From owner-chemistry@ccl.net Mon Jan 21 01:53:02 2008 From: "Nehru Viji Shankaran chat2viji*gmail.com" To: CCL Subject: CCL: Use of mmff94 in charmm Message-Id: <-36076-080121014900-22704-FHIwgotlDKAzjE/ATwZh2Q]^[server.ccl.net> X-Original-From: "Nehru Viji Shankaran" Date: Mon, 21 Jan 2008 01:48:56 -0500 Sent to CCL by: "Nehru Viji Shankaran" [chat2viji*gmail.com] Dear CCLers, I'm new to Charmm. I've installed charmm c33b2 in my system. I want to use the mmff94 force field available in Charmm to calculate the energy of the small molecule. I tried doing it but i always get error. so kindly can someone help me in doing so. I have my small molecule in pdb format. I don't know to convert it into .mrk format. Thanks for any help provided. Nehru viji.S. From owner-chemistry@ccl.net Mon Jan 21 10:32:00 2008 From: "Aurelie Perrier perrier:-:itodys.jussieu.fr" To: CCL Subject: CCL:G: G03 compilation: compilers? Message-Id: <-36077-080121102817-23121-dUCGwPz5JgwMk+ZhzLiDsQ-$-server.ccl.net> X-Original-From: "Aurelie Perrier" Date: Mon, 21 Jan 2008 10:28:12 -0500 Sent to CCL by: "Aurelie Perrier" [perrier,itodys.jussieu.fr] Dear CCLers, I would like to compile Gaussian 03 source code on an AMD Athlon 64-bit machine (linux system). I would like to know if it is compulsory to have pgf77 compiler or if it is possible to use another compiler (ifort for instance)? Any information or help would be much appreciated. Thanks, Aurelie ------------------------------------------- Dr. Aurelie Perrier Laboratoire ITODYS - CNRS UMR7086 Universit PARIS 7 Denis Diderot 1, rue Guy de la Brosse 75005 Paris - France Email : perrier**itodys.jussieu.fr ------------------------------------------- From owner-chemistry@ccl.net Mon Jan 21 11:42:01 2008 From: "nadia boutabba nadboutabba++gmail.com" To: CCL Subject: CCL:G: learning gaussian Message-Id: <-36078-080121081916-22382-NH8x1V7EVdyEWGFmzTqLiw]~[server.ccl.net> X-Original-From: "nadia boutabba" Date: Mon, 21 Jan 2008 08:19:13 -0500 Sent to CCL by: "nadia boutabba" [nadboutabba,,gmail.com] i am learning gaussian ,im physics and im new in the field of computational chemistray, i considered the water dimer, i write the z-matrix of this molecule thanks to molden, and i m doing an optimal structure of this, i got results. now i want to scan the interaction energy of water dimer as a function of the distance between the centre of mass of the two molecules for a given configuration, what is this distance that i will vary in my input file? use HF and a basis set aug-cc-pvdz please can anyone help me thank you From owner-chemistry@ccl.net Mon Jan 21 13:57:00 2008 From: "Rick Venable venabler+*+nhlbi.nih.gov" To: CCL Subject: CCL: Use of mmff94 in charmm Message-Id: <-36079-080121135516-29601-vOKITbvbVlvDirihK9C+4w*|*server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Mon, 21 Jan 2008 13:22:16 -0500 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler_._nhlbi.nih.gov] Some of the online CHARMM course notes (Pittsburgh Supercomputing Center (PSC), also Scripps Research, San Diego) discuss using MMFF Also, try a post in the "Parameters" forum at www.charmm.org -- Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 1/21/08 1:48 AM, "Nehru Viji Shankaran chat2viji*gmail.com" wrote: > Dear CCLers, > > I'm new to Charmm. I've installed charmm c33b2 in my system. > I want to use the mmff94 force field available in Charmm to calculate the > energy of the small molecule. > I tried doing it but i always get error. so kindly can someone help me in > doing so. I have my small molecule in pdb format. I don't know to convert it > into .mrk format. Thanks for any help provided. From owner-chemistry@ccl.net Mon Jan 21 16:59:00 2008 From: "Jayashree Nagesh yfpjaya . gmail.com" To: CCL Subject: CCL:G: CASSCF: Localisation and Visualisation of Orbitals Message-Id: <-36080-080121142337-11749-bEMRMVi0SUDaVAfW5ryP2g^_^server.ccl.net> X-Original-From: "Jayashree Nagesh" Date: Mon, 21 Jan 2008 14:23:34 -0500 Sent to CCL by: "Jayashree Nagesh" [yfpjaya . gmail.com] One of the checks for casscf calculations, I believe is to localise the orbitals and view them to see if they are 'localised' on the desired atoms. I am running a casscf calculation for methoxy molecule, using Gaussian 98. I know that one can ask G98 to localise the active orbitals (IOP(5/42=1), but I am not sure how I visualise them with Molden, for example? Molden does not seem to know that there is more than one set of orbitals in the output file, for example, one belonging to the initial guess, and one, after the casscf calculation is done. So my questions are - 1. Is there a way to get the localised orbitals separately in the output file apart from the orbitals belonging to the casscf wavefunction? 2. How can I visualise more than one set of orbitals in Molden? Or is there a better viewer that I should be using? Thanks Jayashree yfpjaya##gmail.com From owner-chemistry@ccl.net Mon Jan 21 17:35:00 2008 From: "Michael Krein kreinm2{:}rpi.edu" To: CCL Subject: CCL:G: G03 compilation: compilers? Message-Id: <-36081-080121122832-4504-ikryZ2gvg3Rl/HVn9qkhGQ^^^server.ccl.net> X-Original-From: Michael Krein Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 21 Jan 2008 11:20:15 -0500 Mime-Version: 1.0 (Apple Message framework v915) Sent to CCL by: Michael Krein [kreinm2-#-rpi.edu] While it may be possible, I would strongly recommend against using IFORT/ICC with anything not Intel... IFORT/ICC builds runtime checks into every executable... if it's found that your machine isn't GenuineIntel, well, you're executing the i386 non-optimized codepath, if you can execute at all. A better option might be to investigate Sun Solaris on AMD Opteron. The Sun Studio Compilers are free to download (as is Solaris) and appear to be supported by Gaussian. I have not benchmarked this, however, nor have I tried the Linux version of the Sun Studio Compliers (also free). Both would probably be better places to start. Cheers, -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Michael Krein Breneman Research Group Rensselaer Exploratory Center for Cheminformatics Research Rensselaer Polytechnic Institute -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- On Jan 21, 2008, at 10:28 AM, Aurelie Perrier perrier:-:itodys.jussieu.fr wrote: > > Sent to CCL by: "Aurelie Perrier" [perrier,itodys.jussieu.fr] > Dear CCLers, > > I would like to compile Gaussian 03 source code on an AMD Athlon 64- > bit machine (linux system). I would like to know if it is compulsory > to have pgf77 compiler or if it is possible to use another compiler > (ifort for instance)? > > Any information or help would be much appreciated. > Thanks, > > Aurelie > > ------------------------------------------- > Dr. Aurelie Perrier > Laboratoire ITODYS - CNRS UMR7086 > Universit PARIS 7 Denis Diderot > 1, rue Guy de la Brosse > 75005 Paris - France > Email : perrier(-)itodys.jussieu.fr > ------------------------------------------- > > > > -= 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)> > >