From owner-chemistry@ccl.net Thu Jan 22 02:04:01 2009 From: "jbrandao===ualg.pt" To: CCL Subject: CCL: energy of H+ Message-Id: <-38479-090121032343-5452-pWuOQY6hNzcEJYDSBVGa7g*server.ccl.net> X-Original-From: jbrandao]^[ualg.pt Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 21 Jan 2009 07:22:34 +0000 MIME-Version: 1.0 Sent to CCL by: jbrandao#%#ualg.pt No. You should use statistical themodynamics to answer that question. This result only means that the process can be endothermic (there is =20 missing data on the zero point energy, vibrational frequencies, =20 rotational constants, solvent(?)...). Although H+ is a zero for =20 energy, this dissociation may increase the entropy of the system =20 (there is again missing data...). At the end, I would like to emphasize that a process is =20 thermodinamically allowed or forbiden (second law) depending on the =20 conditions (temperature, etc.) Jo=E3o Brand=E3o Quoting "Serge Dom serge.dom[a]gmail.com" : > Thank you for your answer. > If energy of H+ is zero I need only calculate pyridine-h and pyridine (-) = in > order to calculate difference in energy between > product and reactant. Pyridine-h (0,2) has total energy -248.8282688 au at > PW91/cc-pVTZ level and pyridine (-) (-1,2) has energy > -248.2369938. So elimination of the proton from pyridine-h molecule is not > thermodynamically favorable. Is it correct? > > Serge > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Thu Jan 22 09:06:01 2009 From: "Tamar Ansbacher tamar.ansbacher-x-mail.huji.ac.il" To: CCL Subject: CCL:G: 'charge' calculation in Gaussian Message-Id: <-38480-090122022259-30864-ZJlsyfeNbMsydqnUonUZig(0)server.ccl.net> X-Original-From: Tamar Ansbacher Content-Type: multipart/alternative; boundary=00151751149a02256d04610d0969 Date: Thu, 22 Jan 2009 09:15:20 +0200 MIME-Version: 1.0 Sent to CCL by: Tamar Ansbacher [tamar.ansbacher- -mail.huji.ac.il] --00151751149a02256d04610d0969 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All. I'm running a single point charge calculation in Gaussian I wonder how to get the total energy. I see the usual SCF value,(HF=-...) beside that I see a Self energy of the charges term and an MM energy of the charges term and a Nuclear-Charge attraction term Does the HF value include these terms? I reduced those from the HF value- and Im not getting the SCF value with no charge contributions (like running a simple SCF job) Any help would be appreciated Tamar --00151751149a02256d04610d0969 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All.
I'm running a single point charge calculation in Gaussian
I wonder how to get  the total energy.
I see the usual SCF value,(HF=-...) beside that I see
  a Self energy of the charges term  and
an MM   energy of the charges term and
a Nuclear-Charge attraction term
Does the HF value include these terms?
I reduced those from the HF value- and Im not getting the SCF value with no charge contributions (like running a simple
SCF job)
Any help would be appreciated
Tamar

--00151751149a02256d04610d0969-- From owner-chemistry@ccl.net Thu Jan 22 10:08:02 2009 From: "Gabriele Cruciani gabri ~~ chemiome.chm.unipg.it" To: CCL Subject: CCL: descriptors for peptides Message-Id: <-38481-090122065025-29832-fVfUhFkupBPKBJcErUR73g*o*server.ccl.net> X-Original-From: Gabriele Cruciani Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Thu, 22 Jan 2009 11:50:27 +0100 MIME-Version: 1.0 Sent to CCL by: Gabriele Cruciani [gabri : chemiome.chm.unipg.it] 2D-3D descriptors for peptides can be easily obtained with VolSurf+ Please see the VS+ home page at www.moldiscovery.com Best G.Cruciani > Sent to CCL by: "atul agarwal" [aagarwal .. achillion.com] > Hi, > > Are there any 2D and 3D descriptors available for peptides? References of their application and availability for pharma will be highly appreciated. > > thanks! > Atul> > From owner-chemistry@ccl.net Thu Jan 22 11:53:01 2009 From: "sumit mukherjee sooomitin .. hotmail.com" To: CCL Subject: CCL:G: memory requirement Message-Id: <-38482-090121200113-16488-Z9vtNUPuEsbdMkVlln6txg .. server.ccl.net> X-Original-From: "sumit mukherjee" Date: Wed, 21 Jan 2009 20:01:10 -0500 Sent to CCL by: "sumit mukherjee" [sooomitin[A]hotmail.com] i am looking forward to doing the following calculation: # opt freq=noraman b3lyp/6-31+g(d) geom=connectivity i am using a desktop computer with winxp OS and with quad-core processor and 4 GB RAM. what is the memory and processor requirement for this job if # of atoms is 40-50? gaussian website talks about it more or less, but i am confused. can somebody tell me how to calculate exact requirement? your help is appreciated. From owner-chemistry@ccl.net Thu Jan 22 13:25:00 2009 From: "Nir London nir[A]rosettadesigngroup.com" To: CCL Subject: CCL: Rosetta Academic Training Workshop Message-Id: <-38483-090122131924-15157-uqFB7ywyCL0vkFhCEUU11Q..server.ccl.net> X-Original-From: "Nir London" Date: Thu, 22 Jan 2009 13:19:20 -0500 Sent to CCL by: "Nir London" [nir ~ rosettadesigngroup.com] Due to public demand, Rosetta Design Group is organizing a Rosetta software training workshop, aimed for academic groups. The format of the workshop will be a webinar - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.