From owner-chemistry@ccl.net Sat May 8 01:11:01 2010 From: "Soaring Bear soaringbear*_*yahoo.com" To: CCL Subject: CCL: Method for Hydrogen Bonding Message-Id: <-41821-100507231827-32633-B/UIWzXOEFksnrWAQDCWgw*|*server.ccl.net> X-Original-From: Soaring Bear Content-Type: multipart/alternative; boundary="0-1982886831-1273285092=:59610" Date: Fri, 7 May 2010 19:18:12 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Soaring Bear [soaringbear##yahoo.com] --0-1982886831-1273285092=:59610 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable H bonds are weak and variable so poorly parameterized by any comp method - = an opportunity for further development.=A0=20 Soaring Bear Ph.D. Pharmacology soaringbear at yahoo.com =0Ahttp://soaringbear.com/nature/WeedsforNeeds.html =0Ahttp://www.nlm.nih.gov/mesh/presentations/bear_2005_aug/index.htm =0Aauthor of http://HerbMed.org & http://HerbInsight.com --- On Thu, 5/6/10, Sanjay Bharathwaj computationalchemist.:.gmail.com wrote: > From: Sanjay Bharathwaj computationalchemist.:.gmail.com=20 Subject: CCL: Method for Hydrogen Bonding Could you please let me know the methodseither HF, DFT (if so which functio= nal) that helpsme to study the hydrogen bonded interaction. I find from literatures, that MP2/Lanl2dz provides=0Athe best.But i think i= t takes me long time for my system.In this regard, could you please let me = know any othermethods (computationally cheap) that help me tosolve the prob= lem.Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, Andhra pradhesh,India. =0A=0A --0-1982886831-1273285092=:59610 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
H bonds are weak and variable so poorly param= eterized by any comp method - an opportunity for further development. =

Soaring Bear Ph.D. Pharmacology soaringbear at yahoo.com
=0Aht= tp://soaringbear.com/nature/WeedsforNeeds.html
=0Ahttp://www.nlm.nih.gov= /mesh/presentations/bear_2005_aug/index.htm
=0Aauthor of http://HerbMed.= org & http://HerbInsight.com

--- On Thu, 5/6/10, Sanjay Bhara= thwaj computationalchemist.:.gmail.com <owner-chemistry() ccl.net> wrote:

From: Sanjay Bharathwaj compu= tationalchemist.:.gmail.com
Subject: CCL: Method for Hydrogen Bonding

Could you please let me know th= e methods
either HF, DFT (if so which functional) that helps
me to study the hydrogen bonded interaction.

