From owner-chemistry@ccl.net Mon May 5 06:49:00 2008 From: "Karl Kirschner (kkirschn) kkirschn{:}hamilton.edu" To: CCL Subject: CCL:G: Undergraduate research question Message-Id: <-36890-080505063707-29387-0DuxoG6Ps6N+0SEu3wbymg~!~server.ccl.net> X-Original-From: "Karl Kirschner (kkirschn)" Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_CMj3MvasY9YxYGqF5NmTag)" Date: Mon, 05 May 2008 12:36:49 +0200 MIME-version: 1.0 Sent to CCL by: "Karl Kirschner (kkirschn)" [kkirschn()hamilton.edu] This is a multi-part message in MIME format. --Boundary_(ID_CMj3MvasY9YxYGqF5NmTag) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: quoted-printable Content-disposition: inline Hi Barbara=2C =A0=A0=A0 At Hamilton=2C have several undergraduate students conducing c= omputational research=2E For students to be most successful in this=2C i= t is important that you catch them early=2C retain them and have them co= nduct research during the summer=2E We have a few students begin as earl= y as the summer before their freshman year=2E During the summer we run a= n 11 week program that requires the students to work a 40 hour week for = 10 weeks=2C with one week that they can choose to use as a vacation=2E T= hey are paid for their work during these 10 weeks=2E Our older students = (juniors and seniors) attend and present posters at conferences such as = the Sanibel Symposium and/or regional ACS meetings=2E These meetings are= important for the student=27s research experience because it broadens t= heir understanding of how their research extends beyond the walls of our= science building and they realize that they are a part of a larger comm= unity=2E They always return to the college with renewed enthusiasm to co= nduct research to the best of their abilities=2E At the end of each summ= er we host the MERCURY conference (founded by George C=2E Shields)=2C wh= ich is specifically for undergraduate research in computational chemistr= y=2C and is a resource for those who are conducting research with underg= raduates=2E You can find the website here=3A http=3A//mercury=2Echem=2Eh= amilton=2Eedu/modules/content/=3Fid=3D1 =2E =A0=A0=A0 The summer research is very important because that is when the= most research can be accomplished=2E During the school year=2C the stud= ents obviously have to focus on class work and many do extracurricular a= ctivities that require attention=2E If possible=2C it is good to have a = productive and enthusiastic student to take research for class credit=2C= enabling them to continue their research into the school year=2E Each o= f our senior chemistry majors do this=2E This is very beneficial because= they continue their learning curve that started in the summer=3B those = who do not conduct research during the school year often require a week = for relearning techniques and remembering where they were on their proje= ct=2E =A0=A0=A0 We also have our students keep detailed lab notebooks=2C which= we retain when they graduate=2C and write weekly progress reports=2E Th= e lab notebooks are helpful for writing manuscripts after the students h= ave graduated=2C and in transferring a project=27s data/ideas to a new s= tudents upon joining the group=2E The weekly reports are helpful for sim= ple communication=2C it keeps the students =22honest=22 with their work = or lack there of by putting responsibility for productivity on their sho= ulders=2E The weekly reports also allows them to think about and see the= ir own progress=2E We ask them to tell us both their successes and their= problems so that we can help solve them=2E At the end of summer they wr= ite a comprehensive report=2C which will be used to remind us of what th= ey did and can be used by them or a new student to pick the project back= up in the next summer=2E =A0=A0=A0 Having returningn students who have worked for us is helpful b= ecause they can answer many simple questions that the new students have=2C= such as learning Linux or how to run a geometry optimization=2E Some st= udents have personalities that enjoy being a mentor to younger students=2C= while others prefer to work alone on a project=2E In terms of personali= ties=2C we try to fit the student to an appropriate project=2E For examp= le=2C if they like programing then we put them on a project that would b= enefit from writing scripts=2E If they like looking at lots of data=2C t= hen we put them on a molecular dynamics project=2C and so on=2E We talk = to each student=2C before