From runeberg@csc.fi Fri Feb 19 12:43:26 1993 From: Nino Runeberg Message-Id: <199302190843.AA18020@csc.fi> Subject: mass effects on vibrational frequencies To: CHEMISTRY@ccl.net Date: Fri, 19 Feb 1993 10:43:26 +0200 (EET) Hi CCML Readers, when calculating vibrational frequencies with Gaussian92 I met the following problem. I would like to substitute mass-centers having virtually any mass(e.g. a hydrogen with a mass of 100u). I am aware of the keyword option ReadIsotopes in Gaussian92 but, as far as I know, this allows only substitution of real isotopes(the program checks the mass against a list of known isotopes). So my questions are 1) Is it possible to solve this problem within the Gaussian92 package. 2) Is there available any free software which could use the G92 Z-matrix and force constants as input and allows recalculation of vibrational frequencies for different masses. Thanks in advance, Nino Runeberg email: runeberg@convex.csc.fi Department of Chemistry phone: int-358-0-191 7247 P.O. Box 19 FIN-00014 fax: int-358-0-406 159 University of Helsinki Finland From vaxinf@chclu.chemie.uni-konstanz.de Fri Feb 19 06:01:30 1993 Date: Fri, 19 Feb 1993 11:42:09 CET From: vaxinf@chclu.chemie.uni-konstanz.de To: CHEMISTRY@ccl.net Message-Id: <009685D3.59C3DB80.23862@chclu.chemie.uni-konstanz.de> Subject: QUIPU-Programs Hi, I looking for the person, who is responsible for the QUIPU-Package, a molecular modeling program, distributed by the quantum theory project at University of Florida. Thanks for your reply in advance Eberhard Heuser-Hofmann Univ.Konstanz Germany From boehme@convex.HRZ.Uni-Marburg.DE Fri Feb 19 14:16:14 1993 Date: Fri, 19 Feb 93 13:16:14 +0100 From: boehme@convex.HRZ.Uni-Marburg.DE (Boehme Marlis) Message-Id: <9302191216.AA11006@convex.HRZ.Uni-Marburg.DE> To: chemistry@ccl.net Subject: BSSE-calculation Dear Netters, There is a problem calculating the BSSE on organocopper-(I)-molecules. I use the basisset and expanded ECP's from Hay and Wadt for cu and the Gaussian programm. The calculation for a dimere involving ghostfunctions for the coppercation gives a higher total energy than the calculation for the corresponding monomer without that functions. One expects a lower energy because of the better discription with the additional ghostfunctions. We assume that it is reasoned by the ECP-calculation. Any ideas? Marlis Boehme boehme@convex.uni-marburg.de From chiremv!andromeda!jeffb@uunet.UU.NET Fri Feb 19 03:46:34 1993 Date: Thu, 18 Feb 93 13:08:55 -0800 From: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) Message-Id: <9302182108.AA16901@andromeda> To: uunet!ccl.net!chemistry-request@uunet.UU.NET Subject: Re: Question about PDB format Joe Leonard asked about: 1H24 | 2H24--N24-- . . . rest of molecule | 3H24 This follows standard Brookhaven PDB rules (paraphrased from the April 1992 PDB Newsletter): Atom names occur in columns 13-16. These four characters are: 1-2 Chemical Symbol - right justified 3 Remoteness indicator (alphabetic) 4 Branch designator (numeric) For protein coordinate sets containing hydrogens, IUPAC-IUB rules are followed, except that rule 4.4 has been modified as follows: "When more than one hydrogen atom is bonded to a single atom, the hydrogen atom number designation is given as the first character of the atom name rather than as the last character (e.g. HB1 is denoted as 1HB)." Perfectly logical, right? Jeff Blaney Chiron From tripos!vela!victor@wupost.wustl.edu Fri Feb 19 03:09:53 1993 Date: Fri, 19 Feb 93 09:09:53 -0600 From: tripos!vela!victor@wupost.wustl.edu (Vic Lewchenko) Message-Id: <9302191509.AA04462@vela.tripos> To: chemistry@ccl.net Subject: Hirschfeld charges? I have always been interested in methods for computing charges on atoms in molecules for use in molecular modeling. Recently I heard that DMOL can compute "Hirschfeld" charges and that at least