David Subject: CCL: single proton calculation with DFT - more info - Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez++dq.unirioja.es] Dear CCL'ers, Thank you all for the interest shown in my last post. It seems that my question has a little sense, doesn`t it?. Well, I want to calculate a single proton energy in order to stablish a reasonable comparison between a protonated specie and a deprotonated one (like a carbanion). Once I have optimized the carbanionic structure, I wonder if I could evaluate the infinitely-separated proton energy in some way, only with comparative purposes. I hope this clarify a little more. Thanks again. Regards, Gonzalohttp://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 Mon Apr 10 10:39:01 2006 From: "Pawel Zawadzki zawpaw:+:soliton.ch.pw.edu.pl" To: CCL Subject: CCL: problem with Monte Carlo in gamess Message-Id: <-31469-060410093401-17704-d13bc3mUg8HuskBwXZnnXQ^server.ccl.net> X-Original-From: Pawel Zawadzki Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 10 Apr 2006 14:43:33 +0200 Mime-Version: 1.0 Sent to CCL by: Pawel Zawadzki [zawpaw]![soliton.ch.pw.edu.pl] Dear CCL readers, I have a problem using GLOBOP option implemented in Gamess. I've tried modified version of exam30.inp from gamess/tests directory: $contrl scftyp=rhf runtyp=globop coord=ZMT $end $system MWORDS=2 $end $basis gbasis=N31 NGAUSS=6 $end $GLOBOP XMIN=-30 XMAX=30 YMIN=-30 YMAX=30 ZMIN=-30 ZMAX=-30 NGEOPT=10 $END $STATPT NSTEP=100 OPTTOL=0.0005 $END $data formamide with three effective fragment waters C1 C O 1 rCO N 1 rCN 2 aNCO H 3 rNHa 1 aCNHa 2 0.0 H 3 rNHb 1 aCNHb 2 180.0 H 1 rCH 2 aHCO 4 180.0 rCO=1.1962565 rCN=1.3534065 rNHa=0.9948420 rNHb=0.9921367 rCH=1.0918368 aNCO=124.93384 aCNHa=119.16000 aCNHb=121.22477 aHCO=122.30822 $end $efrag coord=int fragname=H2ORHF O1 4 1.926 3 175.0 1 180.0 H2 7 0.9438636 4 117.4 3 -175.0 H3 7 0.9438636 8 106.70327 4 95.0 fragname=H2ORHF O1 8 1.901 7 175.0 4 0.0 H2 10 0.9438636 8 110.0 4 -5.0 H3 10 0.9438636 11 106.70327 8 -95.0 fragname=H2ORHF H2 2 1.951 1 150.0 3 0.0 O1 13 0.9438636 2 177.0 3 0.0 H3 14 0.9438636 13 106.70327 3 140.0 $end The problem is when Gamess enters Monte Carlo search, log file is not updated and the process doesn't finish. What should I change in input file? Thank you very much in advance, Pawel From owner-chemistry@ccl.net Mon Apr 10 11:13:01 2006 From: "Shobe, David dshobe-x-sud-chemieinc.com" To: CCL Subject: CCL: GAPT charges - software Message-Id: <-31470-060410102339-15562-EbHVymuh/WfVbFbFLvF5IQ!A!server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C65CAA.463210FB" Date: Mon, 10 Apr 2006 16:23:01 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe^^^sud-chemieinc.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C65CAA.463210FB Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable How do I compute GAPT (General Atomic Polar Tensor) charges? Can anyone re= commend a program? --David Shobe, Ph.D., M.L.S. S=FCd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, 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 an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C65CAA.463210FB Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable GAPT charges - software

How do I compute GAPT (General Atomic Pola= r Tensor) charges?  Can anyone recommend a program?

--David Shobe, Ph.D., M.L.S.
S=FCd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a fire= wall.