they start working with us=2C about what they = like and dislike=2E We present them with different projects and ask them= what they would like to do=2E We try to instill as much ownership of th= e project into them (via becoming a group leader=2C writing reports/manu= scripts=2C allowing them to explore their own ideas even though you know= a multiplicity of 3 is wrong=2E=2E=2E)=2C so that it is their project a= nd not just their professors=27 project=2E The student=27s ownership of = their research is very important=2E =A0=A0=A0 In terms of projects=2C I feel that the two most important req= uirements is a) it is interesting to the student and to you=2C and b) it= is presentable at a conference and publishable=2E It could be a molecul= ar dynamics project or a quantum mechanics project=2E For the student=2C= any research experience that they receive as an undergraduate will bene= fit them with obtaining their goals after graduation (medical school=2C = graduate school=2C industry=2E=2E=2E)=2E Publishing with your students w= ill help you obtain future grants for sustaining the research and will m= ake your students be more competitive for national awards=2C thus increa= sing theirs and your success=2E We try to have the students write the fi= rst rough draft of manuscripts=2E Initially=2C they make an outline of t= he literature and their data=2C then they write the methods and introduc= tion=2C followed by the creation of tables and figures=2E Finally=2C the= y take a stab at the writing the results and discussion=2E =A0=A0=A0 From my experience=2C students are more likely to quickly beco= me productive with quantum projects than simulations projects=2E Make su= re to spot check input and out files periodically for errors=2E Make sur= e that students are not burning processors with bad calculations=2C wast= ing resources and valuable research time=2E The model above is one that = we have found successful for undergraduate computational research=2C but= many others have set up different and successful models=2E I hope this = is helpful to you=2E If you have any further questions=2C please let me = know=2E Cheers=2C Karl =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Karl N=2E Kirschner=2C Ph=2ED=2E Center for Molecular Design=2C Co-Director Visiting Assistant Professor Hamilton College=2C Clinton NY 13323 =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F On May 4=2C 2008=2C at 7=3A09 AM=2C Barbara Murray barbara=5Fmurray=7E!=7E= redlands=2Eedu wrote=3A Sent to CCL by=3A Barbara Murray =5Bbarbara=5Fmurray=5D=3D=5Bredlands=2E= edu=5D Let me give the list some background before I try to ask my question=2E=A0= I teach organic chemistry at a small private=2C undergraduate universit= y=2E=A0 I was trained as a solid state synthetic chemist about 30 years = ago=2E=A0 About 15 years ago I became interested in computational chemis= try and have dabbled in it ever since=2E=A0 I say dabbled because a) alt= hough faculty are encouraged to stay professionally active here=2C teach= ing is our first priority (and my first love) and b) for the last 10 yea= rs I=27ve been a half time administrator so I have little time to do res= earch=2E All of our chemistry majors do at least a senior research project and so= me do much more=2E=A0 I=27ve had the occasional student work for me doin= g what I call computational studies of biologically active molecules=2E=A0= A student does a literature search to find a set of biologically intere= sting molecules that all work on the same receptor (one example was prot= ease inhibitors when they were first coming out)=2E=A0 The student then = uses computational chemistry (usually electrostatic potentials) and info= rmation about the receptor=27s active site to determine why one molecule= might work better than another=2E=A0 These are not earth shaking projec= ts (nor publishable)=2C but the students learn a bit about computational= chemistry and I=27m generally happy=2E But my problem (or not) is that I now have one of the smartest students = I=27ve had in over 20 years who wants to work for me=2E=A0 He=27s not on= ly intelligent but incredibly hard-working=2E=A0 He=27s just finished hi= s sophomore year=2C having blown the curve in my organic class away and = he thinks he wants to be a pharmaceutical chemist=2E I feel like he is capable of doing incredible work=2C especially if he s= tays interested in a project and works on it for the next 2 years=2E=A0 = But I don=27t know what to do with him!