one person thinks these work best. Can someone briefly explain to me how Hirschfeld charges are computed or even better also point me to a reference? Thanks Vic Lewchenko victor@tripos.com From wrinn@iris104.biosym.com Fri Feb 19 02:36:43 1993 Date: Fri, 19 Feb 93 10:36:43 -0800 From: wrinn@biosym.com Message-Id: <9302191836.AA05104@iris104.biosym.com> To: CHEMISTRY@ccl.net Subject: hirshfeld charges Vic Lewchenko asks about Hirshfeld charges. The reference is Hirshfeld, F.L., Theor.Chim.Acta 44, 129 (1977) From FR042008@YSUB.YSU.EDU Fri Feb 19 09:49:00 1993 Message-Id: <199302191947.AA19729@oscsunb.ccl.net> Date: Fri, 19 Feb 93 14:49:00 EST From: "Janet Del Bene" To: chemistry@ccl.net Subject: BSSE calculation Marlis, In general, one thing that you need to be concerned about is the monomer geometry. If the monomer distorts in the complex, and you do the monomer calculations with ghost functions at that geometry, then the computed energy of the monomer at the distorted geometry with ghost functions could indeed be higher than the optimized monomer without ghost functions. I might also add that it is probably better to use a better basis set which includes diffuse functions that to do the BSSE correction. I have addressed this in two recent papers, one on proton affinities and one on hydrogen bond energies. Others (Schaefer and Truhlar, for example) have come to similar conclusions. Hope this helps. Janet E. Del Bene From ravishan@swan.wesleyan.edu Fri Feb 19 11:53:17 1993 Date: Fri, 19 Feb 93 11:53:05 -0500 Message-Id: <9302191653.AA20971@swan.wesleyan.edu> From: G. Ravishanker To: vincent@retina.chem.psu.edu Subject: Parallel AMBER Jim We have just finished porting Wesdyn (an MD program derived from GROMOS86 - heavily modified and vectorized for Cray) to run in parallel under Network Linda. It is premature for me to put this out, but I could not resist. Our timings show reasonable numbers for first attempt. This resulted from the work by myself and Tim Mattson (Scientific Computing Associates who market Linda). We see speedups of 30% for two nodes and 50% for 3 nodes. Our initial tests were on EM (10-50 steps) on a dodecamer sequence of DNA with ~2400 water molecules in a hexagonal prizm box with periodic boundary condition with a cutoff of 11.5 A (7.5 A to 11.5 A switching function). We are going to run more benchmarks on 5ps of MD, and on Ethernet vs FDDI. We have several things to sort out including the distribution and other things, so treat this as very preliminary. Things look pretty good at this point and we are looking at possibilities of further speedups. Ravi**************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wesleyan.edu * * Middletown, CT 06457. * **************************************************************************** From SML108@PSUVM.PSU.EDU Fri Feb 19 11:56:36 1993 Message-Id: <199302191656.AA16700@oscsunb.ccl.net> Date: Fri, 19 Feb 93 11:56 EST From: Subject: Re: MM2 energy minimization? To: hcj@gull.uncc.edu > In testing our geometry optimization program that utilizes >genetic algorithms, we were able to obtain a lower energy conformation >than MM2. This is not too suprising, however, when we gave our new >geometry to MM2, it calculated an initial energy of ~9.44 and ended >with a final energy, after _minimization_, of ~10.05!! I was just >curious why this might be? Any ideas? Most likely possibility: A bug in your code... 2nd most liikely possibility: Going from internally represented coordinates to whatever output file format you use caused slight perturbations in your coordinates throwing you out of the minimum you were originally heading towards I'd bet on number one myself based on experience... How big a system were you playing with? If it's really big, I'd start to lean towards number two... Scott From mail Fri Feb 19 13:02:31 1993 Date: Fri, 19 Feb 1993 