From owner-chemistry@ccl.net Thu Jul 22 00:33:01 2010 From: "Adam Zabell adam.zabell]_[gmail.com" To: CCL Subject: CCL: HOW TO GET STARTED ON YASARA Message-Id: <-42321-100721232518-2046-wXG28IjmZJke8VIBgT3TMQ%%server.ccl.net> X-Original-From: Adam Zabell Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Jul 2010 23:25:08 -0400 MIME-Version: 1.0 Sent to CCL by: Adam Zabell [adam.zabell,+,gmail.com] > Instead of watching the same video for three weeks, just try to read a book > on the topic or just follow the old "try & error" strategy until the answer > comes. At the risk of being less serious, try & error looks a lot like this: http://www.xkcd.com/627/ -- Adam From owner-chemistry@ccl.net Thu Jul 22 04:12:00 2010 From: "Ramon Crehuet rcsqtc%a%iqac.csic.es" To: CCL Subject: CCL: HOW TO GET STARTED ON YASARA Message-Id: <-42322-100722035929-7129-lBhT2yEEg1DIZLWeRlgp1g]_[server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Jul 2010 09:59:20 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc||iqac.csic.es] I would like to add that if you are doing your masters thesis you now belong to a research group, probably with grad students, post-doct, tenured researchers, etc. They probably have experience with the kind of project you have to do. You told us "my supervisor is too busy", and what do you think we do all day long? Wait for e-mails un under-supervised people? Assuming that your supervisor is too busy and that we are not is a lack of respect. All the best, Ramon On 07/22/2010 05:48 AM, Dr Ponnadurai Ramasami ramchemi!A!intnet.mu wrote: > > Sent to CCL by: "Dr Ponnadurai Ramasami" [ramchemi(0)intnet.mu] > Dear CCL Users > I strongly agree with Gonzalo. > This is professional form. > > There are many issues that can be addressed with different help services. > All the best. > Ramasami > > ----- Original Message ----- >> From: "JOEL NKEM EGWUONWU joel_nkem**yahoo.com" >> > To: "Ramasami, Ponnadurai " > Sent: Wednesday, July 21, 2010 9:02 PM > Subject: CCL: HOW TO GET STARTED ON YASARA > > >> From owner-chemistry@ccl.net Thu Jul 22 04:47:00 2010 From: "Chris Swain swain*mac.com" To: CCL Subject: CCL: ChemSpider Safari Extension Updated Message-Id: <-42323-100722042231-14314-v6xXTkHzr5CdUy2eDZ1Kiw ~ server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Boundary_(ID_x9WQ3iFLQoBCNPywRkgqWw)" Date: Thu, 22 Jul 2010 09:22:20 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain() mac.com] --Boundary_(ID_x9WQ3iFLQoBCNPywRkgqWw) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Hi, A few people contacted me about the ChemSpider Safari Extension with helpful comments so i thought I'd mention that the ChemSpider Safari Extension has now been updated. http://homepage.mac.com/swain/Macinchem/page5/files/8e05b503736444c024bc9a456fdaa464-569.html The new version builds on the brilliant work of the ChemSpider team and now displays 2D and 3D structures, allows the user to zoom in on a structure and download a structure. Works with Safari on both Macs and Windows Cheers, Chris --Boundary_(ID_x9WQ3iFLQoBCNPywRkgqWw) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT Hi,

A few people contacted me about the ChemSpider Safari Extension with helpful comments so i thought I'd mention that the ChemSpider Safari Extension has now been updated.

http://homepage.mac.com/swain/Macinchem/page5/files/8e05b503736444c024bc9a456fdaa464-569.html

The new version builds on the brilliant work of the ChemSpider team and now displays 2D and 3D structures, allows the user to zoom in on a structure and download a structure.