=A0 I=27m so used to having okay = students who are happy with okay little projects=2C and I=27ve been conc= entrating on administration=2C that I need help or suggestions or someth= ing=2E=2E=2E=2E=2E I=27ve been an on and off member of this list and realize that this is n= ot exactly the typical question=2C but I thought it couldn=27t hurt to a= sk=2E So if you had a willing young worker who wanted to be a pharmaceutical c= hemist when he grows up what would you have him do=3F=A0 I have Spartan = and Gaussian available=2E=A0 He=27s been playing around with Spartan for= the last few weeks=2E=A0 I also am willing to get other programs if the= re are other types of calculations that people do=2E=A0 I=27m also willi= ng to collaborate with someone who=27s doing pharmaceutical research and= thinks they could use us=2E=A0 I don=27t want to shortchange this stude= nt=3B I=27d like to give him a real taste of what pharmaceutical computa= tional chemists do=3B and I think he=27s capable of doing really high qu= ality work=2E=A0 Besides=2C I=27d like to learn along with him=2E Any help or suggestions are welcome=2E=A0 barbara=5Fmurray*redlands=2Eed= u -- = *********************************************************** Barbara Murray=A0=A0=A0 =A0=A0=A0=A0 barbara=5Fmurray*redlands=2Eedu Director The Center for Science and Mathematics University of Redlands Redlands=2C CA --Boundary_(ID_CMj3MvasY9YxYGqF5NmTag) Content-type: text/html; charset=us-ascii Content-transfer-encoding: quoted-printable Content-disposition: inline Hi Barbara=2C=3Cbr=3E=3Cbr=3E=26nbsp=3B=26nbsp=3B=26nbsp=3B At Hamilton=2C= have several undergraduate students conducing computational research=2E= For students to be most successful in this=2C it is important that you = catch them early=2C retain them and have them conduct research during th= e summer=2E We have a few students begin as early as the summer before t= heir freshman year=2E During the summer we run an 11 week program that r= equires the students to work a 40 hour week for 10 weeks=2C with one wee= k that they can choose to use as a vacation=2E They are paid for their w= ork during these 10 weeks=2E Our older students (juniors and seniors) at= tend and present posters at conferences such as the Sanibel Symposium an= d/or regional ACS meetings=2E These meetings are important for the stude= nt=27s research experience because it broadens their understanding of ho= w their research extends beyond the walls of our science building and th= ey realize that they are a part of a larger community=2E They always ret= urn to the college with renewed enthusiasm to conduct research to the be= st of their abilities=2E At the end of each summer we host the MERCURY c= onference (founded by George C=2E Shields)=2C which is specifically for = undergraduate research in computational chemistry=2C and is a resource f= or those who are conducting research with undergraduates=2E You can find= the website here=3A http=3A//mercury=2Echem=2Ehamilton=2Eedu/modules/co= ntent/=3Fid=3D1 =2E=3Cbr=3E=3Cbr=3E=26nbsp=3B=26nbsp=3B=26nbsp=3B The su= mmer research is very important because that is when the most research c= an be accomplished=2E During the school year=2C the students obviously h= ave to focus on class work and many do extracurricular activities that r= equire attention=2E If possible=2C it is good to have a productive and e= nthusiastic student to take research for class credit=2C enabling them t= o continue their research into the school year=2E Each of our senior che= mistry majors do this=2E This is very beneficial because they continue t= heir learning curve that started in the summer=3B those who do not condu= ct research during the school year often require a week for relearning t= echniques and remembering where they were on their project=2E=3Cbr=3E=3C= br=3E=26nbsp=3B=26nbsp=3B=26nbsp=3B We also have our students keep detai= led lab notebooks=2C which we retain when they graduate=2C and write wee= kly progress reports=2E The lab notebooks are helpful for writing manusc= ripts after the students have graduated=2C and in transferring a project= =27s data/ideas to a new students upon joining the group=2E The weekly r= eports are helpful for simple communication=2C it keeps the students =22= honest=22 with their work or lack there of by putting responsibility for= productivity on their shoulders=2E The weekly reports also allows them = to think about and see their own