From chemistry-request@server.ccl.net Mon Oct 22 03:01:08 2001 Received: from popeye.latrobe.edu.au ([131.172.4.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9M716B27057 for ; Mon, 22 Oct 2001 03:01:07 -0400 Received: from [131.172.148.97] (gln.chem.latrobe.edu.au [131.172.148.97]) by popeye.latrobe.edu.au (8.9.3/8.9.3) with ESMTP id RAA19218 for ; Mon, 22 Oct 2001 17:03:51 +1000 (EST) Mime-Version: 1.0 X-Sender: chemgn@pop.latrobe.edu.au Message-Id: Date: Mon, 22 Oct 2001 17:05:00 +1000 To: chemistry@ccl.net From: "Graeme L. Nyberg" Subject: GAMESS - $SURF Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear GAMESS users, How do I utilise $SURF to get a potential energy scan? Whem I try, I get an error message indicating IVEC1 ("an array of two atoms") is incorrectly specified. Unfortunately there is no example given in the documentation, and I've tried all the alternatives I can think of. Taking HCN as an example (atom numbers 1,2,3 resp), and wanting the energy as a function of the H-C bond length, I would have thought IVEC=1,2 [or, maybe, (1,2)] {and the related IGRP1=2,3 [or (2,3)]} but this doesn't work. What's the required format? Thanks, Graeme Nyberg. From chemistry-request@server.ccl.net Mon Oct 22 06:45:27 2001 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9MAjQB32391 for ; Mon, 22 Oct 2001 06:45:26 -0400 Received: from imim.es (diana.imim.es [193.147.240.77]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id V277DS6X; Mon, 22 Oct 2001 12:48:53 +0200 Sender: mbarbany@ccl.net Message-ID: <3BD3F984.C501C2C2@imim.es> Date: Mon, 22 Oct 2001 12:48:36 +0200 From: Montserrat Barbany Puig X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-2smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: rotatable bonds Content-Type: multipart/alternative; boundary="------------F7A1B422F69CF437C2BCAA75" --------------F7A1B422F69CF437C2BCAA75 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL's: I am interested in a program that could detect rotatable bonds automatically, without user interventention. Thanks in advance -- Institut Municipal d'Investigació Mèdica Montserrat Barbany Puig c/Dr.Aiguader,80 08803-Barcelona (Spain) email: mbarbany@imim.es Tel: 93 2211009 Fax:93 2213237 --------------F7A1B422F69CF437C2BCAA75 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL's:

I am interested in a program that could detect rotatable bonds
automatically,  without user interventention.
 

Thanks in advance
 
  

