From owner-chemistry@ccl.net Thu Feb 7 06:30:01 2008 From: "Barabara Jagoda-Cwiklik barbara]|[fh.huji.ac.il" To: CCL Subject: CCL:G: Understanding Gaussian 03 output of simple geometry optimization Message-Id: <-36243-080207062735-18818-bP80qyjeyaNQQXdqqsnzsg .. server.ccl.net> X-Original-From: "Barabara Jagoda-Cwiklik" Content-Type: multipart/alternative; boundary="----=_Part_8561_21442867.1202379705805" Date: Thu, 7 Feb 2008 12:21:45 +0200 MIME-Version: 1.0 Sent to CCL by: "Barabara Jagoda-Cwiklik" [barbara(a)fh.huji.ac.il] ------=_Part_8561_21442867.1202379705805 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline On Feb 6, 2008 7:45 PM, Sebastian Krapf science],[k78.eu < owner-chemistry-*-ccl.net> wrote: > > Sent to CCL by: "Sebastian Krapf" [science],[k78.eu] > Dear CCL users, > > I am using Gaussian 03 as a beginner and I have got a little problem in > understanding the output of a simple geometry optimization of CsOH. Can > anybody tell me what the two different angles in the output tell me and what > do the negative numbers in the "Definition part" mean? > ---------------------------- > ! Optimized Parameters ! > ! (Angstroms and Degrees) ! > -------------------------- > -------------------------- > ! Name Definition Value Derivative Info. > ! > > -------------------------------------------------------------------------------- > ! R1 R(1,2) 2.6143 -DE/DX = 0.0 > ! > ! R2 R(2,3) 0.978 -DE/DX = 0.0 > ! > ! A1 L(1,2,3,-2,-1) 177.0425 -DE/DX = 0.0 > ! > ! A2 L(1,2,3,-1,-2) 180.0 -DE/DX = 0.0 > ! > > ------------------------------------------------------------------------------- > Hi Sebastian, "Definition" column you have shown contains redundant internal coordinates which are default during Gaussian's optimization. This extra angle is added automatically by Berny optimizer because your molecule is almost linear (the second angle is introduced when 175owner-chemistry-*-ccl.net> wrote:

Sent to CCL by: "Sebastian  Krapf" [science],[k78.eu]
Dear CCL users,

I am using Gaussian 03 as a beginner and I have got a little problem in understanding the output of a simple geometry optimization of CsOH. Can anybody tell me what the two different angles in the output tell me and what do the negative numbers in the "Definition part" mean?
               ----------------------------
                          !   Optimized Parameters   !
                          ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  2.6143         -DE/DX =    0.0                 !
 ! R2    R(2,3)                  0.978          -DE/DX =    0.0                 !
 ! A1    L(1,2,3,-2,-1)        177.0425         -DE/DX =    0.0                 !
 ! A2    L(1,2,3,-1,-2)        180.0            -DE/DX =    0.0                 !
 -------------------------------------------------------------------------------


Hi Sebastian,

"Definition" column you have shown contains redundant internal coordinates which are default during Gaussian's optimization.
This extra angle is added automatically by Berny optimizer because your molecule is almost linear (the second angle is introduced when 175<angle<180deg), but it doesn't mean that there is something wrong with your calculation! The subsequent table called "Input orientation" gives final coordinates.