progress=2E We ask them to tell us both= their successes and their problems so that we can help solve them=2E At= the end of summer they write a comprehensive report=2C which will be us= ed to remind us of what they did and can be used by them or a new studen= t to pick the project back up in the next summer=2E=3Cbr=3E=3Cbr=3E=26nb= sp=3B=26nbsp=3B=26nbsp=3B Having returningn students who have worked for= us is helpful because they can answer many simple questions that the ne= w students have=2C such as learning Linux or how to run a geometry optim= ization=2E Some students have personalities that enjoy being a mentor to= younger students=2C while others prefer to work alone on a project=2E I= n terms of personalities=2C we try to fit the student to an appropriate = project=2E For example=2C if they like programing then we put them on a = project that would benefit from writing scripts=2E If they like looking = at lots of data=2C then we put them on a molecular dynamics project=2C a= nd so on=2E We talk to each student=2C before they start working with us= =2C about what they like and dislike=2E We present them with different p= rojects and ask them what they would like to do=2E We try to instill as = much ownership of the project into them (via becoming a group leader=2C = writing reports/manuscripts=2C allowing them to explore their own ideas = even though you know a multiplicity of 3 is wrong=2E=2E=2E)=2C so that i= t is their project and not just their professors=27 project=2E The stude= nt=27s ownership of their research is very important=2E=3Cbr=3E=3Cbr=3E=26= nbsp=3B=26nbsp=3B=26nbsp=3B In terms of projects=2C I feel that the two = most important requirements is a) it is interesting to the student and t= o you=2C and b) it is presentable at a conference and publishable=2E It = could be a molecular dynamics project or a quantum mechanics project=2E = For the student=2C any research experience that they receive as an under= graduate will benefit them with obtaining their goals after graduation (= medical school=2C graduate school=2C industry=2E=2E=2E)=2E Publishing wi= th your students will help you obtain future grants for sustaining the r= esearch and will make your students be more competitive for national awa= rds=2C thus increasing theirs and your success=2E We try to have the stu= dents write the first rough draft of manuscripts=2E Initially=2C they ma= ke an outline of the literature and their data=2C then they write the me= thods and introduction=2C followed by the creation of tables and figures= =2E Finally=2C they take a stab at the writing the results and discussio= n=2E=3Cbr=3E=3Cbr=3E=26nbsp=3B=26nbsp=3B=26nbsp=3B From my experience=2C= students are more likely to quickly become productive with quantum proj= ects than simulations projects=2E Make sure to spot check input and out = files periodically for errors=2E Make sure that students are not burning= processors with bad calculations=2C wasting resources and valuable rese= arch time=2E The model above is one that we have found successful for un= dergraduate computational research=2C but many others have set up differ= ent and successful models=2E I hope this is helpful to you=2E If you hav= e any further questions=2C please let me know=2E=3Cbr=3E=3Cbr=3ECheers=2C= =3Cbr=3EKarl=3Cbr=3E=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=3Cbr=3E Karl N=2E Kirschner=2C Ph=2ED=2E=3Cbr=3E Center for Molecular Design=2C Co-Director=3Cbr=3E Visiting Assistant Professor=3Cbr=3E Hamilton College=2C Clinton NY 13323=3Cbr=3E =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=3Cbr=3E =3Cbr=3E =3Cbr=3EOn May 4=2C 2008=2C at 7=3A09 AM=2C Barbara Murray barbara=5Fmur= ray=7E!=7Eredlands=2Eedu wrote=3A=3Cbr=3E=3Cbr=3E=3Cbr=3ESent to CCL by=3A= Barbara Murray =5Bbarbara=5Fmurray=5D=3D=5Bredlands=2Eedu=5D=3Cbr=3ELet= me give the list some background before I try to ask my question=2E=26n= bsp=3B I teach organic chemistry at a small private=2C undergraduate uni= versity=2E=26nbsp=3B I was trained as a solid state synthetic chemist ab= out 30 years ago=2E=26nbsp=3B About 15 years ago I became interested in = computational chemistry and have dabbled in it ever since=2E=26nbsp=3B I= say dabbled because a) although faculty are encouraged to stay professi= onally active here=2C teaching is our first priority (and my first love)= and b) for the last 10 years I=27ve been a half time administrator so I= have little time to do research=2E=3Cbr=3E=3Cbr=3EAll