From owner-chemistry@ccl.net Tue Jan 15 02:08:00 2008 From: "etamar,,fh.huji.ac.il" To: CCL Subject: CCL: charge keyword with fixing atoms in gaussian Message-Id: <-36036-080115020631-27436-vj/eRwjKxq4DW6CL7oabVw{=}server.ccl.net> X-Original-From: etamar=-=fh.huji.ac.il Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Tue, 15 Jan 2008 09:09:02 +0200 MIME-Version: 1.0 Sent to CCL by: etamar .. fh.huji.ac.il Hi All i wonder if there is a possibility to fix atoms/bonds when using the charge keyword. the error massage I get is "Cannot AddRedundant with Cartesian or Z-matrix opts." probably because the charge keyword requires opt=z-matrix with z matrix or symbolic Cartesian coordinated. Also , is there a way to skip this opt=z-matrix demand and use regular coordinates with "charge"? Thanks Tamar ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Tue Jan 15 08:42:01 2008 From: "Chris Moth chris.moth{=}Vanderbilt.Edu" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36037-080114105333-2558-r3mbaxFFHjL9cEAd5MxYFA|a|server.ccl.net> X-Original-From: "Chris Moth" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 14 Jan 2008 09:12:49 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: "Chris Moth" [chris.moth(0)Vanderbilt.Edu] C# is a beautiful language for business software development on the Windows platform. The .NET environment shields software development from many problems (opportunities) that lower level languages (C especially) can create. For a nice language to "learn how to program", I would say C# is fine - just as PASCAL was good long ago. You can load Microsoft Visual Studio and be writing your first program very quickly. If you are developing a modern, interactive computational chemistry application with a rich user interface, and you want it to run on a variety of platforms, you might look at Java. Java is a conceptual precursor of .NET - and is perhaps more inherently cross-platform. However, many applications in computational chemistry have no user interface to speak of - and are fundamentally dedicated to computation of results as quickly as possible. Thus compiled FORTRAN and C (vs interprested Java/C#) are going to haev a role in our field for the forseeable future. But yes, they are very old now. Python is certainly interesting - and I would suggest you look at "chimera" as an example of what has been done with it. I was about to write that Python has not caught on with the main-stream software development community - but a quick search at hotjobs.com for "Python" category=Tech Jobs shows 600 listings. That's quite impressive. > > Sent to CCL by: "Mahmoud Arafat Ibrahim" [M_Arafat82 * Yahoo.Com] > Dear Dr. / Prof. > In the fact, I am a new researcher in Computational Chemistry Subject and > I am going to specialized in Drug Design. I have started studying C sharp > as a programming language as my first step in this new field (it was an > advise from one professor). After an intermediate step in C sharp, I am > now confusing about its usage in my new field. Indeed, I found that all > programs have been used in Computational Chemistry are based on FORTRAN or > C language. So, I am now hesitating about my step and asking for advice. > > May you direct me to the best step? > -Stop studying Programming languages as whole where they are usefulness in > Computational Chemistry. > -Study FORTRAN or C language where they are more abundant in Computational > Chemistry. > or > -Continue studying C sharp where it is the most modern language. > I hope to read from you as soon as possible. > Sincerely; > M. Arafat, > Chemistry Department, > Faculty of Science, > Minia university, > Egypt.> > > From owner-chemistry@ccl.net Tue Jan 15 10:28:00 2008 From: "Agrafiotis, Dimitris K. PRDUS DAGRAFIO!