Best,
Basia

--
Barbara Jagoda-Cwiklik, Ph.D
The Fritz Haber Research Center for Molecular Dynamics
Institute of Chemistry
The Hebrew University of Jerusalem
Jerusalem, ISRAEL
e-mail: barbara-*-fh.huji.ac.il ------=_Part_8561_21442867.1202379705805-- From owner-chemistry@ccl.net Thu Feb 7 08:57:00 2008 From: "=?ISO-8859-15?Q?Nicola_Giacch=E8?= nicolag]~[chimfarm.unipg.it" To: CCL Subject: CCL: PseudoReceptor FREE Software Message-Id: <-36244-080207060102-17069-NHuruiNtkWZV7d/Z8TMcRA-,-server.ccl.net> X-Original-From: =?ISO-8859-15?Q?Nicola_Giacch=E8?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 07 Feb 2008 11:28:29 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-15?Q?Nicola_Giacch=E8?= [nicolag++chimfarm.unipg.it] Hi, i would like to know if there a list of FREE Academic software to develop "pseudoreceptors" and QSAR analysis. thanks -- Nicola Giacchè, PhD Student Bachelor Degree in Medicinal Chemistry and Technology of Drugs University of Perugia Department of Medicinal Chemistry and Technology of Drugs Via del Liceo, 1 - 06123 Perugia (Italy) Tel ++39 075 585 5169/5156 E-mail: nicolag%chimfarm.unipg.it From owner-chemistry@ccl.net Thu Feb 7 09:32:00 2008 From: "Steve Williams willsd#appstate.edu" To: CCL Subject: CCL: AIM for non minimum structures Message-Id: <-36245-080207085923-24361-W30/KHsYu3Lb8/rvJed+Ng]-[server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Feb 2008 08:53:41 -0500 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd[-]appstate.edu] Following the recent discussion of AIM on CCL, I have a question for the AIM experts out there: In his book (Atoms in Molecules, and Introduction) Popelier, on pages 60 and 61, makes the point that AIM analysis of bonding is only valid for energy minimum structures, and not for such molecular structures as points on an IRC, or for transition states. There have however, been some recent publications (like Salazar et al. J. Phys. Chem. A, 2007, 111, p 7848 and Wagner et al. Tetrahedron, 2007, 63, p5251) that explicity discuss and attribute meaning to bond critical points for TS or IRC structures. What is the current opinion (and why is it what it is) on AIM applied to molecules in non energy minimum geometries? Thanks, Steve Williams From owner-chemistry@ccl.net Thu Feb 7 11:33:00 2008 From: "Iain Wallace iain.m.wallace(0)gmail.com" To: CCL Subject: CCL: Another Pipeline Pilot Question: Loops Message-Id: <-36246-080206225209-10127-6i8k+Lz3DnZp1ZWrL4Gp8Q],[server.ccl.net> X-Original-From: "Iain Wallace" Content-Type: multipart/alternative; boundary="----=_Part_42042_13147915.1202354567613" Date: Wed, 6 Feb 2008 22:22:47 -0500 MIME-Version: 1.0 Sent to CCL by: "Iain Wallace" [iain.m.wallace!^!gmail.com] ------=_Part_42042_13147915.1202354567613 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I was wondering if any one would be able to help me. I can not figure out how to "loop" over a PipeLine pilot protocol that I have written. I would like to run it a number of times and generate some statistics. I have written a protocol to build a model to classify drugs from non-drugs. It takes in actives/inactives and splits them into a training and test set. The model is then build using the training set, and then validated on the test set. I am wondering if there is any way I can loop over this procedure, to turn it into a cross validation procedure? As an aside, does anybody know of a good resource for example PipeLine pilot protocols? This is all rather new to me! Thanks for any help :) Iain ------=_Part_42042_13147915.1202354567613 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all,

I was wondering if any one would be able to help me. I can not figure out how to "loop" over a PipeLine pilot protocol that I have written. I would like to run it a number of times and generate some statistics.
I have written a protocol to build a model to classify drugs from non-drugs.
It takes in  actives/inactives and splits them into a training and test set. The model is then build using the training set, and then validated on the test set.
I am wondering if there is any way I can loop over this procedure, to turn it into a cross validation procedure?

As an aside, does anybody know of a good resource for example PipeLine pilot protocols? This is all rather new to me!

Thanks for any help :)

Iain




------=_Part_42042_13147915.1202354567613-- From owner-chemistry@ccl.net Thu Feb 7 21:40:01 2008 From: "J Chen chenzhz|*|sohu.com" To: CCL Subject: CCL: cutoff distances for VDW interactions of site-site pairing Message-Id: <-36247-080207212705-12075-u512Y/WY8aiW/DAwk9eLrg*_*server.ccl.net> X-Original-From: "J Chen" Date: Thu, 7 Feb 2008 21:27:01 -0500 Sent to CCL by: "J Chen" [chenzhz__sohu.com] Hello, CCLer. Are there any literatures that include cutoff distances for VDW interactions of site-site pairing, such as (C)H---O pair? I will appreciate any help from you. Thanks. J. Chen