of our chemistry = majors do at least a senior research project and some do much more=2E=26= nbsp=3B I=27ve had the occasional student work for me doing what I call = computational studies of biologically active molecules=2E=26nbsp=3B A st= udent does a literature search to find a set of biologically interesting= molecules that all work on the same receptor (one example was protease = inhibitors when they were first coming out)=2E=26nbsp=3B The student the= n uses computational chemistry (usually electrostatic potentials) and in= formation about the receptor=27s active site to determine why one molecu= le might work better than another=2E=26nbsp=3B These are not earth shaki= ng projects (nor publishable)=2C but the students learn a bit about comp= utational chemistry and I=27m generally happy=2E=3Cbr=3E=3Cbr=3EBut my p= roblem (or not) is that I now have one of the smartest students I=27ve h= ad in over 20 years who wants to work for me=2E=26nbsp=3B He=27s not onl= y intelligent but incredibly hard-working=2E=26nbsp=3B He=27s just finis= hed his sophomore year=2C having blown the curve in my organic class awa= y and he thinks he wants to be a pharmaceutical chemist=2E=3Cbr=3E=3Cbr=3E= I feel like he is capable of doing incredible work=2C especially if he s= tays interested in a project and works on it for the next 2 years=2E=26n= bsp=3B But I don=27t know what to do with him!=26nbsp=3B I=27m so used t= o having okay students who are happy with okay little projects=2C and I=27= ve been concentrating on administration=2C that I need help or suggestio= ns or something=2E=2E=2E=2E=2E=3Cbr=3E=3Cbr=3EI=27ve been an on and off = member of this list and realize that this is not exactly the typical que= stion=2C but I thought it couldn=27t hurt to ask=2E=3Cbr=3E=3Cbr=3ESo if= you had a willing young worker who wanted to be a pharmaceutical chemis= t when he grows up what would you have him do=3F=26nbsp=3B I have Sparta= n and Gaussian available=2E=26nbsp=3B He=27s been playing around with Sp= artan for the last few weeks=2E=26nbsp=3B I also am willing to get other= programs if there are other types of calculations that people do=2E=26n= bsp=3B I=27m also willing to collaborate with someone who=27s doing phar= maceutical research and thinks they could use us=2E=26nbsp=3B I don=27t = want to shortchange this student=3B I=27d like to give him a real taste = of what pharmaceutical computational chemists do=3B and I think he=27s c= apable of doing really high quality work=2E=26nbsp=3B Besides=2C I=27d l= ike to learn along with him=2E=3Cbr=3E=3Cbr=3EAny help or suggestions ar= e welcome=2E=26nbsp=3B barbara=5Fmurray*redlands=2Eedu=3Cbr=3E=3Cbr=3E--= =3Cbr=3E***********************************************************=3Cb= r=3EBarbara Murray=26nbsp=3B=26nbsp=3B=26nbsp=3B =26nbsp=3B=26nbsp=3B=26= nbsp=3B=26nbsp=3B barbara=5Fmurray*redlands=2Eedu=3Cbr=3EDirector=3Cbr=3E= The Center for Science and Mathematics=3Cbr=3EUniversity of Redlands=3Cb= r=3ERedlands=2C CA=3Cbr=3E --Boundary_(ID_CMj3MvasY9YxYGqF5NmTag)-- From owner-chemistry@ccl.net Mon May 5 10:15:00 2008 From: "Breton, Gary gbreton..berry.edu" To: CCL Subject: CCL:G: Undergraduate research question Message-Id: <-36891-080505092444-2023-dWTTvNmCVsFNdr8SMR68KQ(a)server.ccl.net> X-Original-From: "Breton, Gary" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 5 May 2008 08:50:24 -0400 MIME-Version: 1.0 Sent to CCL by: "Breton, Gary" [gbreton#%#berry.edu] Hi Barbara, We began a Medicinal Chemistry Course a few years ago, and I was put in charge of developing the lab portion of the course. The lab is strictly computational in nature. I looked at a host of different available = software to see which might be most user-friendly and offer the most "real-world-like" (at least in my opinion) sort of protein-ligand = modeling. I found that the BioMedCache software was an excellent choice. At any = given point in time, half of the students worked on BioMedCache and half = worked on Spartan....and then they traded. Biomedcache can be found here: http://www.computers.us.fujitsu.com/www/products_bioscience.shtml?product= s/b ioscience/bio_med_cache Now, to the point... I found that once students worked through the BioMedCache tutorials, and had an idea how to build and do simple minimizations on Spartan, that they could create their own molecules and = add them to the libraries that BioMedCache used in their tutorials. They = were then able to test these novel molecules for