From owner-chemistry@ccl.net Tue Oct 24 09:42:01 2006 From: "Markus Thut markus.thut^-^iac.unibe.ch" To: CCL Subject: CCL:G: AW: G: Electron Densities Message-Id: <-32860-061023112202-17053-bW3cz6eyOzBJDGgLY9CJXQ_+_server.ccl.net> X-Original-From: Markus Thut Content-Transfer-Encoding: 8bit Content-type: text/plain; charset="iso-8859-1" Date: Mon, 23 Oct 2006 16:23:29 +0200 MIME-version: 1.0 Sent to CCL by: Markus Thut [markus.thut#,#iac.unibe.ch] Hi Diana Gaussian: You need to create .cube files. See in the Gaussian manual the entry for the cubegen-program. You need a program such as molekel or molden, which are able to plot *.cube files. Regards, Markus -----Ursprüngliche Nachricht----- Von: owner-chemistry^^ccl.net [mailto:owner-chemistry^^ccl.net] Gesendet: Samstag, 21. Oktober 2006 20:46 An: Thut, Markus Betreff: CCL:G: Electron Densities Sent to CCL by: "diana yepes" [yepes61[a]gmail.com] ------=_Part_162083_22166930.1161383386871 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear people, Does anyone know how to obtain the electron density from Gaussian or Gamess? We need it either as a function or as a set of points that can be plotted in a 3-D fashion. We appreciate any help we can get. Thanks a lot. Diana Yepes Instituto de Quimica Universidad de Antioquia Medellin, Colombia ------=_Part_162083_22166930.1161383386871 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Dear people,

 

Does anyone know how to obtain the electron density from Gaussian or Gamess?

We need it either as a function or as a set of points that can be plotted in a 3-D fashion.

 

We appreciate any help we can get. Thanks a lot.

 