^!prdus.jnj.com" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36038-080115102308-17305-ewLo7Rm734N7K6f3yEZRcA]*[server.ccl.net> X-Original-From: "Agrafiotis, Dimitris K. [PRDUS]" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 15 Jan 2008 10:22:59 -0500 MIME-Version: 1.0 Sent to CCL by: "Agrafiotis, Dimitris K. [PRDUS]" [DAGRAFIO**prdus.jnj.com] This is a very timely thread for me for a variety of self-serving = reasons. Frankly, I don't think you will get the right advise in this = forum, as it all boils down to personal preferences and familiarity. I = must confess that I am surprised by the foresight of your advisor. C# is = one heck of a programming language, built on one heck of a platform = (.Net) which runs on 90+% of the world's computers. This is something = that the computational chemisty community never really realized and = exploited. If you want to see what can be done in C#, have a look at our = ABCD paper that was recently published in J. Chem. Info. Model. = (http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2007/47/i06/abs/ci700267= w.html), and go to the section on Third Dimension Explorer (3DX). The = application is written entirely in C#, and its performance and = sophistication are astounding. There is a fair amount of C++ code behind = it, but the .Net framework allows it to be seamlessly integrated with = the rest of the application. This project has received a lot of = attention in the press (see, for example, the highlight in the latest = issue of Nature Reviews: = http://www.nature.com/nrd/journal/v6/n12/full/nrd2471.html), so I think = it's worth reading. You may think that this is more of an "IT" type of = application, but you will be astonished by how much hard-core = computational chemistry algorithms you will find in there. So, if I were = to offer my advise, I would say go with C#. You will become familiar = with an envionment that is poised for dominance in the software = industry, and you will have acquired a modern set of skills that will = differentiate you from most of your colleagues who are still left in = Fortran and Perl :-) Which brings me to the self-serving part. If any of you want to be part = of such an effort (ABCD, that is), have experience in .Net, C#, and C++, = and want to live in Belgium, pleae drop me a note (off line). We have = some job openings in our team there, and we are looking for top = programming talent, with a strong background in computational chemistry, = computational biology and informatics, who are not limited by their = training, are able to work in different problem domains, are skilled in = engaging the users and responding to their needs, and are able to work = as part of a larger team. Hint for Mr. Arafat: there are a lot more = skills that you need to acquire to have a successful career in today's = world. Programming is just one of them. Don't underestimate the others. Best regards, ____________________________________________________ Dimitris K. Agrafiotis, Ph.D. Johnson & Johnson Pharmaceutical Research & Development, LLC 665 Stockton Drive, Exton, PA 19341, USA Tel: (610) 458-6045 Fax: (610) 458-8249 E-mail: dagrafio]*[prdus.jnj.com http://www.dimitris-agrafiotis.com -----Original Message----- > From: owner-chemistry]*[ccl.net [mailto:owner-chemistry]*[ccl.net] Sent: Monday, January 14, 2008 10:13 AM To: Agrafiotis, Dimitris K. [PRDUS] Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Sent to CCL by: "Chris Moth" [chris.moth(0)Vanderbilt.Edu] C# is a beautiful language for business software development on the Windows platform. The .NET environment shields software development = > from many problems (opportunities) that lower level languages (C especially) can create. For a nice language to "learn how to program", I would say C# is fine - just as PASCAL was good long ago. You can load Microsoft Visual Studio and be writing your first program very quickly. If you are developing a modern, interactive computational chemistry application with a rich user interface, and you want it to run on a variety of platforms, you might look at Java. Java is a conceptual precursor of .NET - and is perhaps more inherently cross-platform. However, many applications in computational chemistry have no user interface