I find from literatures, that MP2/Lanl2dz provides
=0A
the best.B= ut i think it takes me long time for my system.
In this regard, c= ould you please let me know any other
methods (computationally ch= eap) that help me to
solve the problem.
Dr. Sanjay Bhar= athwaj Kumar,
Dharmendra Institute of Technology,
Andhra pradhesh,
India.
=0A
=0A
--0-1982886831-1273285092=:59610-- From owner-chemistry@ccl.net Sat May 8 09:35:00 2010 From: "Rudolf Herrmann rudolf.herrmann^physik.uni-augsburg.de" To: CCL Subject: CCL: Needed help in interpretation of the results. Message-Id: <-41822-100507135816-544-cbXAvwQ4KVSSmkz4khgnVA]=[server.ccl.net> X-Original-From: "Rudolf Herrmann" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 7 May 2010 19:16:56 +0200 MIME-Version: 1.0 Sent to CCL by: "Rudolf Herrmann" [rudolf.herrmann,+,physik.uni-augsburg.de] Hello, > Hii CCL readers, > > I am using Turbomole, i have performed a calculation on carboxylic acid, > I > used Restricted Hartree-fock method and convergence factor used is 10-7, > asked the application to calculate the NMR shielding. > > The job was successful it gave me an output file, its a human readable > file but i am unable to interpret its results. > i am here with pasting the results, if any one can help me in interpreting > the results, can explain me briefly what are those values, i will be much > thankful. > it depends on what information you want to obtain from your calculation. Let's say, you want to compare the chemical shifts with experimental values from solution NMR. Then take the isotropic values and relate them to that of the standards used in NMR spectroscopy, i.e. TMS for C and H, and water for O. You have to calculate these values with the same method and basis set as used in your example. The delta value to be compared with the experiment is then: delta(compound) = isotr(standard) - isotr(compound) Hope this helps Rudolf. > > $nmr rhf shielding constants > # NO. TYPE MULT. ISOTROPIC ANISOTROPIC dD/dB-CONTRIBUTION > 1 o 1 161.66655533 249.88593341 -233.44145446 > 2 c 1 36.06703273 169.33675006 -212.86538167 > 3 o 1 -85.83832058 624.85981932 -480.92857026 > 4 h 1 27.03601664 10.65610582 -2.21326829 > 5 h 1 24.99107514 4.78581852 -2.99780226 > $end > > your help will be much appreciated. > > > Thanks > Rocky > -- Dr. Rudolf Herrmann Institut für Physik Universität Augsburg D-86159 Augsburg From owner-chemistry@ccl.net Sat May 8 13:28:00 2010 From: "amr hamed dramr83_-_gmail.com" To: CCL Subject: CCL: Receptor Based Pharmacophore Model Message-Id: <-41823-100507141431-8722-kEJd5ZsaOPQsBwoekLX4eg.@.server.ccl.net> X-Original-From: amr hamed Content-Type: multipart/alternative; boundary=0015173fe53cc9efe30486041883 Date: Fri, 7 May 2010 20:07:40 +0300 MIME-Version: 1.0 Sent to CCL by: amr hamed [dramr83^gmail.com] --0015173fe53cc9efe30486041883 Content-Type: text/plain; charset=ISO-8859-1 Ligandscout is the main software to do that in automatic fashion and can export the result to accelrys ds or phase from schrodinger or MOE U can use guides in Discovery studio to do it manually though and adjust it On Fri, May 7, 2010 at 1:31 PM, Anup Shah shahanup86*_*gmail.com < owner-chemistry[-]ccl.net> wrote: > > Sent to CCL by: "Anup Shah" [shahanup86:_:gmail.com] > Dear all, > > Can anyone recommend me a tool for structure/receptor based pharmacophore > model > generation using various crystal structure of a receptor in different > conformation? > > Thanking you in anticipation. > > ANUP SHAH > M.S. (Pharm) > Center for Pharmacoinformatics, > National Institute of Pharmaceutical Education & Research, > Sector 67, S.A.S. Nagar, Mohali > Punjab-160062, INDIA> > > --0015173fe53cc9efe30486041883 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Ligandscout is the main software to do that in automatic f= ashion and can export the result to accelrys ds or phase from schrodinger o= r MOE
U can use guides in Discovery studio to do it manually though and= adjust it

On Fri, May 7, 2010 at 1:31 PM, Anup Shah sh= ahanup86*_*gmail.com <= ;owner-chemistry[-]ccl.net>= wrote:

Sent to CCL by: "Anup =A0Shah" [shahanup86:_:gmail.com]
Dear all,

Can anyone recommend me a tool for structure/receptor based pharmacophore m= odel
generation using various crystal structure of a receptor in different
conformation?

Thanking you in anticipation.

ANUP SHAH
M.S. (Pharm)
Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education & Research,
Sector 67, S.A.S. Nagar, Mohali
Punjab-160062, INDIA