activity against various proteins. By examining the structures of the molecules already in the library, and making informed choices as to the structures of the "novel" molecules, they were amazed to find that they could (logically and deliberately) increase the binding energies of their molecules relative = to those already found in the library. I actually had them create = molecules that they expected to bind tighter, then also create some molecules that they expected to bind even worse...and then test them. This exercise, = which served as the culminating project for the semester, proved to be a hit = with the students, and was essentially "novel" research. Hope this helps, Gary W. Breton Chair and Prof. of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 Ph. (706) 290-2661 Fax. (706) 238-7855 =20 On 5/4/08 1:09 AM, "Barbara Murray barbara_murray~!~redlands.edu" wrote: >=20 > Sent to CCL by: Barbara Murray [barbara_murray]=3D[redlands.edu] > Let me give the list some background before I try to ask my question. = I > teach organic chemistry at a small private, undergraduate university. = I > was trained as a solid state synthetic chemist about 30 years ago. > About 15 years ago I became interested in computational chemistry and > have dabbled in it ever since. I say dabbled because a) although > faculty are encouraged to stay professionally active here, teaching is > our first priority (and my first love) and b) for the last 10 years = I've > been a half time administrator so I have little time to do research. >=20 > All of our chemistry majors do at least a senior research project and > some do much more. I've had the occasional student work for me doing > what I call computational studies of biologically active molecules. A > student does a literature search to find a set of biologically > interesting molecules that all work on the same receptor (one example > was protease inhibitors when they were first coming out). The student > then uses computational chemistry (usually electrostatic potentials) = and > information about the receptor's active site to determine why one > molecule might work better than another. These are not earth shaking > projects (nor publishable), but the students learn a bit about > computational chemistry and I'm generally happy. >=20 > But my problem (or not) is that I now have one of the smartest = students > I've had in over 20 years who wants to work for me. He's not only > intelligent but incredibly hard-working. He's just finished his > sophomore year, having blown the curve in my organic class away and he > thinks he wants to be a pharmaceutical chemist. >=20 > I feel like he is capable of doing incredible work, especially if he > stays interested in a project and works on it for the next 2 years. = But > I don't know what to do with him! I'm so used to having okay students > who are happy with okay little projects, and I've been concentrating = on > administration, that I need help or suggestions or something..... >=20 > I've been an on and off member of this list and realize that this is = not > exactly the typical question, but I thought it couldn't hurt to ask. >=20 > So if you had a willing young worker who wanted to be a pharmaceutical > chemist when he grows up what would you have him do? I have Spartan = and > Gaussian available. He's been playing around with Spartan for the = last > few weeks. I also am willing to get other programs if there are other > types of calculations that people do. I'm also willing to collaborate > with someone who's doing pharmaceutical research and thinks they could > use us. I don't want to shortchange this student; I'd like to give = him > a real taste of what pharmaceutical computational chemists do; and I > think he's capable of doing really high quality work. Besides, I'd = like > to learn along with him. >=20 > Any help or suggestions are welcome. > barbara_murray*redlands.edu From owner-chemistry@ccl.net Mon May 5 11:25:01 2008 From: "Stefan Richter mcmsoft^-^eml-r.villa-bosch.de" To: CCL Subject: CCL: webPIPSA: a webserver for comparing protein interaction properties Message-Id: <-36892-080505103436-15765-F1EbEtLWh3SwM664RsSjAA]~[server.ccl.net> X-Original-From: "Stefan Richter" Date: Mon, 5 May 2008 10:34:32 -0400 Sent to CCL by: "Stefan Richter" [mcmsoft]|[eml-r.villa-bosch.de] We would like to announce the availability of webPIPSA, a webserver for comparing protein interaction properties: http://pipsa.eml.org/. The