11:57:48 -0500 From: hyper!hurst (Graham Hurst) Message-Id: <9302191657.AA10083@hyper.hyper.com> To: chemistry@ccl.net, jle@world.std.com (Joe M Leonard) Subject: Re: Question about PDB format > Date: Thu, 18 Feb 1993 12:50:05 -0500 > From: jle@world.std.com (Joe M Leonard) > Message-Id: <199302181750.AA09614@world.std.com> > Subject: Question about PDB format > > Large molecule folks... > > I've seen a lot of PDB formats in my time, but recently I've seen one that > looks unusual. The "standard" format seems to have a 2 character atom > label field (such as " C" and "CA") and a 2 digit index field. Ok... > Recently, I've been sent a file with the following functional group: > > 1H24 > | > 2H24--N24-- . . . rest of molecule > | > 3H24 > > The obvious convention is that there are the three H's on N24. However, > it places a number in the atom label field. I thought the PDB > "legal" format was somewhat strict (can you say F77?) on column layouts > and contents. Am I missing something (and is this legal)? Or am I seeing > yet another custom extension to the malleable PDB format? > > Joe Leonard > jle@world.std.com The PDB standard file format is quite strict (and restrictive). As Bob Whiteside pointed out, H names which would follow the published rules won't fit in the four characters provided! When the standard won't work, depositors are required to put in remarks describing the naming convention that they have used. The usual (i.e. in a dozen or so protein entries in the Brookhaven database) remark section uses the following text: REMARK 7 HYDROGEN AND DEUTERIUM ATOMS IN THIS ENTRY HAVE BEEN 6RSA 108 REMARK 7 ASSIGNED NAMES CONSISTENT WITH THE RECOMMENDATIONS OF THE 6RSA 109 REMARK 7 IUPAC-IUB COMMISSION ON BIOCHEMICAL NOMENCLATURE (E.G. 6RSA 110 REMARK 7 J.MOL.BIOL. (1970) VOL.52, PP 1-17). WE HAVE FOLLOWED RULE 6RSA 111 REMARK 7 4.4 OF THE RECOMMENDATIONS WITH THE FOLLOWING MODIFICATION- 6RSA 112 REMARK 7 WHEN MORE THAN ONE HYDROGEN ATOM IS BONDED TO A SINGLE 6RSA 113 REMARK 7 NON-HYDROGEN ATOM, THE HYDROGEN ATOM NUMBER DESIGNATION IS 6RSA 114 REMARK 7 GIVEN AS THE FIRST CHARACTER OF THE ATOM NAME RATHER THAN 6RSA 115 REMARK 7 AS THE LAST CHARACTER (E.G. H*BETA*1 IS DENOTED AS 1HB ). 6RSA 116 Note that even though ' HB1' would fit, '1HB ' is used. This seems to be a de facto standard in the database. The only (slight) exception I've seen in the deposited structures is for the DNA files where the following remark is found: REMARK 6 THIS ENTRY INCLUDES HYDROGEN ATOMS. EACH HYDROGEN ATOM HAS 2ZNA 64 REMARK 6 BEEN ASSIGNED A NAME IN WHICH THE THIRD AND FOURTH 2ZNA 65 REMARK 6 CHARACTERS REPRESENT THE NUMBER WITHIN THE RESIDUE 2ZNA 66 REMARK 6 (NUCLEOTIDE) OF THE NON-HYDROGEN ATOM TO WHICH IT IS 2ZNA 67 REMARK 6 BONDED. IN THE CASE OF MORE THAN ONE HYDROGEN ATOM BONDED 2ZNA 68 REMARK 6 TO THE SAME NON-HYDROGEN ATOM, THE FIRST CHARACTER OF THE 2ZNA 69 REMARK 6 NAME OF THE HYDROGEN ATOM IS ASSIGNED A NUMBER (1, 2, ...). 2ZNA 70 REMARK 6 FOR EXAMPLE, IN THE NUCLEOTIDE C A 1 THERE ARE TWO HYDROGEN 2ZNA 71 REMARK 6 ATOMS BONDED TO ATOM C5*. BECAUSE ATOM C5* IS THE FIFTH 2ZNA 72 REMARK 6 ATOM IN THIS RESIDUE (NUCLEOTIDE), THE HYDROGEN ATOMS HAVE 2ZNA 73 REMARK 6 BEEN ASSIGNED THE NAMES 1H 5 AND 2H 5. WITHIN A RESIDUE 2ZNA 74 REMARK 6 (NUCLEOTIDE) THE NON-HYDROGEN ATOMS WILL BE LISTED FIRST, 2ZNA 75 REMARK 6 FOLLOWED BY THE HYDROGEN ATOMS IN ASCENDING ORDER. 2ZNA 76 As Bob said, Brookhaven is aware of the limitation for atom names and will address them in a future format. As I suspect you have found, most software doesn't adhere to the published PDB standard, and few seem to know about the above de facto standard. Of those that do, none that I know of will add remarks like the above (though HyperChem will keep the remarks if they are already there). Good luck, Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com