From jkl@ccl.net Fri Jul 17 13:29:42 1992 Date: Fri, 17 Jul 1992 13:29:39 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: mopac.man postscript file? Status: R Posted to the list for: = Date: Thu, 16 Jul 1992 9:07:27 -0700 (PDT) = From: F0418950@JAGUAR.CSC.WSU.EDU Does anyone have, or know where I can find a postscript version of the mopac6.0 manual (the mopac.man file)? Whenever I print the mopac.man file I have, the pages are shifted so I use up almost twice as much paper as it should take (189 pages). I have tried various formaters and ported it to ms word and wordperfect as well, but to no avail. Thanks in advance, Andrew f0418950@jaguar.csc.wsu.edu From jkl@ccl.net Fri Jul 17 13:38:09 1992 Date: Fri, 17 Jul 1992 13:38:06 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Re: A Semiempirical Life Status: R Sent to the list for: = Date: Thu, 16 Jul 1992 14:12:05 -0400 = From: hyper!slee (Thomas Slee) ,or slee@hyper.com Following up Brian Duke's question: the task of giving semi-empirical methods a firm theoretical grounding has been addressed by Karl Freed, of the University of Chicago. It is likely that the paper Dr. Duke recalls seeing in J. Chem. Phys. is one of Freed's. Freed does not to my knowledge ask about the limitations of Hartree-Fock theory, however; instead he argues that the essential approximation of semi-empirical methods is the use of valence orbitals only. Freed shows that you can write out an equation that yields the exact energies of the valence states of the system in such a limited basis if you are prepared to use an effective Hamiltonian that has many (more than two-) body effective interactions. A recent review by Thiel (Tetrahedron, vol 44, No 24, p 7393) summarizes the work briefly, and gives several of the key references. Freed's work does not seem to have had much in the way of practical consequences that I have seen (and I may well be wrong, of course ... ). It does suggest some ways forward in terms of writing out semi-empirical Hamiltonians, but perhaps semi-empirical methods are not at a stage where their structure can be directed by formal considerations. Tom Slee, Hypercube -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 From jkl@ccl.net Fri Jul 17 13:40:03 1992 Date: Fri, 17 Jul 1992 13:39:59 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: CHARMm .DCD READ/WRITE SELE ATOMS Status: R Sent to the list for: = Date: 16-JUL-1992 18:37:57.27 = From: WSONNEN@EAGLE.WESLEYAN.EDU This is a question for any CHARMm guru on the net. I would like to create a trajectory file (.DCD file) from an existing .DCD file. I want the new .DCD file to contain only selected atoms from the entire coordinate set. I have tried a number of variations without success. Any help would be appreciated. Below are two excerpts, each followed by the relevant CHARMm .LOG output, from two files. As you can see i tried two commands: the COOR READ and the TRAJ READ/TRAJ WRITE. Thank you Wayne Sonnen wsonnen@eagle.wesleyan.edu ************************************************************************** ...........STUFF DELETED........................ OPEN READ UNIT 51 FILE NAME TEST.DCD OPEN WRITE UNIT 52 FILE NAME DNA2.DCD WRITE COOR UNIT 52 FILE * SET 1 1 LABEL LOOP READ COOR UNIT 51 FILE IFILE @1 WRITE COOR UNIT 52 FILE INCR 1 BY 1 IF 1 LT 2.5 GOTO LOOP STOP END *******************LOG FILE FOR ABOVE STUFF:**************************** ******************** ... STUFF DELETED ....................