Works with Safari on both Macs and Windows

Cheers,

Chris

--Boundary_(ID_x9WQ3iFLQoBCNPywRkgqWw)-- From owner-chemistry@ccl.net Thu Jul 22 05:22:00 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis[#]borealisgroup.com" To: CCL Subject: CCL: HOW TO GET STARTED ON YASARA Message-Id: <-42324-100722045305-22872-fBht3qFGN25AyEERTNH8gw- -server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 22 Jul 2010 10:52:52 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis:_:borealisgroup.com] Joel I would recommend you look for some on-line tutorials. They tend to be very good and helpful (well most of the times). Also the program's web page can be a good place to start http://www.yasara.org/movies.htm Usually people have two types of problems with these highly complex mathematically based software. They either can't understand how to use the software or a particular application of it (but understand the theories behind the maths) or they don't understand the actual theories and assumptions used to derive the equations. If your problem is the first one then just try to calculate something easy and simple that you already know the answer. That way you should be able to see how the program works and follow the iterations. After you understand the basics you can start increasing the level of complexity towards the types of simulations you're interested in. If your problem is the second one then I'm afraid no help in terms of software usage will be useful to you. In that case you need to pick up a book and read through the theories and assumptions on how the types of calculations you're are interested in are setup. After you do this you will see that all these programs work in more or less the same manner, and as soon as you know how to use one you're almost proficient in the vast majority of them. In this quest your colleagues and supervisors will be your best source of information (at least in the beginning), so use them well! I hope this helps Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com::ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com::ccl.net] On Behalf Of Ramon Crehuet rcsqtc%a%iqac.csic.es Sent: Thursday, July 22, 2010 9:59 AM To: Gkourmpis, Thomas Subject: CCL: HOW TO GET STARTED ON YASARA Sent to CCL by: Ramon Crehuet [rcsqtc||iqac.csic.es] I would like to add that if you are doing your masters thesis you now belong to a research group, probably with grad students, post-doct, tenured researchers, etc. They probably have experience with the kind of project you have to do. You told us "my supervisor is too busy", and what do you think we do all day long? Wait for e-mails un under-supervised people? Assuming that your supervisor is too busy and that we are not is a lack of respect. All the best, Ramon On 07/22/2010 05:48 AM, Dr Ponnadurai Ramasami ramchemi!A!intnet.mu wrote: > > Sent to CCL by: "Dr Ponnadurai Ramasami" [ramchemi(0)intnet.mu] > Dear CCL Users > I strongly agree with Gonzalo. > This is professional form. > > There are many issues that can be addressed with different help services. > All the best. > Ramasami > From owner-chemistry@ccl.net Thu Jul 22 05:57:00 2010 From: "Kurt De Grave Kurt.DeGrave]_[cs.kuleuven.be" To: CCL Subject: CCL: iPad question Message-Id: <-42325-100722053627-11731-lpRQCuaQAG0QhC413CUmYA^_^server.ccl.net> X-Original-From: Kurt De Grave Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Jul 2010 11:36:07 +0200 MIME-Version: 1.0 Sent to CCL by: Kurt De Grave [Kurt.DeGrave~~cs.kuleuven.be] Joe Leonard jleonard42,gmail.com wrote: > Sent to CCL by: Joe Leonard [jleonard42:+:gmail.com] Folks, I figure > some of CCL's readers have iPads and have played with them a bit. I > am aware of how people use them for reading literature and books, but > I wonder whether anybody has tried to get graphics applications like > PyMOL (or even modeling packages) to use the iPad as a front-end. > > I have seen an iX11 application, but this would require both X11 and > OpenGL (menus and graphics). I would think the iPad could perform at > least as well as a 4-5 year old PC, That's a bit too optimistic, 4-5 years ago we already had 2+GHz dual core superscalar OoOE CPUs. It'll be more comparable to a 7-10 year old PC. Also, you can't run arbitrary programs on it, only those blessed by the manufacturer, and only for as long as they stay blessed. An Android-based tablet may be better suited in that regard. best regards, kurt. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Thu Jul 22 06:47:01 2010 From: "Emran Heshmati heshmaty/a\yahoo.com" To: CCL Subject: CCL:G: gaussian view and antechamber Message-Id: <-42326-100722064121-20162-aWrnx/gsYWYGuGjGFRmmFQ^^^server.ccl.net> X-Original-From: Emran Heshmati Content-Type: multipart/alternative; boundary="0-1847498827-1279795274=:50523" Date: Thu, 22 Jul 2010 03:41:14 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Emran Heshmati [heshmaty%%yahoo.com] --0-1847498827-1279795274=:50523 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Lamees=20 After drawing an saving your molecule, open it in a text editor such as wor= dpad, and change its=A0charge and mutiplesity.=20 =A0 Best Regards Emran Heshmati P Save a tree... please don't print this e-mail unless you really need to --- On Thu, 22/7/10, lamees hegazy lameesshams=3Dyahoo.com wrote: > From: lamees hegazy lameesshams=3Dyahoo.com Subject: CCL:G: gaussian view and antechamber To: "Heshmati, Emran " Date: Thursday, 22 July, 2010, 4:59 AM Hi CCl, I'm trying to build a charged molecule using gaussian view and I don't find= any option which allows me to do that.=20 Also, I'm trying to use mol2 file generated by gaussian view in antechamber= program but antechamber can't read the mol2 file. Does any one has these e= rrors before. =A0 =0A=0A --0-1847498827-1279795274=:50523 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Lamees

After drawing an saving your molecule, open it in a text editor such a= s wordpad, and change its charge and mutiplesity.

