From chemistry-request@server.ccl.net Mon Nov 12 07:48:06 2001 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fACCm6B26596 for ; Mon, 12 Nov 2001 07:48:06 -0500 Received: from localhost (scifac209-194.dhcp.csuohio.edu [137.148.209.194]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0GMO002PRUFWZA@sims.csuohio.edu> for chemistry@ccl.net; Mon, 12 Nov 2001 07:52:44 -0500 (EST) Date: Mon, 12 Nov 2001 07:48:15 -0500 From: Deley Sulton Subject: 3-D glasses To: ccl Message-id: <89E1A5BC-D76B-11D5-95CE-0003934FCAB2@csuohio.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.472) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7BIT Thank you all so much for your guidance towards finding high quality 3-D glasses. I look forward to following your leads. Y'all have a nice day, Deley Sulton From chemistry-request@server.ccl.net Mon Nov 12 07:54:52 2001 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fACCsqB26805 for ; Mon, 12 Nov 2001 07:54:52 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id HAA01553 for ; Mon, 12 Nov 2001 07:54:47 -0500 (EST) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id fACCskA07021 for chemistry@ccl.net; Mon, 12 Nov 2001 07:54:46 -0500 (EST) From: Wai-To Chan Message-Id: <200111121254.fACCskA07021@curl.gkcl.yorku.ca> Subject: anharmonic oscillator wavefunctions To: chemistry@ccl.net Date: Mon, 12 Nov 2001 07:54:45 -0500 (EST) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< I have a colleague who is interested in computing Franck-Condon factors, for which he needs anharmonic oscillator wavefunctions. I think that I can provide him with some good potentials (he is interested in first row diatomics) from something like ccsd(t) scans with one of the aug-cc basis sets. My plan was to fit the resulting potential to a Morse function, then get the anharmonic wavefunctions by diagonalizing the anharmonic (Morse) Hamiltonian on a basis of harmonic oscillator functions. I am not certain that this fit will be good enough, particularly in the repulsive regime. I have poked about in the literature some, but have not yet found the definitive "best" way to do this. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Potential functions slightly more complex than the Morse function should give reasonably good fit for diatomics. You may refer to John Murrell's text: "Molecular potential functions" Wiley, 1984, for something like an extended Morse function. In a paper I coauthored from 3 years ago we reported a fitting procedure for triatomics which entails the use of the Aguado-Paniagua potential function for diatomics. The functional form includes from 4 to 10 linear parameters and 2 exponential parameters. I fitted the function to a set of ab initio energy points for the OH radical and the O2 anion over a range of about 2 angstroms and extrapolated it to the dissociation limits. The accuracy of the fitting procedure is far from the best for triatomics but the errors of the fits I obtained for the diatomics are essentially negligible. The work was reported in Chemical physics letters, vol 292, (1998), pg 57-62 W.-T. Chan and I. P. Hamilton <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< I suspect there are some ccl users who know about getting good quality vibrational wavefunctions from ab initio potentials, and there may be some existing code out there to help solve this problem. I'd appreciate any suggestions, pointers to papers that I have overlooked, or codes. I'll post a summary on this topic soon. Steve Williams >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.. The program LEVEL by Bob Le Roy at the University of Waterloo may suit your purpose. The program was written to solve the (nuclear) Schrodinger equation for a given diatomic potential and can calculate Frank-Condon factor as well. Prof Le Roy's homepage is at http://sciborg.uwaterloo.ca/~leroy/ Click 'Computer Programs' from there and you will find the description of LEVEL and other related programs. Wai-To Chan From chemistry-request@server.ccl.net Mon Nov 12 06:05:43 2001 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fACB5gB23867 for ; Mon, 12 Nov 2001 06:05:42 -0500 Received: from imim.es (i21.imim.es [193.147.240.127]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id V0GDD7N4; Mon, 12 Nov 2001 12:06:26 +0100 Sender: hteran@ccl.net Message-ID: <3BEFAC1E.71655587@imim.es> Date: Mon, 12 Nov 2001 12:01:50 +0100 From: "Hugo G. de Teran" X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Autodock errors Content-Type: multipart/alternative; boundary="------------ECFBB186EDE72D14734045D8" --------------ECFBB186EDE72D14734045D8 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, When running autodock, I found the next problem: DPF> ga_run 10 # do this many GA or LGA runs NOTE: Command mode has been set. Sorry, genetic algorithm-local search cannot be performed. DPF> DPF> # Perform Cluster Analysis DPF> analysis # do cluster analysis on results NOTE: Command mode has been set, so cluster analysis cannot be performed. >>> Closing the docking parameter file (DPF)... ________________________________________________________________________________ /usr/local/modelling/AutoDock_3.0/bin/sgi4D.IRIX64_6.5_R10000/autodock3: NOW IN COMMAND MODE. And The calculation stays on standby. The parameters of the dpf are exactly the same to those of a previous calculation that works fine. The only difference is that the macromolecule is in other conformation (the sidechains), but the new pdbqs, gpf, and grid maps are all ok. I don't know what it means "Command mode has been set", but I did not introduce any new parameters. Any ideas? Thanks -- Hugo G. de Teran Castañon G. R. Informatica Biomedica Institut Municipal d'Investigacio Medica - IMIM C/ Dr Aiguader, 80, E-08003/ Barcelona (SPAIN) Ph: +34 93 221 10 09 ext 2340 Fax: Fax: +34 93 221 3237 http://www1.imim.es/modeling/ --------------ECFBB186EDE72D14734045D8 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  
Dear all,
When running autodock, I found the next problem:

DPF> ga_run 10          # do this many GA or LGA runs

NOTE: Command mode has been set.  Sorry, genetic algorithm-local search cannot be performed.