This e-mail message may contain confidential and / or privileged infor= mation. 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 th= is 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-ma= il and delete this message.
Thank you.
------_=_NextPart_001_01C65CAA.463210FB-- From owner-chemistry@ccl.net Mon Apr 10 11:48:00 2006 From: "Shobe, David dshobe|-|sud-chemieinc.com" To: CCL Subject: CCL: AIM charges - HF or DFT? Message-Id: <-31471-060410104547-30329-+2999OuyxCP9hTQkBQ42+w_+_server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C65CAD.71370941" Date: Mon, 10 Apr 2006 16:45:41 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe===sud-chemieinc.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C65CAD.71370941 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I have some questions about current "best practices" regarding AIM charges. First of all, is a HF or a DFT wave function better? What about the hybrid= B3LYP?=20=20 Second, is a large basis set still considered to be important? What about = diffuse functions?=20=20 Third, I am considering purchasing AIM2000. Are AIM2000 users satisfied? = Does it have limitations I should be aware of? Is there competing software= I should consider? For non-computational-chemistry reasons, I have only W= indows XP operating system. --David Shobe, Ph.D., M.L.S. S=FCd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, 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 an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C65CAD.71370941 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable AIM charges - HF or DFT?

I have some questions about current "= best practices" regarding AIM charges.

First of all, is a HF or a DFT wave functi= on better?  What about the hybrid B3LYP? 

Second, is a large basis set still conside= red to be important?  What about diffuse functions? 

Third, I am considering purchasing AIM2000= .  Are AIM2000 users satisfied?  Does it have limitations I shoul= d be aware of?  Is there competing software I should consider?  F= or non-computational-chemistry reasons, I have only Windows XP operating sy= stem.

--David Shobe, Ph.D., M.L.S.
S=FCd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a fire= wall.


This e-mail message may contain confidential and / or privileged infor= mation. 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 th= is 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-ma= il and delete this message.
Thank you.
------_=_NextPart_001_01C65CAD.71370941-- From owner-chemistry@ccl.net Mon Apr 10 12:23:01 2006 From: "Gopakumar Gopinadhanpillai gopakumar]![chem.kuleuven.be" To: CCL Subject: CCL: FMO analysis Message-Id: <-31472-060410120126-26796-TEXtMUhB7lpQDeisQ9yW0A . server.ccl.net> X-Original-From: "Gopakumar Gopinadhanpillai" Date: Mon, 10 Apr 2006 12:01:24 -0400 Sent to CCL by: "Gopakumar Gopinadhanpillai" [gopakumar:+:chem.kuleuven.be] Hello members, Could any one tell me what is the best program to perform FMO analysis, which is available free for academic purpose. Thanking you all -Gopakumar From owner-chemistry@ccl.net Mon Apr 10 12:58:01 2006 From: "Sergio Emanuel Galembeck segalemb]-[usp.br" To: CCL Subject: CCL:G: GAPT charges - software Message-Id: <-31473-060410121744-1903-a4e1RSOr9LFRD2BhHkgQbg%a%server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 10 Apr 2006 13:17:31 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb|*|usp.br] Dear David, I recomend Gaussian03, because the GAPT are listed when the frequency calculations are performed, as APT charges. Best regards, Sergio ============================================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av Bandeirantes, 3900 Ribeirao Preto, SP Brasil phone: +55-16-602-37-65 fax: +55-16-633-81-51 e-mail: segalemb(0)usp.br ============================================================== Citando "Shobe, David dshobe-x-sud-chemieinc.com" : > Sent to CCL by: "Shobe, David" [dshobe^^^sud-chemieinc.com] > This is a multi-part message in MIME format. > ------_=_NextPart_001_01C65CAA.463210FB > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > How do I compute GAPT (General Atomic Polar Tensor) charges? Can anyone re= > commend a program? > > --David Shobe, Ph.D., M.L.S. > S=FCd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > This e-mail message may contain confidential and / or privileged informatio= > n. If you are not an addressee or otherwise authorized to receive this mess= > age, 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 an= > d delete this message.=20 > Thank you. > ------_=_NextPart_001_01C65CAA.463210FB > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > > 1"> > > GAPT charges - software > > > > >

How do I compute GAPT (General Atomic Pola= > r Tensor) charges?  Can anyone recommend a program? >