webserver provides a workflow for some of the functions of PIPSA version 3.0 (http://projects.eml.org/mcm/software/pipsa). The webPIPSA server compares the electrostatic potentials of proteins for which coordinates have been provided in uploaded pdb files or pdb entries specified via PDB codes. The proteins should be structurally related and superimposable. The resulting pairwise similarity indices for the electrostatic potentials are then displayed in a colored matrix view (heat map) and a tree based clustering (epogram). The webserver also allows use of the new PIPSA 3.0 feature to restrict the comparison to a region (eg a binding site) of the proteins. webPIPSA is described in an early access publication of the the Nucleic Acid Research webserver edition 2008 (Stefan Richter, Anne Wenzel, Matthias Stein, Razif R. Gabdoulline and Rebecca C. Wade, Nucleic Acids Research, doi:10.1093/nar/gkn181, http://nar.oxfordjournals.org/cgi/content/abstract/gkn181). The authors can be contacted via mcmsoft~!~eml-r.villa-bosch.de Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Fax: +49 (0)6221 - 533 - 298 From owner-chemistry@ccl.net Mon May 5 14:49:01 2008 From: "Kalju Kahn kalju]|[chem.ucsb.edu" To: CCL Subject: CCL:G: Undergraduate research question Message-Id: <-36893-080505144627-15047-UBYGUH3eSeYoR1xe8OMhUQ**server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 5 May 2008 11:46:06 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju%x%chem.ucsb.edu] Dear Barbara, I saw many excellent answers already to your question, but wanted to pitch in with another viewpoint. While a research project focusing on QM study of ligands or simulation of receptors is clearly interesting, there is so much more in computer-aided pharmaceutical chemistry that one can learn. It may be the case that your bright student will benefit from a little broader background before plunging into a specific project. You indicate that you have used electrostatic potential calculations to optimize ligands. This is related to the broad area of description of molecular similarity, and people have also used ELP features in QSAR. Maybe he could look into these fields, and formulate ideas on what can be done better. The calculation of protein electrostatic potentials has nowadys became almost trivial, thanks to the availability of APBS and PyMOL. Beyond that, docking has been a generally uplifting experience to our students. While I would not suggest this as the main focus for undergrad research, students clearly enjoy tinkering with structures to improve the docking scores. The programs DOCK and AutoDock are free and not too complex. The main point thus is to get him a little more familiar with the big picture, and with the tools that are needed at various stages of computational drug development. I tend to agree that QM is a better start than protein simulations. Gaussian and Spartan come with clearly written books that not only show how to get things done but also teach the basic principles of calculations and the meaning of results. Spartan is a great one to start with! Manuals for many common simulation programs are more geared toward people who know what they are doing. And it is much more difficult to spot errors in the MD simulation as compared to the QM calculation. P.S. There are few tutorials and practice problems available in the "Assignments" section at http://www.chem.ucsb.edu/~kalju/chem162/ that your student might enjoy. 2,3,4,and 5 are computational ones and fairly independent of the password-protected lecture notes. Please do not hesitate to contact me if you have any questions. Best wishes, Kalju > > Sent to CCL by: Barbara Murray [barbara_murray]=[redlands.edu] > Let me give the list some background before I try to ask my question. I > teach organic chemistry at a small private, undergraduate university. I > was trained as a solid state synthetic chemist about 30 years ago. > About 15 years ago I became interested in computational chemistry and > have dabbled in it ever since. I say dabbled because a) although > faculty are encouraged to stay professionally active here, teaching is > our first priority (and my first love) and b) for the last 10 years I've > been a half time administrator so I have little time to do research. > > All of our chemistry majors do at least a senior research project and > some do much more. I've had the occasional student work for me doing > what I call computational studies of biologically