DPF>
DPF> # Perform Cluster Analysis
 

DPF> analysis           # do cluster analysis on results

NOTE: Command mode has been set, so cluster analysis cannot be performed.

>>> Closing the docking parameter file (DPF)...

________________________________________________________________________________

/usr/local/modelling/AutoDock_3.0/bin/sgi4D.IRIX64_6.5_R10000/autodock3: NOW IN COMMAND MODE.

And The calculation stays on standby.
The parameters of the dpf are exactly the same to those of a previous calculation that works fine. The only difference is that the macromolecule is in other conformation (the sidechains), but the new pdbqs, gpf, and grid maps are all ok. I don't know what it means "Command mode has been set", but I did not introduce any new parameters.
Any ideas?
Thanks 

-- 
Hugo G. de Teran Castañon
G. R. Informatica Biomedica
Institut Municipal d'Investigacio Medica - IMIM
C/ Dr Aiguader, 80, E-08003/ Barcelona (SPAIN)

Ph: +34 93 221 10 09 ext 2340
Fax: Fax: +34 93 221 3237
                    
                    http://www1.imim.es/modeling/
  --------------ECFBB186EDE72D14734045D8-- From chemistry-request@server.ccl.net Mon Nov 12 04:31:10 2001 Received: from rbadb2.rbacpxclu.bas.roche.com ([196.3.50.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAC9V8B21191 for ; Mon, 12 Nov 2001 04:31:09 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KAM3AXKDHC9AQ4BN@Roche.COM> for chemistry@ccl.net; Mon, 12 Nov 2001 10:28:51 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KAM3AKATTM9AQ4EH@Roche.COM>; Mon, 12 Nov 2001 10:28:33 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Mon, 12 Nov 2001 10:28:53 +0100 Content-return: allowed Date: Mon, 12 Nov 2001 10:28:50 +0100 From: "Borosy, Andras {Basi~Basel}" Subject: RE: 3-D glasses To: "'Deley Sulton'" , chemistry@ccl.net Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA858@rbamsem3.bas.roche.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAC9VAB21192 Dear Mr. Sulton, > > I am looking for some high quality red/blue 3-D glasses for viewing > large molecule dynamics in Spartan and other programs with 3-D > capabilities. If anyone knows of a company which carries > this, please > let me know. http://www.nuvision3d.com/ Best, Borosy, András Basilea Pharmaceutica Ltd POB 3255, 65/316 4002 Basel tel: +41-61-6885469 fax: +41-61-6882139 www.basileapharma.com From chemistry-request@server.ccl.net Mon Nov 12 12:48:00 2001 Received: from mail.rochester.edu (root@[128.151.224.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fACHm0B02414 for ; Mon, 12 Nov 2001 12:48:00 -0500 Received: from ice (ice.chem.rochester.edu [128.151.195.5]) by mail.rochester.edu (8.11.6/8.11.6) with SMTP id fACHmH92634844 for ; Mon, 12 Nov 2001 12:48:17 -0500 (EST) Message-Id: <200111121748.fACHmH92634844@mail.rochester.edu> Date: Mon, 12 Nov 2029 13:3:54 -0500 From: wei zhuang To: "chemistry@ccl.net" Subject: doing MD to an organic molecule with aromatic group X-mailer: FoxMail 3.11 Release [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear all: I want to do MD to a organic molecule which has a quinoline group.I am using MM3 force field.however,they deal with pi system with a SCF(or VESCF)method and it can only do the minimization,for the dynamic,it is not so accurate.could anybody tell me what can I do,is that any new method or program that I can use? thank you best regards wei zhuang weiz@mail.rochester.edu From chemistry-request@server.ccl.net Mon Nov 12 14:26:24 2001 Received: from seas.marine.usf.edu ([131.247.136.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fACJQOB05109 for ; Mon, 12 Nov 2001 14:26:24 -0500 Received: from seas (ms139dhcp231.marine.usf.edu [131.247.139.231]) by seas.marine.usf.edu (8.11.4/8.11.4) with SMTP id fACJQJg18512 for ; Mon, 12 Nov 2001 14:26:19 -0500 (EST) Message-ID: <000b01c16bc8$f324f000$e78bf783@marine.usf.edu.seas.marine.usf.edu> From: "luo" To: Subject: Molecular Volumes, Free Softeware? Date: Mon, 12 Nov 2001 14:25:35 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0008_01C16B85.E48490C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_0008_01C16B85.E48490C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I am searching a free software to predict organic molecular volumes.=20 Who would help me? Your help is appreciated greatly. Yu-Ran Luo, Ph.D. luo@seas.marine.usf.edu ------=_NextPart_000_0008_01C16B85.E48490C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
I am searching a free software to predict organic = molecular=20 volumes.
 
Who would help me?
 
Your help is appreciated greatly.
 
Yu-Ran Luo, Ph.D.
 
luo@seas.marine.usf.edu
 
------=_NextPart_000_0008_01C16B85.E48490C0-- From chemistry-request@server.ccl.net Mon Nov 12 14:10:12 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fACJA9B04629 for ; Mon, 12 Nov 2001 14:10:10 -0500 Received: from ppp-212.56.193.78.mldnet.com (ppp-212.56.193.78.mldnet.com [212.56.193.78]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id VAA00849 for ; Mon, 12 Nov 2001 21:09:59 +0200 Date: Mon, 12 Nov 2001 21:18:06 +0200 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <212846887.20011112211806@yahoo.com> To: chemistry@ccl.net Subject: Basis set for Fe, Co, Mn, Mg MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear chemistry, Could anybody point me out good basis set for Fe, Co, Mn, Mg (to be used in GAMESS for calculation of Fe in porphyrin ring)? Best regards, Mike mailto:MikePeleah@yahoo.com