> >

--David Shobe, Ph.D., M.L.S. > >
S=FCd-Chemie, Inc. > >
phone (502) 634-7409 > >
fax (502) 634-7724 >

> >

Don't bother flaming me: I'm behind a fire= > wall. >

>
> > >
This e-mail message may contain confidential and / or privileged infor= > mation. 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 th= > is 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-ma= > il and delete this message.
> Thank you.
>
> > > ------_=_NextPart_001_01C65CAA.463210FB--> > > > From owner-chemistry@ccl.net Mon Apr 10 13:33:00 2006 From: "Sergio Emanuel Galembeck segalemb[a]usp.br" To: CCL Subject: CCL: AIM charges - HF or DFT? Message-Id: <-31474-060410130227-31700-aNFWrOSxLbTqfvTpwaXihg!^!server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 10 Apr 2006 14:02:12 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb]![usp.br] Dear David, - DFT normally produces better results than HF, because of the inclusion of electron correlation and B3LYP is the most applied functional. - Normally the largest basis set produces better results, but a medium basis that produces good results is 6-31+G(d,p). In my opinion diffuse functions are important, specially in the study of non-bonded interactions, as hydrogen bonds and pi-pi interactions. - I use AIM2000, because it has a very nice graphical interface, and Morphy. Morphy is more robust than AIM2000 and you can do the integration of all atoms in only one step. Best regards, Sergio ============================================================== Sergio Emanuel Galembeck Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av Bandeirantes, 3900 Ribeirao Preto, SP Brasil phone: +55-16-602-37-65 fax: +55-16-633-81-51 e-mail: segalemb.!^!.usp.br ============================================================== Citando "Shobe, David dshobe|-|sud-chemieinc.com" : > Sent to CCL by: "Shobe, David" [dshobe===sud-chemieinc.com] > This is a multi-part message in MIME format. > ------_=_NextPart_001_01C65CAD.71370941 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > I have some questions about current "best practices" regarding AIM charges. > > First of all, is a HF or a DFT wave function better? What about the hybrid= > B3LYP?=20=20 > > Second, is a large basis set still considered to be important? What about = > diffuse functions?=20=20 > > Third, I am considering purchasing AIM2000. Are AIM2000 users satisfied? = > Does it have limitations I should be aware of? Is there competing software= > I should consider? For non-computational-chemistry reasons, I have only W= > indows XP operating system. > > --David Shobe, Ph.D., M.L.S. > S=FCd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > This e-mail message may contain confidential and / or privileged informatio= > n. If you are not an addressee or otherwise authorized to receive this mess= > age, 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 an= > d delete this message.=20 > Thank you. > ------_=_NextPart_001_01C65CAD.71370941 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > > 1"> > > AIM charges - HF or DFT? > > > > >

I have some questions about current "= > best practices" regarding AIM charges. >

> >

First of all, is a HF or a DFT wave functi= > on better?  What about the hybrid B3LYP?  >

> >

Second, is a large basis set still conside= > red to be important?  What about diffuse functions?  >

> >

Third, I am considering purchasing AIM2000= > .  Are AIM2000 users satisfied?  Does it have limitations I shoul= > d be aware of?  Is there competing software I should consider?  F= > or non-computational-chemistry reasons, I have only Windows XP operating sy= > stem.

> >

--David Shobe, Ph.D., M.L.S. > >
S=FCd-Chemie, Inc. > >
phone (502) 634-7409 > >
fax (502) 634-7724 >