to speak of - and are fundamentally dedicated to computation = of results as quickly as possible. Thus compiled FORTRAN and C (vs interprested Java/C#) are going to haev a role in our field for the forseeable future. But yes, they are very old now. Python is certainly interesting - and I would suggest you look at "chimera" as an example of what has been done with it. I was about to write that Python has not caught on with the main-stream software development community - but a quick search at hotjobs.com for "Python" category=3DTech Jobs shows 600 listings. That's quite impressive. > > Sent to CCL by: "Mahmoud Arafat Ibrahim" [M_Arafat82 * Yahoo.Com] > Dear Dr. / Prof. > In the fact, I am a new researcher in Computational Chemistry Subject = and > I am going to specialized in Drug Design. I have started studying C = sharp > as a programming language as my first step in this new field (it was = an > advise from one professor). After an intermediate step in C sharp, I = am > now confusing about its usage in my new field. Indeed, I found that = all > programs have been used in Computational Chemistry are based on = FORTRAN or > C language. So, I am now hesitating about my step and asking for = advice. > > May you direct me to the best step? > -Stop studying Programming languages as whole where they are = usefulness in > Computational Chemistry. > -Study FORTRAN or C language where they are more abundant in = Computational > Chemistry. > or > -Continue studying C sharp where it is the most modern language. > I hope to read from you as soon as possible. > Sincerely; > M. Arafat, > Chemistry Department, > Faculty of Science, > Minia university, > Egypt.> > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jan 15 11:07:01 2008 From: "Klon, Anthony aklon- -pcop.com" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36039-080115103153-19295-4HyiBXQ1PrwhYvvtq2TXoQ|,|server.ccl.net> X-Original-From: "Klon, Anthony" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 15 Jan 2008 09:30:05 -0500 MIME-Version: 1.0 Sent to CCL by: "Klon, Anthony" [aklon]*[pcop.com] We=20use=20both=20C#=20and=20C++=20internally.=20One=20of=20the=20nicer=20= features=20about=20C#=20is the=20ability=20for=20desktop=20developers=20to=20take=20all=20of=20the=20= code=20written=20by comp.=20chemists=20and=20make=20it=20available=20to=20Windows=20user.=20On= e=20member=20of=20our group=20is=20writing=20code=20in=20C#=20so=20that=20the=20software=20can=20= be=20deployed=20on chemists'=20and=20biologists'=20desktops.=20This=20program=20is=20mainly=20= a=20GUI=20that takes=20advantage=20of=20our=20existing=20code=20base.=20At=20the=20back-e= nd,=20the=20rest=20of us=20write=20code=20in=20C++=20in=20a=20linux=20environment. Anthony=20E.=20Klon Research=20Scientist Molecular=20Modeling Pharmacopeia P.O.=20Box=205350 Princeton,=20NJ=2008543-5350 609.452.3676 -----Original=20Message----- > From:=20owner-chemistry*ccl.net=20[mailto:owner-chemistry*ccl.net]=20 Sent:=20Monday,=20January=2014,=202008=2010:13=20AM To:=20Klon,=20Anthony Subject:=20CCL:=20Asking=20for=20"Usage=20of=20C=20sharp=20in=20Computatio= nal=20Chemistry" Sent=20to=20CCL=20by:=20"Chris=20Moth"=20[chris.moth(0)Vanderbilt.Edu] C#=20is=20a=20beautiful=20language=20for=20business=20software=20developme= nt=20on=20the Windows=20platform.=20=20The=20.NET=20environment=20shields=20software=20d= evelopment > from many=20problems=20(opportunities)=20that=20lower=20level=20languages=20(C=20= especially) can=20create. For=20a=20nice=20language=20to=20"learn=20how=20to=20program",=20I=20would= =20say=20C#=20is=20fine=20- just=20as=20PASCAL=20was=20good=20long=20ago.=20=20You=20can=20load=20Micr= osoft=20Visual=20Studio and=20be=20writing=20your=20first=20program=20very=20quickly. If=20you=20are=20developing=20a=20modern,=20interactive=20computational=20= chemistry application=20with=20a=20rich=20user=20interface,=20and=20you=20want=20it=20= to=20run=20on=20a variety=20of=20platforms,=20you=20might=20look=20at=20Java.