-- 
Institut Municipal d'Investigació Mèdica
Montserrat Barbany Puig
c/Dr.Aiguader,80
08803-Barcelona (Spain)
email: mbarbany@imim.es
Tel: 93 2211009 Fax:93 2213237
  --------------F7A1B422F69CF437C2BCAA75-- From chemistry-request@server.ccl.net Mon Oct 22 10:22:22 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9MEMLB04113 for ; Mon, 22 Oct 2001 10:22:22 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id KAA02319; Mon, 22 Oct 2001 10:25:11 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 22 Oct 2001 10:25:05 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GLM00H3Y2HL34@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Mon, 22 Oct 2001 10:20:09 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id <4YZZ74AY>; Mon, 22 Oct 2001 10:24:51 -0400 Content-return: allowed Date: Mon, 22 Oct 2001 10:24:51 -0400 From: "Shobe, Dave" Subject: T.sub.e energies from "cis opt" in G98 To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C1565E@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 When one does a CIS single point calculation in G98, the output includes the excitation energy at that particular geometry, i.e. a vertical transition energy. Typically this is done at the minimum-energy geometry for the ground state. However, many researchers report T.sub.e energies, which are "well-to-well", i.e. from the minimum-energy geometry of the ground state to the minimum-energy geometry of the excited state. The keywords CIS(ROOT=n) OPT take the molecule to the minimum geometry for the excited state, but it's not obvious how to calculate T.sub.e from the output. (Yes, I can make an intelligent guess of how to do that, but I don't have high confidence that it's the most correct way of obtaining T.sub.e). --David Shobe From chemistry-request@server.ccl.net Mon Oct 22 13:23:08 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9MHN8B07049 for ; Mon, 22 Oct 2001 13:23:08 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA11110; Mon, 22 Oct 2001 13:25:57 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 22 Oct 2001 13:25:51 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GLM00IODAUVW8@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Mon, 22 Oct 2001 13:20:55 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id <4YZZ74ZA>; Mon, 22 Oct 2001 13:25:37 -0400 Content-return: allowed Date: Mon, 22 Oct 2001 13:25:37 -0400 From: "Shobe, Dave" Subject: Is TD or Zindo better than CIS? To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15666@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 A question related to the last one. I'm aware that CIS has its shortcomings and the results should be considered only a rough sketch of the molecule's spectrum. Gaussian has two other methods (neither of which I've used) for calculating excited states: Zindo and TD. Are these significatnly better than CIS? Zindo being a semiempirical method, is it only good for certain kinds of molecules? Should I be looking at programs other than Gaussian for this type of calculation? I've noticed that the T.sub.e values are typically calculated at the same level of theory as the ground state (using guess=alter I presume). I suppose this is preferable when it succeeds. This is often possible for diatomics, but once symmetry constraints are removed it's difficult to keep the electron configuration from "falling" into the ground state. --David Shobe From chemistry-request@server.ccl.net Mon Oct 22 15:09:27 2001 Received: from borzoi.bq.ub.es ([161.116.154.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9MJ9QB08937 for ; Mon, 22 Oct 2001 15:09:26 -0400 Received: from borzoi.bq.ub.es (localhost [127.0.0.1]) by borzoi.bq.ub.es (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id VAA61544 for ; Mon, 22 Oct 2001 21:10:13 -0700 (PDT) Sender: robert@borzoi.bq.ub.es Message-ID: <3BD4EDA5.F201A7A0@borzoi.bq.ub.es> Date: Tue, 23 Oct 2001 06:10:13 +0200 From: Robert Soliva X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: autodock cryst.str. minimisation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Autodock users, I have a couple of questions regarding the use of autodock to minimise with the local search method. I apologise if they seem too obvious (I have just started using the program). 1- I want to minimise a ligand-receptor structure taken from the pdb. I understand I am supposed to use the do_local_only command, but I do not know how to tell the program to optimise without moving the ligand randomly out of the active site. Could anybody send me an example of a dpf input file that can do this? 2-Is is possible once the minimisation has taken place, to have not only the value for the total interaction, but also the value for the different terms of the scoring function (i.e. to have the value and its composition in terms of vdW, electrostatic, H bonding torsion and desolvation?). Is there a command to ask the program for those values? Please reply to robert@sgmol.bq.ub.es Thank you very much for your help. Robert. From chemistry-request@server.ccl.net Mon Oct 22 16:28:44 2001 Received: from femail43.sdc1.sfba.home.com ([24.254.60.37]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9MKSeB09703 for ; Mon, 22 Oct 2001 16:28:44 -0400 Received: from C1353359A ([65.4.172.51]) by femail43.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011022203125.XEZT29972.femail43.sdc1.sfba.home.com@C1353359A>; Mon, 22 Oct 2001 13:31:25 -0700 Message-ID: <00e601c15b38$2c169c20$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: "Shobe, Dave" , "'CCL'" References: <157A51F55AAAD3119CD70008C7B1629D01C15666@lvlxch01.unitedcatalysts.com> Subject: Re: CCL:Is TD or Zindo better than CIS? Date: Mon, 22 Oct 2001 13:28:55 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Actually, they are the same thing.....as far as the equations used to generate the CI matrix. > A question related to the last one. I'm aware that CIS has its shortcomings > and the results should be considered only a rough sketch of the molecule's > spectrum. Gaussian has two other methods (neither of which I've used) for > calculating excited states: Zindo and TD. Are these significatnly better > than CIS? Zindo being a semiempirical method, is it only good for certain > kinds of molecules? Should I be looking at programs other than Gaussian for > this type of calculation? > Gaussian likely calculates excited states for Zindo and ab initio Hamiltonians with a single-excitation CI (the Tamm-Dankoff approximation) > from a singlet, single-reference ground state using a fixed geometry that was used to generate the ground state SCF. Certainly, more sophisticated schemes are possible, such as including double excited configurations, non-singlet ground states, etc. I'm not sure if Gaussian supports these (at least for the ZINDO Hamiltonian). From chemistry-request@server.ccl.net Mon Oct 22 23:25:14 2001 Received: from relay.it.northwestern.edu ([129.105.16.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9N3PEB22720 for ; Mon, 22 Oct 2001 23:25:14 -0400 Received: (from mailnull@localhost) by relay.it.northwestern.edu (8.9.3/8.9.3) id WAA02266; Mon, 22 Oct 2001 22:28:05 -0500 (CDT) Received: from [129.105.186.87] (quandong-67-186087.nuts.nwu.edu [129.105.186.87]) by relay.acns.nwu.edu via smap (V2.0) id xma001889; Mon, 22 Oct 01 22:27:54 -0500 Mime-Version: 1.0 X-Sender: hutchisn@mercury.chem.northwestern.edu (Unverified) Message-Id: In-Reply-To: <157A51F55AAAD3119CD70008C7B1629D01C15666@lvlxch01.unitedcatalysts.com> References: <157A51F55AAAD3119CD70008C7B1629D01C15666@lvlxch01.unitedcatalysts.com> Date: Mon, 22 Oct 2001 22:27:44 -0500 To: "Shobe, Dave" From: Geoff Hutchison Subject: Re: CCL:Is TD or Zindo better than CIS? Cc: "'CCL'" Content-Type: text/plain; charset="us-ascii" ; format="flowed" At 1:25 PM -0400 10/22/01, Shobe, Dave wrote: >spectrum. Gaussian has two other methods (neither of which I've used) for >calculating excited states: Zindo and TD. Are these significatnly better >than CIS? Zindo being a semiempirical method, is it only good for certain >kinds of molecules? Should I be looking at programs other than Gaussian for >this type of calculation? It's strange this should come up as I'm working on a manuscript along these lines for a certain set of molecules. But first there's a nomenclature issue. Normally when people say "Zindo," they mean "INDO/S CIS," and so you can't compare "Zindo" to "CIS." Also, I'm not quite sure I know what you mean when you say "TD" since you usually refer to TD-HF or TD-DFT for time-dependent HF or time dependent DFT. If you compare Zindo CIS to HF-CIS for most neutral organic molecules, you'll find Zindo is more accurate. If you compare TD-HF (say the RPA) to HF-CIS, the HF-RPA is better--no surprise since the RPA is one step past the Tamm-Dancoff approximation (CIS). But HF-RPA is not as good as Zindo for most neutral organic molecules. TD-DFT seems to be slightly worse than Zindo for neutral organic molecules, but not by much. Also keep in mind that Zindo CIS as a semiempirical method sometimes incorrectly identifies the composition of certain excitations even if the energy is pretty good. Can't say how Gaussian does on these sorts of things--we can't get it here. As Mark Thompson pointed out, you can also go beyond CIS to CISD, etc. The original ZINDO program from Zerner does let you do things like this, though YMMV. Other programs as well have CISD, CISDT and other higher-order methods. (Dalton springs to mind.) -- -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.nwu.edu/