> >

Don't bother flaming me: I'm behind a fire= > wall. >

>
> > >
This e-mail message may contain confidential and / or privileged infor= > mation. 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 th= > is 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-ma= > il and delete this message.
> Thank you.
>
> > > ------_=_NextPart_001_01C65CAD.71370941--> > > > From owner-chemistry@ccl.net Mon Apr 10 14:09:01 2006 From: "Gardner, Elizabeth A. eagardner~~utep.edu" To: CCL Subject: CCL: Gamess Source code for PC WINDOWS Message-Id: <-31475-060410115358-14245-jj1+QAMqzniJEl7ZBl8r4w ~~ server.ccl.net> X-Original-From: "Gardner, Elizabeth A." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 10 Apr 2006 09:06:46 -0600 MIME-Version: 1.0 Sent to CCL by: "Gardner, Elizabeth A." [eagardner ~ utep.edu] The nanotechnology center at www.nanohub.org offers free access to GAMESS. The nanoHUB is an NSF funded center that offers computational resources and simulations for nanotechnology. You have to register, but that's so that we can track usage. There are both research and educational level tools available. Beth Elizabeth Gardner Assistant Professor Department of Chemistry University of Texas at El Paso El Paso, TX 79968 Phone: (915) 747-7551 Fax: (915) 747-5748 Office: 121D Physical Sciences Bldg. -----Original Message----- > From: owner-chemistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net] Sent: Monday, April 10, 2006 6:11 AM To: Gardner, Elizabeth A. Subject: CCL: Gamess Source code for PC WINDOWS Sent to CCL by: "Serguey Alekseevich Pozdneev" [pozdneev++sci.lebedev.ru] Dear Cllegs, If it is possible I schould like to have Gamess Source code for PC WINDOWS Sincerely yours S.Pozdneevhttp://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 Mon Apr 10 14:43:00 2006 From: "Christopher Cramer cramer__chem.umn.edu" To: CCL Subject: CCL: single proton calculation with DFT - more info - Message-Id: <-31476-060410135116-32758-daBrbj8vfZvjRJCYJujJnA-x-server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-6-1024429232 Date: Mon, 10 Apr 2006 11:51:10 -0500 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: Christopher Cramer [cramer%x%chem.umn.edu] --Apple-Mail-6-1024429232 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed While I too find the application of a million lines of code to a bare proton mildly amusing, we may as well be careful and accurate about this. For the proton (a.u.): E(elec) = 0.000 00 (for the reasons already posted by others) U(T) = E(elec) + ZPVE + 3/2 RT = 0.001 42 at 298 K (the proton has no zero-point vibrational energy, and 3/2 RT translational energy) H(T) = U(T) + PV = 5/2 RT = 0.002 36 at 298 K (from ideal gas approximation for PV) G(T) = H(T) - TS(T) = -0.009 99 at 298 K (from translational entropy, standard-state volume of 1 mol per 24.45 L (1 atm ideal gas)) Proton affinity is usually reported as an enthalpy, often at 298 K. For pKa calculations in water (a free energy), the aqueous solvation free energy of the proton will also be needed (-265.9 kcal/mol for 1 atm gas phase to 1 M solution). Chris Cramer -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer .. pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-6-1024429232 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
While I too find the = application of a million lines of code to a bare proton mildly amusing, = we may as well be careful and accurate about this. For the proton = (a.u.):

E(elec)= =3D 0.000 00 (for the reasons already posted by others)

U(T) =3D E(elec) + ZPVE + = 3/2 RT =3D 0.001 42 at 298 K (the proton has no zero-point vibrational = energy, and 3/2 RT translational energy)

H(T) =3D U(T) + PV =3D 5/2 = RT =3D 0.002 36 at 298 K (from ideal gas approximation for = PV)

G(T) =3D = H(T) - TS(T) =3D -0.009 99 at 298 K=A0 (from translational entropy, = standard-state volume of 1 mol per 24.45 L (1 atm ideal = gas))

Proton = affinity is usually reported as an enthalpy, often at 298 = K.

For pKa = calculations in water (a free energy), the aqueous solvation free energy = of the proton will also be needed (-265.9 kcal/mol for 1 atm gas phase = to 1 M solution).