&nb= sp;

Best Regards
Emran = Heshmati
P Save a tree... please don't print this e-mail unless y= ou really need to

--- On Thu, 22/7/10, lamees h= egazy lameesshams=3Dyahoo.com <owner-chemistry,+,ccl.net> wr= ote:

From: lamees hegazy lameesshams=3Dyahoo.com <o= wner-chemistry,+,ccl.net>
Subject: CCL:G: gaussian view and antechamber=
To: "Heshmati, Emran " <heshmaty,+,yahoo.com>
Date: Thur= sday, 22 July, 2010, 4:59 AM

Hi CCl,

I'm trying to build a charged molecule usin= g gaussian view and I don't find any option which allows me to do that. Also, I'm trying to use mol2 file generated by gaussian view in antechambe= r program but antechamber can't read the mol2 file. Does any one has these = errors before.

<= /DIV>

--0-1847498827-1279795274=:50523-- From owner-chemistry@ccl.net Thu Jul 22 08:32:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim]=[compchem.net" To: CCL Subject: CCL:G: gaussian view and antechamber Message-Id: <-42327-100722082834-6322-Mh2NgHyVjwFt052Pzw3BSg\a/server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6dbe2bc5dfd98048bf90dc7 Date: Thu, 22 Jul 2010 13:28:13 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim%x%compchem.net] --0016e6dbe2bc5dfd98048bf90dc7 Content-Type: text/plain; charset=ISO-8859-1 Dear Lamees I don't remember well what's the problem with mol2 file generated by GaussView. You can save your file in PDB formate by Gaussview, and then use OpenBabel to convert it to mol2. This mol2 file works well with antechamber. I have just one more note, I do recommend to use R.E.D. software to generate your molecular charge, instead of antechamber. Sincerely; M. Ibrahim On Thu, Jul 22, 2010 at 1:29 AM, lamees hegazy lameesshams=yahoo.com < owner-chemistry(a)ccl.net> wrote: > Hi CCl, > > I'm trying to build a charged molecule using gaussian view and I don't find > any option which allows me to do that. > Also, I'm trying to use mol2 file generated by gaussian view in antechamber > program but antechamber can't read the mol2 file. Does any one has these > errors before. > > > > > > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim(a)compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6dbe2bc5dfd98048bf90dc7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Lamees

I don't remember well what's the problem with mol2 = file generated by GaussView.

You can save your file in PDB format= e by Gaussview, and then use OpenBabel to convert it to mol2. This mol2 fil= e works well with antechamber.

I have just one more note, I do recommend to use R.E.D. software to ge= nerate your molecular charge, instead of antechamber.

Sincerely;<= /div>

M. Ibrahim

On Thu, Jul 2= 2, 2010 at 1:29 AM, lamees hegazy lameesshams=3Dyahoo.com <owner-chemistry(a)ccl.net> wrote:

Hi CCl,
I'm trying to build a charged molecule using gaussian view and I = don't find any option which allows me to do that.
Also, I'm trying to use mol2 file generated by gaussian view in antecha= mber program but antechamber can't read the mol2 file. Does any one has= these errors before.

=A0

--
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Univ= ersity of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim(a)compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601

--0016e6dbe2bc5dfd98048bf90dc7-- From owner-chemistry@ccl.net Thu Jul 22 22:49:01 2010 From: "Aimee Tomlinson altomlinson..northgeorgia.edu" To: CCL Subject: CCL:G: Gaussian, TDDFT & MO percentages Message-Id: <-42328-100722161554-16728-ZwLwkEEX84pIn/wNYsdY1A{:}server.ccl.net> X-Original-From: "Aimee Tomlinson" Date: Thu, 22 Jul 2010 16:15:53 -0400 Sent to CCL by: "Aimee Tomlinson" [altomlinson-*-northgeorgia.edu] Does anyone know what the keyword is to generate percent contributions to excited states using a TDDFT in Gaussian?