Diana Yepes

Instituto de Quimica   

Universidad de Antioquia

Medellin, Colombia

------=_Part_162083_22166930.1161383386871--http://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 Tue Oct 24 10:17:00 2006 From: "Hans De Winter hans.dewinter(0)silicos.com" To: CCL Subject: CCL: Silicos releases SiMath under BSD License Message-Id: <-32861-061024084756-19029-K//0jVkEH0dI70caoSPBiQ#,#server.ccl.net> X-Original-From: "Hans De Winter" Date: Tue, 24 Oct 2006 08:47:56 -0400 Sent to CCL by: "Hans De Winter" [hans.dewinter%%silicos.com] SiMath is Silicos' open source library for the manipulation of data matrices and the subsequent mathematical and statistical modeling. SiMath tries to provide a simple C++ API that is data matrix centered and that covers the model building procedure from data preprocessing to training and evaluation of the model. The goal is to provide a library that can be easily integrated into standalone applications. The rationale of SiMath is not to invent the wheel again but to integrate available open source packages and also newly implemented algorithms into one comprehensive library. Several well established libraries exist nowadays, but they all have a different interface and work with their own matrix representation. These tools are incorporated into SiMath and adapted such that their interface is consistent over all tools. For instance, all clustering algorithms are initiated by defining a set of parameters and the actual clustering is done by calling the cluster method with the data matrix. Currently, SiMath contains modules for PCA (or SVD), matrix discretisation, SVM training and evaluation, several clustering algorithms, self-organing map and several general mathematical utilities. More information about SiMath and how to download the source code can be found at: http:// www.silicos.com/simath.html. Silicos is a chemoinformatics-based biotechnology company empowering proprietary multi-target virtual screening technologies for the discovery of novel and high-quality lead compounds. From owner-chemistry@ccl.net Tue Oct 24 10:52:01 2006 From: "Lubos Vrbka lists- -vrbka.net" To: CCL Subject: CCL: rigid body MD Message-Id: <-32862-061024100158-2109-pCM3kiOP07ZRWnqrsCr+yQ()server.ccl.net> X-Original-From: Lubos Vrbka Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Tue, 24 Oct 2006 21:56:06 +0900 MIME-Version: 1.0 Sent to CCL by: Lubos Vrbka [lists^^vrbka.net] > I'm looking for a molecular dynamics package that is able to rigidify > some portion of the system during simulation. So far I have to use an > all-atom force field such as Amber. I heard that there was a program > called MBO(N)D developed by Moldyn. It disappeared long time ago since > the company was bought and its parent company is later gone too. Can > anyone point out any available similar programs? Thanks. you can try dl_poly as well... regards, -- Lubos _%_" http://www.lubos.vrbka.net From owner-chemistry@ccl.net Tue Oct 24 11:26:00 2006 From: "Keith Butler keeeto2000[#]yahoo.co.uk" To: CCL Subject: CCL:G: questions about scrf calculation: ua0/uaff (gaussian) Message-Id: <-32863-061024103930-21827-Mg8pfjGiQCzjNpv+Rkdt/g/./server.ccl.net> X-Original-From: Keith Butler Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 24 Oct 2006 14:37:12 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Keith Butler [keeeto2000*yahoo.co.uk] 4 I have big difficulties to converge the geometries > in solution (both in UA0 and UAHF). Even increase > TSNUM to 300 I could only converge the geometries > with "loose" criteria but not with the default > convergence criteria. Can I use anything to further > converge the geometry? One method which I have used quite sucessfully is to optimise with a larger cavity using Alpha=1.8 for example then optimise this output at Alpha=1.6 and so on until Alpha=1.2 (which is the default). Hope this helps. Keith --- "Xie Wang xie.wang.:.gmail.com" wrote: > Sent to CCL by: "Xie Wang" [xie.wang,+,gmail.com] > Hello, > > I am trying to describe dissociation processes of a > dimeric complex of small organic molecules in > solution. Several questions: > > 1. what is the difference between UA0 and UAFF? Is > there a reference that discussed the details of how > those models are built? > > 2. gaussian output: "Error on total polarization > charges = 0.01466" Is this the total error of the > nuclear and electronic apparant charge? This number > from UA0 model is about 10 times bigger than that > from UAHF. Does this mean UAHF is more accurate? > > 3. Both UA0 and UAHF show this kind of output: > > Partition over spheres: > Sphere on Atom Surface Charge GEl GCav > GDR > 1 C1 2.10 -0.022 -0.04 0.48 > -0.13 > 2 C2 1.53 -0.014 -0.02 0.48 > -0.15 > 3 C3 1.49 0.003 -0.09 0.63 > -0.11 > 4 C4 1.69 0.002 -0.08 0.49 > -0.11 > 5 C5 4.30 -0.028 0.21 1.23 > -0.34 > 6 N6 17.24 0.096 -3.31 2.32 > -1.44 > 7 C7 4.30 -0.028 0.21 1.23 > -0.34 > 8 N8 17.24 0.096 -3.31 2.32 > -1.44 > 9 C9 5.32 -0.037 0.28 1.23 > -0.35 > 10 N10 17.53 0.097 -3.33 2.32 > -1.45 > 11 C11 5.31 -0.037 0.28 1.23 > -0.34 > 12 N12 17.53 0.097 -3.33 2.32 > -1.44 > 13 C13 4.19 -0.005 0.17 1.24 > -0.34 > 14 N14 17.80 0.176 -8.53 2.32 > -1.46 > 15 C15 4.19 -0.005 0.17 1.24 > -0.34 > 16 N16 17.80 0.176 -8.53 2.32 > -1.53 > 17 C17 4.88 -0.008 0.24 1.24 > -0.34 > 18 N18 17.80 0.177 -8.53 2.32 > -1.46 > 19 C19 4.88 -0.008 0.24 1.24 > -0.34 > 20 N20 17.80 0.177 -8.53 2.32 > -1.46 > Added spheres: 100.17 -0.030 -4.55 0.00 > 0.00 > > My first guess is that these are the exposed surface > area/charge/free energy distributed over different > atoms. However, these partitioned numbers do not add > up to the number in the last line (Added > spheres:...). So what do all these information mean? > What is the relation of all these charges to the > "Error on total polarization charges" (question 2)? > > 4 I have big difficulties to converge the geometries > in solution (both in UA0 and UAHF). Even increase > TSNUM to 300 I could only converge the geometries > with "loose" criteria but not with the default > convergence criteria. Can I use anything to further > converge the geometry? > > Any information will be appreciated. Thanks in > advance! > > > > -= 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/> > > > Send instant messages to your online friends http://uk.messenger.yahoo.com From owner-chemistry@ccl.net Tue Oct 24 22:28:00 2006 From: "06900535r-$-polyu.edu.hk" To: CCL Subject: CCL:G: force field parameter change in Gaussian 03 Message-Id: <-32864-061022223421-20580-E5tY7DZ828U7hiJNIq1vMQ[-]server.ccl.net> X-Original-From: <06900535r:polyu.edu.hk> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 23 Oct 2006 09:55:57 +0800 MIME-Version: 1.0 Sent to CCL by: [06900535r,polyu.edu.hk] Sent to CCL by: "elaine chan" [06900535r]_[polyu.edu.hk] > > I want to use molecular mechanics (force field parameters) of gaussian 03 > to optimize platinium complex with toxin substance. But, I don't know how > to create the input file of molecualr mechanics. What parameters and force > field parameters should be set up? > Elaine Chan>