Chris Cramer

--


Christopher J. Cramer

University of Minnesota

Department of Chemistry

207 Pleasant St. = SE

Minneapolis, MN 55455-0431

--------------------------

=

Phone:=A0 (612) 624-0859 || FAX:=A0 (612) 626-2006

Mobile: (952) = 297-2575

cramer .. pollux.chem.umn.edu<= /FONT>

http://pollux.chem.umn.edu/~cr= amer

(website = includes information about the textbook "Essentials

=A0 =A0 of Computational = Chemistry:=A0 Theories and = Models, 2nd Edition")


= --Apple-Mail-6-1024429232-- From owner-chemistry@ccl.net Mon Apr 10 16:20:00 2006 From: "Ramiro Arratia rarratia^^^unab.cl" To: CCL Subject: CCL: 5th Workshop of Computational Chemistry and Molecular Spectroscopy Message-Id: <-31477-060410145052-8767-Go2tmmv4z0ex0XKpXuupvA[#]server.ccl.net> X-Original-From: "Ramiro Arratia" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0018_01C65CA6.3B493DA0" Date: Mon, 10 Apr 2006 13:54:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Ramiro Arratia" [rarratia{:}unab.cl] This is a multi-part message in MIME format. ------=_NextPart_000_0018_01C65CA6.3B493DA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, We would like to invite you to participate in the 5th Workshop of = Computational Chemistry and Molecular Spectroscopy to be held in Punta = de Tralca (Banco Central Resort) during October 17-20, 2006. Punta de = Tralca is a beatiful south pacific beach which is next to Isla Negra = where Pablo Neruda's musseum is located. For more information, please visit: Please visit: http://www.unab.cl/workshop=20 Ramiro Arratia Perez, Ph.D. Director, Doctorado Fisicoquimica Molecular Facultad de Ecologia y Recursos Naturales Universidad Andres Bello Republica 275, Santiago Ph: (562) 661-8232 (562) 661-8226 Fax: (562)-661-8269 rarratia_+_unab.cl ------=_NextPart_000_0018_01C65CA6.3B493DA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
Dear Colleagues,
 We would like to invite you to = participate in=20 the 5th Workshop of Computational Chemistry and Molecular Spectroscopy = to be=20 held in Punta de Tralca (Banco Central Resort) during October 17-20, = 2006. =20 Punta de Tralca is a beatiful south =  pacific=20 beach which is next to Isla Negra where Pablo Neruda's musseum is=20 located.
 
For more information, please = visit:
 
Please visit: http://www.unab.cl/workshop 
 
Ramiro Arratia Perez, = Ph.D.
Director, Doctorado=20 Fisicoquimica Molecular
Facultad de Ecologia y Recursos=20 Naturales
Universidad Andres Bello
Republica 275, Santiago
Ph: = (562)=20 661-8232
      (562)  661-8226
Fax:=20 (562)-661-8269
rarratia_+_unab.cl
= ------=_NextPart_000_0018_01C65CA6.3B493DA0-- From owner-chemistry@ccl.net Mon Apr 10 17:32:00 2006 From: "Christos Deligkaris cdeligka.:.purdue.edu" To: CCL Subject: CCL: Autodock questions Message-Id: <-31478-060410173035-13920-Tk+iduTdxtbY7Ux9T0XXJw!^!server.ccl.net> X-Original-From: "Christos Deligkaris" Date: Mon, 10 Apr 2006 17:30:33 -0400 Sent to CCL by: "Christos Deligkaris" [cdeligka__purdue.edu] Dear All, when I try to do my grid parameter file (.gpf) I get these two warnings: "Warning! Oxygen with no bonded atoms, atom serial number 106 Warning! Oxygen with no bonded atoms, atom serial number 107 .." "Warning! Attempt to divide by zero was just prevented. Are the coordinates of atoms 350 and 575 the same?" I found the atom with number 350 but there is no atom with number 575, so the last warning seems a little bit strange .. If anyone knows if these messages are important and whether they have an impact on the calculations please let me know. Is there any way I can fix these problems? Thank you in advance, Christos Deligkaris cdeligka=-=purdue.edu From owner-chemistry@ccl.net Mon Apr 10 22:33:00 2006 From: "jz7(!)duke.edu" To: CCL Subject: CCL: Free QSAR (CoMFA) software Message-Id: <-31479-060410151715-29702-5cY3l86rit5A2Rgsg74OWQ],[server.ccl.net> X-Original-From: jz7{}duke.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 7 Apr 2006 14:47:24 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: jz7-.-duke.edu Dear all, Does anyone know any free programs that can do QSAR analysis (using CoMFA)? Sybyl does this but it is not free. Thanks a lot!