From owner-chemistry@ccl.net Sun Jan 13 10:05:00 2008 From: "Mahmoud Arafat Ibrahim M_Arafat82(~)Yahoo.Com" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36017-080113035645-20474-wBzRzJXyANFlptQ3dmwg1g~!~server.ccl.net> X-Original-From: "Mahmoud Arafat Ibrahim" Date: Sun, 13 Jan 2008 03:56:41 -0500 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 Sun Jan 13 12:29:01 2008 From: "Jozsef Csontos jozsefcsontos[]creighton.edu" To: CCL Subject: CCL: extrapolation schemes Message-Id: <-36018-080113122645-11883-qFAeJuu0oV0CroGtBJXKvQ{}server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sun, 13 Jan 2008 11:26:35 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos%x%creighton.edu] Dear All, could you point me to papers which compare different extrapolation procedures to the basis set limit. Thank you, Jozsef -- Jozsef Csontos, Ph.D. (jozsefcsontos_at_creighton_dot_edu) Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Sun Jan 13 13:03:01 2008 From: "Joe Leonard jleonard42/./gmail.com" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36019-080113123947-16360-uWlhDK/N7XS3Dj6BU+iKgQ(~)server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary=Apple-Mail-1-747873791 Date: Sun, 13 Jan 2008 12:38:09 -0500 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Joe Leonard [jleonard42]-[gmail.com] --Apple-Mail-1-747873791 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed On Jan 13, 2008, at 3:56 AM, Mahmoud Arafat Ibrahim M_Arafat82(~) Yahoo.Com wrote: > > 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. Do not feel bad asking these questions - there is a lot of experience here on CCL that should be used, remembered and passed along before it's lost! Regarding language usage, recall that most computational chemistry programs are (quite) old. If they were started today, the language (s) used would be different. However, there are far more useful things to study in computational chemistry than programming languages... > > May you direct me to the best step? > -Stop studying Programming languages as whole where they are > usefulness in Computational Chemistry. What do you want to do? Do you want to do drug design in support of medchem project teams? Do you want to create the software that is used by modelers and increasingly medchemists? Do you want to take the academic route and train others to enter this field? Knowing the answer to these questions should determine what you must study. Whatever you want to do, I would start with a scripting language: Python, Perl, Ruby, etc. These are more than sufficient for learning programming, and knowing how to use them will be directly helpful in any aspect of computational chemistry. These languages are replacing traditional Unix scripting tools, and many groups/vendors are releasing toolkits in at least one of these languages. But I would not study languages or programming in any great depth unless you wish to create software. The critical skill of application modelers is medicinal chemistry expertise. All else is secondary. If you know medchem, and have sufficient interpersonal skills to present and defend your ideas (and, of course, the ideas are worthwhile), you will be of use to project teams. If you wish to go into academia, you need to make sure you write well and often. You also need good interpersonal skills to participate in the tenure process, and you need to be a source of good ideas for both yourself and your students. To date, academia's not been as successful in training medicinal chemists as it would like - this might be helped by more industrial people returning along with the drop in the cost of hardware (not just computer hardware). Finally, if you want to create software, several things come to mind: (1) Do you really want to do this, as the employment possibilities are more limited than for applications modelers. I do not have direct experience, but I suspect that one's chances in academia are better than in developing software. (2) You must be good, and you must be visible. Like many areas of chemistry, this is a small community that is well-connected. Be known as the source of good work, good ideas and good implementations. (3) You have to understand the whole program development process, the business aspects and how these things are used. We use at least two distinct platforms, Linux and Windows, and "interconversion" between the two has a significant activation energy. > -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. C#, as I understand it, is a Windows-only environment. Fortran and C have historical importance due to sheer amount of code (still) written in them. As I wrote above, I would start with a scripting language, and possible end with them - you will have to learn the environment(s) you work in, which will require a fair bit of flexibility regarding language choice. As I wrote above, when you know what you want to do, many of these questions answer themselves. Joe Leonard jleonard42(a)gmail.com > I hope to read from you as soon as possible. > Sincerely; > M. Arafat, > Chemistry Department, > Faculty of Science, > Minia university, > Egypt. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -- Canada could have enjoyed: English government, French culture, and American know-how. Instead it ended up with English know-how, French government, and American culture. --Apple-Mail-1-747873791 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
On Jan 13, 2008, at = 3:56 AM, Mahmoud Arafat Ibrahim M_Arafat82(~)Yahoo.Com wrote:


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.=A0 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.

Do not feel bad asking these = questions - there is a lot of experience here on CCL that should be = used, remembered and passed along before it's lost!

Regarding language usage, = recall that most computational chemistry programs are (quite) old. =A0If = they were started today, the language(s) used would be different. = =A0However, there are far more useful things to study in computational = chemistry than programming languages...


May you direct me to the best step?
-Stop studying Programming languages as whole where = they are usefulness in Computational = Chemistry.