=20=20Java=20is= =20a=20conceptual precursor=20of=20.NET=20-=20and=20is=20perhaps=20more=20inherently=20cross= -platform. However,=20many=20applications=20in=20computational=20chemistry=20have=20n= o=20user interface=20to=20speak=20of=20-=20and=20are=20fundamentally=20dedicated=20= to=20computation of results=20as=20quickly=20as=20possible.=20=20Thus=20compiled=20FORTRAN=20a= nd=20C=20(vs interprested=20Java/C#)=20are=20going=20to=20haev=20a=20role=20in=20our=20= field=20for=20the forseeable=20future.=20=20But=20yes,=20they=20are=20very=20old=20now. Python=20is=20certainly=20interesting=20-=20and=20I=20would=20suggest=20yo= u=20look=20at "chimera"=20as=20an=20example=20of=20what=20has=20been=20done=20with=20it.= =20=20I=20was=20about=20to write=20that=20Python=20has=20not=20caught=20on=20with=20the=20main-stream= =20software development=20community=20-=20but=20a=20quick=20search=20at=20hotjobs.com=20= for=20"Python" category=3DTech=20Jobs=20shows=20600=20listings.=20=20That's=20quite=20imp= ressive. > >=20Sent=20to=20CCL=20by:=20"Mahmoud=20Arafat=20Ibrahim"=20[M_Arafat82=20*= =20Yahoo.Com] >=20Dear=20Dr.=20/=20Prof. >=20In=20the=20fact,=20I=20am=20a=20new=20researcher=20in=20Computational=20= Chemistry=20Subject and >=20I=20am=20going=20to=20specialized=20in=20Drug=20Design.=20I=20have=20s= tarted=20studying=20C sharp >=20as=20a=20programming=20language=20as=20my=20first=20step=20in=20this=20= new=20field=20(it=20was an >=20advise=20from=20one=20professor).=20After=20an=20intermediate=20step=20= in=20C=20sharp,=20I am >=20now=20confusing=20about=20its=20usage=20in=20my=20new=20field.=20=20In= deed,=20I=20found=20that all >=20programs=20have=20been=20used=20in=20Computational=20Chemistry=20are=20= based=20on FORTRAN=20or >=20C=20language.=20So,=20I=20am=20now=20hesitating=20about=20my=20step=20= and=20asking=20for advice. > >=20May=20you=20direct=20me=20to=20the=20best=20step? >=20-Stop=20studying=20Programming=20languages=20as=20whole=20where=20they= =20are usefulness=20in >=20Computational=20Chemistry. >=20-Study=20FORTRAN=20or=20C=20language=20where=20they=20are=20more=20abu= ndant=20in Computational >=20Chemistry. >=20or >=20-Continue=20studying=20C=20sharp=20where=20it=20is=20the=20most=20mode= rn=20language. >=20I=20hope=20to=20read=20from=20you=20as=20soon=20as=20possible. >=20Sincerely; >=20M.=20Arafat, >=20Chemistry=20Department, >=20Faculty=20of=20Science, >=20Minia=20university, >=20Egypt.> > > -=3D=20This=20is=20automatically=20added=20to=20each=20message=20by=20the=20= mailing=20script=20=3D- To=20recover=20the=20email=20address=20of=20the=20author=20of=20the=20mess= age,=20please=20change the=20strange=20characters=20on=20the=20top=20line=20to=20the=20*=20sign.=20= You=20can=20also look=20up=20the=20X-Original-From:=20line=20in=20the=20mail=20header. E-mail=20to=20subscribers:=20CHEMISTRY*ccl.net=20or=20use: =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail=20to=20administrators:=20CHEMISTRY-REQUEST*ccl.net=20or=20use =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=20 =20=20=20=20=20=20http://www.ccl.net/chemistry/sub_unsub.shtml Before=20posting,=20check=20wait=20time=20at:=20http://www.ccl.net Job:=20http://www.ccl.net/jobs=20 Conferences:=20http://server.ccl.net/chemistry/announcements/conferences/ Search=20Messages:=20http://www.ccl.net/htdig=20=20(login:=20ccl,=20Passwo= rd: search) If=20your=20mail=20bounces=20from=20CCL=20with=205.7.1=20error,=20check: =20=20=20=20=20=20http://www.ccl.net/spammers.txt RTFI:=20http://www.ccl.net/chemistry/aboutccl/instructions/ ________________________________________________________________________ Scanned=20by=20IBM=20Email=20Security=20Management=20Services=20powered=20= by MessageLabs. ________________________________________________________________________ ________________________________________________________________________ Scanned=20by=20IBM=20Email=20Security=20Management=20Services=20powered=20= by=20MessageLabs. ________________________________________________________________________