From owner-chemistry@ccl.net Tue Nov 3 09:05:01 2009 From: "Jamie Platts Platts-*-cardiff.ac.uk" To: CCL Subject: CCL: MGMS Silver Jubilee Prize Message-Id: <-40593-091103085934-11514-CGPFO8wZmGzeJLkDWbCDdg * server.ccl.net> X-Original-From: Jamie Platts Content-Type: multipart/alternative; boundary="=_alternative 004CD18B80257663_=" Date: Tue, 3 Nov 2009 13:58:59 +0000 MIME-Version: 1.0 Sent to CCL by: Jamie Platts [Platts:-:cardiff.ac.uk] This is a multipart message in MIME format. --=_alternative 004CD18B80257663_= Content-Type: text/plain; charset="US-ASCII" Dear CCL I am pleased to announce that Dr Cherif Matta, of Mount Saint Vincent University & Dalhousie University, Canada, has been awarded the MGMS Silver Jubilee Prize for 2009. This recognises his outstanding research record in recent years, as well as his work in popularisation of scientific advances. We hope to invite Cherif to present his research at a forthcoming MGMS meeting - details to be finalised. The standard of nominations was very high this year, which I hope bodes well for the future of this initiative. I hope you will join me in congratulating Cherif on coming first out of an excellent group of young scientists. Jamie ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts(a)cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy --=_alternative 004CD18B80257663_= Content-Type: text/html; charset="US-ASCII"
Dear CCL
 
I am pleased to announce that Dr Cherif Matta, of Mount Saint Vincent University & Dalhousie University, Canada, has been awarded the MGMS Silver Jubilee Prize for 2009. This recognises his outstanding research record in recent years, as well as his work in popularisation of scientific advances. We hope to invite Cherif to present his research at a forthcoming MGMS meeting - details to be finalised.

The standard of nominations was very high this year, which I hope bodes well for the future of this initiative. I hope you will join me in congratulating Cherif on coming first out of an excellent group of young scientists.