What do you want to do? =A0Do = you want to do drug design in support of medchem project teams? =A0Do = you want to create the software that is used by modelers and = increasingly medchemists? =A0Do you want to take the academic route and = train others to enter this field? =A0Knowing the answer to these = questions should determine what you must study.

Whatever you want to do, I = would start with a scripting language: Python, Perl, Ruby, etc. =A0These = are more than sufficient for learning programming, and knowing how to = use them will be directly helpful in any aspect of computational = chemistry. =A0These languages are replacing traditional Unix scripting = tools, and many groups/vendors are releasing toolkits in at least one of = these languages.

But I would not study = languages or programming in any great depth unless you wish to create = software. =A0The critical skill of application modelers is medicinal = chemistry expertise. =A0All else is secondary. =A0If you know medchem, = and have sufficient interpersonal skills to present and defend your = ideas (and, of course, the ideas are worthwhile), you will be of use to = project teams.

If you wish to go into = academia, you need to make sure you write well and often. =A0You also = need good interpersonal skills to participate in the tenure process, and = you need to be a source of good ideas for both yourself and your = students. =A0To date, academia's not been as successful in training = medicinal chemists as it would like - this might be helped by more = industrial people returning along with the drop in the cost of hardware = (not just computer hardware).

Finally, if you want to = create software, several things come to mind: =A0(1) Do you really want = to do this, as the employment possibilities are more limited than for = applications modelers. =A0I do not have direct experience, but I suspect = that one's chances in academia are better than in developing software. = =A0(2) You must be good, and you must be visible. =A0Like many areas of = chemistry, this is a small community that is well-connected. =A0Be known = as the source of good work, good ideas and good implementations. =A0(3) = You have to understand the whole program development process, the = business aspects and how these things are used. =A0We use at least two = distinct platforms, Linux and Windows, and "interconversion" between the = two has a significant activation = energy.

-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.

C#, as I understand it, is a = Windows-only environment. =A0Fortran and C have historical importance = due to sheer amount of code (still) written in them. =A0As I wrote = above, I would start with a scripting language, and possible end with = them - you will have to learn the environment(s) you work in, which will = require a fair bit of flexibility regarding language = choice.
As I wrote above, when you know what you want to do, = many of these questions answer themselves.

Joe Leonard
I hope to read from you as soon = as possible.
Sincerely;
M. Arafat,
Chemistry = Department,
Faculty of Science,
Minia university,



-=3D This is = automatically added to each message by the mailing script =3D-
To recover the email address of the author of the = message, please change
the strange characters on = the top line to the (a) sign. You can also
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If your mail bounces from CCL with 5.7.1 error, = check:




=

= --Apple-Mail-1-747873791-- From owner-chemistry@ccl.net Sun Jan 13 13:38:00 2008 From: "Lukasz Cwiklik cwiklik::gmail.com" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36020-080113124152-17225-52JxvaxB5nO8We46dz3AnA!=!server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 13 Jan 2008 18:41:41 +0100 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik::gmail.com] On Jan 13, 2008 9:56 AM, Mahmoud Arafat Ibrahim M_Arafat82(~)Yahoo.Com wrote: > 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. Dear Mahmoud, Your question and my answer can start a "flame war" at CCL list, however, I will try to write what I think as a computational chemist who is doing quite a lot of software development in everyday work. Of course, my opinion can be biased by my experience/environment but there are no independent opinions in this topic anyway. 1. As for now, C# is almost completely useless for a computational chemist with one exception: if writes applications for MS Windows. If you do not develop for Windows, C# is not a good choice. 2. A knowledge of C or C++ would be necessary if you want to write a new code. Basic knowledge of Fortran is needed if one need to work with existing Fortran codes. In my biased opinion, in these days starting a new project in Fortran is not an optimal choice. 3. A knowledge of a good, modern and flexible scripting language is also a must and I propose Python. I think, Python would be as useful for a young computational chemist as C, C++ or Fortran. 4. But one must remember - the choice always depends on particualar conditions. If your advisor has a lot of experience in scientific software development and works in this field currently, maybe his/her reasons for choosing C# have a good basis. I hope other CCLers will add their suggestions here. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Sun Jan 13 14:52:00 2008 From: "saif ullah sullah%a%ruc.dk" To: CCL Subject: CCL:G: Error termination request processed by link 9999 Message-Id: <-36021-080113144650-4506-H05SZDKejGYUZNBMzIEFSA+*+server.ccl.net> X-Original-From: "saif ullah" Date: Sun, 13 Jan 2008 14:46:47 -0500 Sent to CCL by: "saif ullah" [sullah,,ruc.dk] Dear CCLers, I am facing a problem in geometry optimization (#BPW91/6-31G(d) OPT=Z-MATRIX) of CH3N+H3 -OOCCH3 molecule with this error, Optimization stopped. -- Number of steps exceeded, NStep= 37 -- Flag reset to prevent archiving. Error termination request processed by link 9999. Error termination via Lnk1e in /net/node0/g03/l9999.exe at Fri Jan 4 18:25:17 2008. Job cpu time: 0 days 1 hours 32 minutes 57.0 seconds. File lengths (MBytes): RWF= 16 Int= 0 D2E= 0 Chk= 7 Scr= 1 I have also tried the keyword opt(MaxCyc=N) but ended with the same error and don't know how could I overcome this problem. Any suggestion or comments in this regard would highly be appreciated. Thanks in advance, Saif From owner-chemistry@ccl.net Sun Jan 13 16:02:00 2008 From: "Michel Petitjean petitjean|a|itodys.jussieu.fr" To: CCL Subject: CCL: Asking for Usage of C sharp in Computational Chemistry Message-Id: <-36022-080113155819-6534-aFhGYQ3gWR1Fmyi4w5AIAQ*|*server.ccl.net> X-Original-From: "Michel Petitjean" Date: Sun, 13 Jan 2008 15:58:15 -0500 Sent to CCL by: "Michel Petitjean" [petitjean(0)itodys.jussieu.fr] To: chemistry=-=ccl.net Subject: CCL: Re: Asking for Usage of C sharp in Computational Chemistry Dear Mahmoud Arafat, If you are willing to develop sophisticated programs in the future, it is much more useful to know a bit of C AND a bit of FORTRAN rather than knowing deeply C. So, you will be able to select the most adequate for a given function to programme. Note that C and FORTRAN are easily mixable (calling or called) on most unix systems, provided that you take some care in the arguments type you use. Furtermore, using advanced features of languages is not a good idea if you would like to generate portable programmes. Most people agree than FORTRAN is better for numerical programming (although it is fine for many other purposes), and than C is better for system-oriented applications. Anyway, please be able to programme by yourself rather than being dependant on somebody else that you will have to pay much and implore on the knees to do the job. Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex Phone: +33(0)1 6908 9681 / Fax: +33(0)1 6908 4007 E-mail: petitjean=-=itodys.jussieu.fr, michel.petitjean=-=cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Formerly: ITODYS (CNRS, UMR 7086), 1 rue Guy de la Brosse, 75005 Paris, France. 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 Sun Jan 13 19:38:00 2008 From: "Igor Filippov Contr igorf[*]helix.nih.gov" To: CCL Subject: CCL: Asking for "Usage of C sharp in Computational Chemistry" Message-Id: <-36023-080113192709-18101-tLsg54XWXBIv+px/7LxsUw^^^server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sun, 13 Jan 2008 17:35:25 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf-x-helix.nih.gov] Dear Mahmoud, I would be very interested to hear the reasoning behind your professor's recommendation for C-sharp. I don't claim to be an expert, but I can think of some examples for almost every other well-known language usage in computational chemistry EXCEPT for C-sharp: C/Fortran - too many to mention ab initio packages/routines C++ - OpenBabel Perl - Daylight toolkit, OpenBabel toolkit Python - PyMol Tcl - CACTVS Java - Chemistry Development Kit (CDK), JME, Jmol This is just off the top of my head, there are many many more; I can think of closed-source examples for Pascal/Delphi, but C-sharp??? Where exactly is it used within the field of computational chemistry? How widespread this usage is? Regards, Igor On Sun, 2008-01-13 at 18:41 +0100, Lukasz Cwiklik cwiklik::gmail.com wrote: > Sent to CCL by: "Lukasz Cwiklik" [cwiklik::gmail.com] > On Jan 13, 2008 9:56 AM, Mahmoud Arafat Ibrahim M_Arafat82(~)Yahoo.Com > wrote: > > 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. > > Dear Mahmoud, > Your question and my answer can start a "flame war" at CCL list, > however, I will try to write what I think as a computational chemist > who is doing quite a lot of software development in everyday work. Of > course, my opinion can be biased by my experience/environment but > there are no independent opinions in this topic anyway. > 1. As for now, C# is almost completely useless for a computational > chemist with one exception: if writes applications for MS Windows. If > you do not develop for Windows, C# is not a good choice. > 2. A knowledge of C or C++ would be necessary if you want to write a > new code. Basic knowledge of Fortran is needed if one need to work > with existing Fortran codes. In my biased opinion, in these days > starting a new project in Fortran is not an optimal choice. > 3. A knowledge of a good, modern and flexible scripting language is > also a must and I propose Python. I think, Python would be as useful > for a young computational chemist as C, C++ or Fortran. > 4. But one must remember - the choice always depends on particualar > conditions. If your advisor has a lot of experience in scientific > software development and works in this field currently, maybe his/her > reasons for choosing C# have a good basis. > > I hope other CCLers will add their suggestions here. > Best, > Lukasz > -- Igor Filippov [Contr]