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--0015173fe53cc9efe30486041883-- From owner-chemistry@ccl.net Sat May 8 17:12:00 2010 From: "Deepa Pandit Deepangi.Pandit|gmail.com" To: CCL Subject: CCL: Modify PDB file of DNA-Protein complexes Message-Id: <-41824-100508171107-21181-XaFf6Z8WQoRk3hqJkLYt4w-.-server.ccl.net> X-Original-From: "Deepa Pandit" Date: Sat, 8 May 2010 17:11:05 -0400 Sent to CCL by: "Deepa Pandit" [Deepangi.Pandit===gmail.com] Hi: I would like to modify an existing PDB file of the protein-DNA complex in such a way that only bases are changed. I would like to keep the phosphate backbone of the DNA unchanged (if possible) and protein structure remains unchanged. What kind of software/server/program is suitable to perform the task? I came across 3D-DART but it is useful for building DNA. Not sure how to address the protein issue. http://haddock.chem.uu.nl/dna/DARTusage.html#buildna Thank you. Deepa From owner-chemistry@ccl.net Sat May 8 19:06:00 2010 From: "amr hamed mahmoud dramr83{}gmail.com" To: CCL Subject: CCL: Best worked examples resource for computational chemistry Message-Id: <-41825-100508190428-305-9A5CpBuvOVp3gXYVcBWGyw]-[server.ccl.net> X-Original-From: "amr hamed mahmoud" Date: Sat, 8 May 2010 19:04:27 -0400 Sent to CCL by: "amr hamed mahmoud" [dramr83**gmail.com] what is the best resource for computational chemistry problems using either hyperchem or spartan ? I mean a source for tutorials and worked examples for both undergraduate and graduate level Thanks in advance From owner-chemistry@ccl.net Sat May 8 21:42:00 2010 From: "Adel A. El-Azhary azhary%a%ksu.edu.sa" To: CCL Subject: CCL:G: Xeon versus Opteron or Athlon processors Message-Id: <-41826-100508064721-28273-o1jdWB5QdN/fspc21uLlbg- -server.ccl.net> X-Original-From: "Adel A. El-Azhary" Date: Sat, 8 May 2010 06:47:20 -0400 Sent to CCL by: "Adel A. El-Azhary" [azhary!=!ksu.edu.sa] Dear all: Did anyone try to run G09 or G03 on Intel Xeon and AMD Opteron or Athlon processors and which one has better price/speed ratio. Adel El-Azhary Azhary : ksu.edu.sa From owner-chemistry@ccl.net Sat May 8 22:17:00 2010 From: "Adam Tenderholt atenderholt{}gmail.com" To: CCL Subject: CCL: Method for Hydrogen Bonding Message-Id: <-41827-100508205933-30469-o5moCMx3dJUWM+94kI7o/g~!~server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 8 May 2010 17:59:22 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt^-^gmail.com] If you're interested in proton NMR, you should look at the following references. These papers have the parameters for linear fits of the calculated isotropic couplings to experimental NMR shifts. Rablen, P. R., et. al. J. Phys. Chem. A, v 103, pp 7357-7363. Wang, B., et. al. J. Comput. Chem., v 22, pp 1887-1895. Others should chime in if they know more recent or appropriate papers... Adam On Fri, May 7, 2010 at 10:27 AM, Nuno A. G. Bandeira nuno.bandeira . ist.utl.pt wrote: > > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[-]ist.utl.pt] > On 06-05-2010 17:46, Sanjay Bharathwaj computationalchemist.:.gmail.com > wrote: >> >> Could you please let me know the methods >> either HF, DFT (if so which functional) that helps >> me to study the hydrogen bonded interaction. >> >> I find from literatures, that MP2/Lanl2dz provides >> the best.But i think it takes me long time for my system. >> > > It's not a guaranteed bet that you'll get a proper description of the H b= ond > using DFT but you could try Barone's modification of PW91 aka mPW91, or P= BE > or any functional using Grimme's empirically dispersion corrected DFT-D > methodology. > > Also make sure you add enough polarisation functions to your atoms (simpl= e > LANL2DZ might not be enough). > > Best wishes > Nuno > > -- > Nuno A. G. Bandeira, AMRSC > Laboratoire de Chimie LR6 > Ecole Normale Superieure de Lyon > 46, Allee d'Italie > 69364 Lyon Cedex 07 - France > http://cqb.fc.ul.pt/intheochem/nuno/ > -- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0> =A0 =A0=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.= shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> =A0 =A0> > >