************* CHARMM> OPEN READ UNIT 51 FILE NAME TEST.DCD UNIT 51 OPENED FOR READONLY ACCESS TO TEST.DCD CHARMM> OPEN WRITE UNIT 52 FILE NAME DNA2.DCD UNIT 52 OPENED FOR WRITE ACCESS TO DNA2.DCD CHARMM> WRITE COOR UNIT 52 FILE RDTITL> * RDTITL MESSAGE: NO TITLE READ. CHARMM> CHARMM> SET 1 1 Parameter # 1 set to "1" CHARMM> LABEL LOOP CHARMM> READ COOR UNIT 51 FILE IFILE @1 RDCMND substituted parameter 1: "1" SPATIAL COORDINATES BEING READ FROM UNIT 51 TITLE: * SCRIPT FILE PRODUCED BY QUANTA TITLE: * DATE: 5/24/92 13:47:40 CREATED BY USER: quanta TITLE: * READING FROM COORDINATE TRAJECTORY, IFILE = 1 ** WARNING ** MULTIPLE COORDINATES FOR **** **NOTE: AFTER GRNERATING THIS STUFF THE MACHINE JUST 'HUNG'************************************************************ **** SECOND FILE: *********************************************************************** .....STUFF DELETED......... OPEN READ UNIT 51 FILE NAME TEST.DCD OPEN WRITE UNIT 52 FILE NAME DNA2.DCD TRAJ IREAD 51 IWRITE 52 * SET 1 1 LABEL LOOP TRAJ READ SELE BYNUM 1:542 END TRAJ WRITE SELE BYNUM 1:542 END INCR 1 BY 1 IF 1 LT 2.5 GOTO LOOP STOP END **************LOG FILE FOR THIS RUN: THE "SELE ... " IS NOT ALLOWED*** .....STUFF DELETED......... CHARMM> TRAJ WRITE SELE BYNUM 1:542 END TRAJ: WRITING NEXT TRAJECTORY FILE, OPTIONS; SKIP= 500 NPRIV= 15500 NSTEP= 25000 TRAJU= 52 **** Warning **** The following extraneous characters were found while command processing in CHARMM SELE BYNUM 1:542 END CHARMM> INCR 1 BY 1 Parameter # 1 set to "2" **************************************************************** From jkl@ccl.net Fri Jul 17 13:41:45 1992 Date: Fri, 17 Jul 1992 13:41:41 -0400 From: jkl@ccl.net To: tchemistry@ccl.net Subject: Relativistic HF Basis Sets Status: R = Date: Fri, 17 Jul 92 10:12:05 -0500 = From: perkins@tc4.fi.ameslab.gov (Leslie S. Perkins) Dear Colleague, I am looking for relativistic Hartree-Fock basis sets for the 5d transition metals, especially Pt and Au. If you know of any ftp site containing these type of basis sets or have references for relativistic HF basis sets, please e-mail me at the address below. Thank you. Leslie perkins@iastate.edu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Leslie S. Perkins Department of Chemistry - Ames Laboratory 402 Wilhelm Hall e-mail : perkins@tc4.fi.ameslab.gov Iowa State Univ. voice : (515) 294-9925 Ames, Iowa 50011 fax : (515) 294-5204 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@ccl.net Fri Jul 17 14:56:14 1992 Date: Fri, 17 Jul 92 13:21 EDT From: Subject: Amber residue vs. atom based cutoffs To: chemistry@ccl.net Status: R Hi, I have a question. AMBER is billed as a residue based force field. On this account, it is claimed, it uses a residue based cutoff for non-bond interactions. Has anyone ever tested what happens when an atom based cutoff is used? Does it actually make a difference? One can think of reasons why it would and reasons why it might not.. Scott From chemistry-request@ccl.net Fri Jul 17 19:50:28 1992 Date: Fri, 17 Jul 1992 11:32 MST From: YAMAMURA@CGF.chem.Arizona.edu Subject: Interaction Energy and Hydrophobicity To: chemistry@ccl.net Status: R Dear Fellow Netters, Does anyone know of computational models for calculating interaction energies between the planar surface of a solid of a known crystal structure and the surface of an adsorbed protein of known crystal structure? It is especially desirable for the model to include hydrophobic interactions. All information received will be summarized to the net. Any information about references, programs, etc would be very much appreciated. Thank you. Susan Yamamura yamamura@cgf.chem.arizona.edu