* Nir London | Rosetta Design Group http://rosettadesigngroup.com/ * If youre not from an academic group, dont worry, write us anyway From owner-chemistry@ccl.net Thu Jan 22 15:53:01 2009 From: "Amir Taghavi amirtaghavi|*|khayam.ut.ac.ir" To: CCL Subject: CCL: Tinker Installation in Open Suse 10.3 linux? Message-Id: <-38484-090122153509-22832-7+/FsjijJ+2kxAHZs6YdbA:+:server.ccl.net> X-Original-From: "Amir Taghavi" Date: Thu, 22 Jan 2009 15:35:06 -0500 Sent to CCL by: "Amir Taghavi" [amirtaghavi]![khayam.ut.ac.ir] Greetings, I'm going to install Tinker 5(or 4.2) in Linux Open Suse 10.3, If anyone has installed it, so I will be grateful if guide me step by step for installation, because I'm new to working with tinker in Linux, Best Regards From owner-chemistry@ccl.net Thu Jan 22 16:28:00 2009 From: "Sarath Chandra Dantu dsarath||gwdg.de" To: CCL Subject: CCL:G: Error in Gaussian Help required Message-Id: <-38485-090122150323-15790-pi+kybF2yvAt3t2xXt8MVA.@.server.ccl.net> X-Original-From: "Sarath Chandra Dantu" Date: Thu, 22 Jan 2009 15:03:19 -0500 Sent to CCL by: "Sarath Chandra Dantu" [dsarath!A!gwdg.de] Dear Friends, I am using gaussian and amber to generate forcefield parameters for Amber forcefield. I am getting the following error in the log file of the gaussian. I have prepared a log file from pdb file using antechamber then i tried to do structure optimization using gaussian. This entry at a13 is causing an error in the Gaussian. t12= -100.1064 b13= 4.6857 "a13= nan" t13= -100.1064 What can i do to rectify this error? Regards, Sarath dsarath'at'gwdg.de From owner-chemistry@ccl.net Thu Jan 22 20:12:01 2009 From: "N. Sukumar nagams---rpi.edu" To: CCL Subject: CCL: descriptors for peptides Message-Id: <-38486-090122180034-27144-s1IX5cMDFZm75DtspiowMQ|-|server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 22 Jan 2009 16:58:17 -0500 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams]_[rpi.edu] PROTEIN RECON http://reccr.chem.rpi.edu/Software/Protein-Recon/Protein-Recon-index.html constructs 2D electronic property descriptors for peptides using an amino acid fragment library precomputed from ab initio wavefunctions. The online utility accepts both PDB and FASTA input. These descriptors are also available within MOE at http://svl.chemcomp.com/ together with RECON 2D topological autocorrelation descriptors and 3D spatial autocorrelation descriptors (RAD). A description of performance of these descriptors for peptides is reported in C. Bergeron, T. Hepburn, M. Sundling, N. Sukumar, W. P. Katt, K. P. Bennett, C. M. Breneman, "Prediction of peptide bonding affinity: Kernel methods for nonlinear modeling" Protein Peptide Lett, in press, 2008. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ ==============Original message text=============== On Tue, 20 Jan 2009 9:14:10 EST "atul agarwal aagarwal|achillion.com" wrote: Sent to CCL by: "atul agarwal" [aagarwal .. achillion.com] Hi, Are there any 2D and 3D descriptors available for peptides? References of their application and availability for pharma will be highly appreciated. thanks! Atulhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Thu Jan 22 20:46:01 2009 From: "xunlei ding dingxunlei%%gmail.com" To: CCL Subject: CCL:G: memory requirement Message-Id: <-38487-090122203901-16673-TiJbdoUoZ+PmcExQvaT33g**server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Fri, 23 Jan 2009 09:38:45 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei**gmail.com] Hi, Different types of atoms (such as H and O ) have different number of basis functions. The memroy requirement depends on how many basis functions are used in the calculation. You can find lines like " 361 basis functions 1083 primitive gaussians" in the output file. You can try the G03 utility "freqmem" to estimate the memory requirement. Ding 2009/1/22 sumit mukherjee sooomitin .. hotmail.com : > > Sent to CCL by: "sumit mukherjee" [sooomitin[A]hotmail.com] > > i am looking forward to doing the following calculation: > > # opt freq=3Dnoraman b3lyp/6-31+g(d) geom=3Dconnectivity > > i am using a desktop computer with winxp OS and with quad-core processor = and 4 GB RAM. > > what is the memory and processor requirement for this job if # of atoms i= s 40-50? gaussian website talks about it more or less, but i am confused. c= an somebody tell me how to calculate exact requirement? your help is apprec= iated. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 ------------------------------------------------------ Xun-Lei Ding Associate Research Professor of Physical Chemistry State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, The Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China