active molecules. A > student does a literature search to find a set of biologically > interesting molecules that all work on the same receptor (one example > was protease inhibitors when they were first coming out). The student > then uses computational chemistry (usually electrostatic potentials) and > information about the receptor's active site to determine why one > molecule might work better than another. These are not earth shaking > projects (nor publishable), but the students learn a bit about > computational chemistry and I'm generally happy. > > But my problem (or not) is that I now have one of the smartest students > I've had in over 20 years who wants to work for me. He's not only > intelligent but incredibly hard-working. He's just finished his > sophomore year, having blown the curve in my organic class away and he > thinks he wants to be a pharmaceutical chemist. > > I feel like he is capable of doing incredible work, especially if he > stays interested in a project and works on it for the next 2 years. But > I don't know what to do with him! I'm so used to having okay students > who are happy with okay little projects, and I've been concentrating on > administration, that I need help or suggestions or something..... > > I've been an on and off member of this list and realize that this is not > exactly the typical question, but I thought it couldn't hurt to ask. > > So if you had a willing young worker who wanted to be a pharmaceutical > chemist when he grows up what would you have him do? I have Spartan and > Gaussian available. He's been playing around with Spartan for the last > few weeks. I also am willing to get other programs if there are other > types of calculations that people do. I'm also willing to collaborate > with someone who's doing pharmaceutical research and thinks they could > use us. I don't want to shortchange this student; I'd like to give him > a real taste of what pharmaceutical computational chemists do; and I > think he's capable of doing really high quality work. Besides, I'd like > to learn along with him. > > Any help or suggestions are welcome. > barbara_murray*redlands.edu > > -- > *********************************************************** > Barbara Murray barbara_murray*redlands.edu > Director > The Center for Science and Mathematics > University of Redlands > Redlands, CA> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Mon May 5 15:25:01 2008 From: "Boobalan Pachaiyappan boobalanp .. gmail.com" To: CCL Subject: CCL: vdW contact area Message-Id: <-36894-080505152149-13513-ZizFqZ3Ok+6bTy2GfJrhzQ:server.ccl.net> X-Original-From: "Boobalan Pachaiyappan" Date: Mon, 5 May 2008 15:21:45 -0400 Sent to CCL by: "Boobalan Pachaiyappan" [boobalanp-,-gmail.com] Dear All, I want to calculate the vdW contact area (not surface area) between a portion of a ligand and certain residues that surrounds it. Is there a way to do that? Any assistance in this case would be highly appreciated. Thank you. Boobalan. From owner-chemistry@ccl.net Mon May 5 16:15:00 2008 From: "Reinaldo Pis Diez reinaldo.pisdiez-*-gmail.com" To: CCL Subject: CCL:G: Error message in G03 freq job Message-Id: <-36895-080505160647-16459-D7u3/xqXYxPsDvoyf8UYrQ.:.server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 05 May 2008 16:06:02 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez---gmail.com] Hi folks, I'm running a frequency job on a small organic molecule using G03, Rev D.01, with the following route section #p freq(raman) b3lyp gen geom(allcheck) scf(restart) After almost four computation days job crashes with the message AX will form 3 AO Fock derivatives at one time. 3 vectors were produced by pass 1. 3 vectors were produced by pass 2. 3 vectors were produced by pass 3. 3 vectors were produced by pass 4. 3 vectors were produced by pass 5. 3 vectors were produced by pass 6. 3 vectors were produced by pass 7. 3 vectors were produced by pass 8. 3 vectors were produced by pass 9. 3 vectors were produced by pass 10. 3 vectors were produced by pass 11. 3 vectors were produced by pass 12. 3 vectors were produced by pass 13. 2 vectors were produced by pass 14. 2 vectors were produced by pass 15. 1 vectors were produced by pass 16. RR out of range in DoVR1. Error termination via Lnk1e in /usr/local/g03/l1002.exe at Mon May 5 14:47:53 2008. I've never seen that message before. What is the error source in this case? And more important, how can I solve it? Thanks in advance. Regards, Reinaldo