Jamie

----------------------------------------------------------
Jamie Platts
School of Chemistry       Phone: +44 (0) 2920 874950
Cardiff University             Email: platts(a)cf.ac.uk
Park Place                       FAX:   +44 (0) 2920 874030
Cardiff CF10 3AT             www.cf.ac.uk/chemy --=_alternative 004CD18B80257663_=-- From owner-chemistry@ccl.net Tue Nov 3 12:46:00 2009 From: "Lydia Rhyman lyd_rhyman=hotmail.co.uk" To: CCL Subject: CCL: average of predicted bond length Message-Id: <-40594-091103124316-25227-c6EHEPHW19INTVPoDCdd4g^-^server.ccl.net> X-Original-From: "Lydia Rhyman" Date: Tue, 3 Nov 2009 12:43:12 -0500 Sent to CCL by: "Lydia Rhyman" [lyd_rhyman++hotmail.co.uk] Dear ALL Assume that one estimates a bond length using B3LYP/6-31G then estimate again using other functionals with the same basis set, is it meaningful to consider an average of these predicted bond lengths? thanks for your comments From owner-chemistry@ccl.net Tue Nov 3 14:41:00 2009 From: "Aniko Simon aniko*o*simbiosys.ca" To: CCL Subject: CCL: Multi SDF to many files in folder Message-Id: <-40595-091103143631-26944-ZsxcWKXTt4YFD/so/1XTvA*server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 3 Nov 2009 14:36:28 -0500 Sent to CCL by: "Aniko Simon" [aniko ~~ simbiosys.ca] Dear CCL'ers, This posting made me realize that there is generic interest in Linux / Unix scripts useful for the computational chemistry community. Our scripts page contains some scripts that are relevant to eHiTS users, but also a few others that are more general-purpose. They are available free of charge here: http://www.simbiosys.ca/download/scripts/index.html Best wishes, Aniko -- Aniko Simon, Ph.D. | SimBioSys Inc. | Tel: 1-416-741-4263 http://www.simbiosys.ca/ | blog: http://www.simbiosys.ca/blog/ On October 22, 2009, Zsolt Zsoldos zsolt-.-simbiosys.ca wrote: > Hi Chi, > > The attached bash script (works on linux or most Unix systems) does > the heart of what you need, i.e. it extracts a specific molecule given > by the index, i.e. the n-th molecule into a file-name you supply. You > may need to modify it to suit your needs or call it in a loop if you > want all the molecules extracted. Note, it also works for mol2 and tma > formats. > > Best regards, > Zsolt > > On Thu, Oct 22, 2009 at 12:23 PM, c p Mpamhanga > > chido.mpamhanga,+,gmail.com wrote: > > Sent to CCL by: "c p Mpamhanga" [chido.mpamhanga-*-gmail.com] > > Hi all, > > > > Does anyone have a script to split an SDFfile into single sdfs named > > after each after each individual molecule as specified in first line of > > parent multi file? (I have written one but it seems not too robust) > > > > Cheers > > > > Chi From owner-chemistry@ccl.net Tue Nov 3 17:48:00 2009 From: "amit dong dongamit123]=[gmail.com" To: CCL Subject: CCL: PCA analysis tool Message-Id: <-40596-091103174612-20204-RhV1HDCWQaLw7vKHD6EGkw-#-server.ccl.net> X-Original-From: amit dong Content-Type: multipart/alternative; boundary=001636498c5d1aa36304777f42e1 Date: Tue, 3 Nov 2009 16:46:00 -0600 MIME-Version: 1.0 Sent to CCL by: amit dong [dongamit123%a%gmail.com] --001636498c5d1aa36304777f42e1 Content-Type: text/plain; charset=ISO-8859-1 Hi, I want to analyse the distribution of my inhibitors and non-inhibitors using PCA. Is there any tool that can be used for the same? I have already calculated the descriptors for both the groups. Thanks AD --001636498c5d1aa36304777f42e1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
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I want to analyse the distribution of my inhibitors and non-inhibitors= using PCA. Is there any tool that can be used for the same? I have already= calculated the descriptors for both the groups.
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Thanks
AD
--001636498c5d1aa36304777f42e1-- From owner-chemistry@ccl.net Tue Nov 3 22:14:01 2009 From: "Cheri A McFerrin cmcfer1-*-tigers.lsu.edu" To: CCL Subject: CCL: gamess Message-Id: <-40597-091103214648-485-nm1LCRUFgCAqLGEbiQzTvA###server.ccl.net> X-Original-From: "Cheri A McFerrin" Date: Tue, 3 Nov 2009 21:46:44 -0500 Sent to CCL by: "Cheri A McFerrin" [cmcfer1+/-tigers.lsu.edu] hi everyone: i would like to solicit some help on dictionary files and the restart function in gamess, this is what my input file begins with below. i am trying to restart (an irc job) that reads the vibrational frequencies > from a prior dictionary file created. trouble is, i can find a definition of dictionary file in the gamess documentation. is anyone familiar w restarting gamess jobs and dictionary files? cheri mcferrin ********************************************************************************** $contrl scftyp=rohf runtyp=irc geom=daf irest=-1 nprint=8 mult=3 icharg=1 dfttyp=b3lyp1 pp=read maxit=200 $end $system mwords=20 memddi=5 $end $vib $end $guess guess=mosaved $end $irc pace=gs2 saddle=.t. forwrd=.f. npoint=20 stride=0.01 $end $scf sogtol=0.01 shift=.t. soscf=.t. conv=1.d-4 diis=.f. $end $dft switch=6.d-4 swoff=1.d-3 $end $data From owner-chemistry@ccl.net Tue Nov 3 23:35:01 2009 From: "Rajarshi Guha rajarshi.guha[#]gmail.com" To: CCL Subject: CCL: PCA analysis tool Message-Id: <-40598-091103232141-32487-ESZT2ZcAMNC+6f6mVT3d/w=server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 3 Nov 2009 22:50:07 -0500 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Rajarshi Guha [rajarshi.guha_+_gmail.com] On Nov 3, 2009, at 5:46 PM, amit dong dongamit123]=[gmail.com wrote: > Hi, > > I want to analyse the distribution of my inhibitors and non- > inhibitors using PCA. Is there any tool that can be used for the > same? I have already calculated the descriptors for both the groups. R ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Gravity brings me down.