From chemistry-request@ccl.net Tue Nov 5 14:19:19 1991 Date: Tue, 5 Nov 91 09:08:09 PST From: cgorman@XHMEIA.Caltech.Edu (SHIP O' SHRIMP) Subject: Use of sparkles in MOPAC? To: chemistry@ccl.net Status: R I am currently trying to use sparkles in MOPAC 6.0 to simulate solvent effects. Specifically, I am using +/- combinations of sparkles to simulate a dipole across a molecule. The Mopac 6.0 manual, the Mopac 5.0 manual and the Ampac 2.1 manual all contain the same description of sparkles. It reads, in part: Two sparkles of equal and opposite sign can form a dipole for mimicking solvent effects... So far, my use of sparkles has resulted in widely varying gradients during minimization, the message "CALCULATION ABANDONED AT THIS POINT", and no results. I am distressed to find NO references to the use of sparkles in the manual, in the FORTRAN code, or in Chem Abstracts. If anyone has some experience with use of sparkles, or, even better, a reference to the use of sparkles to simulate solvent effects, I would very much appreciate a note! Many thanks in advance!! Chris Gorman Chemistry Department, Caltech cgorman@xhmeia.caltech.edu or cgorman@citchem.bitnet From chemistry-request@ccl.net Tue Nov 5 15:53:04 1991 Date: Tue, 5 Nov 91 15:17:24 EST From: donna@athena.bms.com To: chemistry@ccl.net Status: R HA A D | | HB? | HB? P- B-------C-E \ | / | | \ | / Q F \ | / \ | | CO HB | | | CA HA- CA - CB - CG | | | / | \ N HB / | \ / | \ / | \ i.e. a typical L-amino-acid | CO | N CG According to IUPAC nomenclature (Biochemistry Vol 9 1970 ...Rule 2.2.2). IF A > P,Q and D > E > F ... or two branches are identical, then they are numbered in a clockwise direction when viewed down the B-C bond as follows Case I D > E = E E has highest priority and the smallest nuber Case II D = D > E E has lowest priority and is given the largest number Case II D = D (no E) ... see some other rule Later on in the paper under a section for amino acid side chains (section 4.4) it states that for residues with two hydrogens "they are designated in accordance with Rule 2.2.2 Case I for CH2-R and Case III for NH2." So, if i understand all this right, in the above Newman projection, the HB on the left should be HB1 on the one on the right HB2. Well we have compared a variety of programs that we have including Discover XPLOR and CONGEN and there is no concensus in the numbering. We are currently doing structure determination from NMR constraints, where we the NMR people gave us many assignments called pro- R and Pro - S and we've been trying to relate this to the numbering appropriate numbering schemes above and again there doesn't seem to be a consensus. To make matters worse, we also have some D-amino acids in our structure. We believe that this should have no bearing on the numbering of H's from the B-groups on out. But again the programs differ in the numbering schemes ( and not in the same way as for L-amino acids.) Can anyone out there give us insight to A) what is the proper IUPAC numbering and a more recent reference if there is one and B) is this what most NMR people use ?? Thanks Donna Bassolino Stan Krystek Bristol Myers Squibb Pharmaceutical Research Institute Princeton, New Jersey 08854 Bassolino@BMS.COM krystek@BMS.COM From chemistry-request@ccl.net Tue Nov 5 16:57:01 1991 Date: Tue, 5 Nov 91 16:21:56 -0500 From: Iosif Vaisman To: chemistry@ccl.net Subject: Re: Z-Matrix into Cartesian Coordinates Status: R In article <7C37343220208289@UMAECS> Katrina Werpetinski writes: >Does anyone have a (preferrably fortran) algorithm for >converting a Z-matrix (ie bond length, angle, and >dihedral angle of a set of four atoms) into cartesian >coordinates? Fortran programs for such transformation are published in: H. Essen On the General Transformation from Molecular Geometric Parameters to Cartesian Coordinates, J.Comp.Chem. 1983, 4, 2, 136-141 J.E.Nordlander et al. ATCOOR: A Program for Calculation and Utilization of Molecular Atomic Coordinates from Bond Parameters, Comp.Chem. 1985,9,3,209-235 =============================================================================== Iosif Vaisman Internet: vaisman@gibbs.oit.unc.edu Department of Chemistry ivaisman@uncvx1.oit.unc.edu University of North Carolina Bitnet: ivaisman@uncvx1, @uncvm1 Chapel Hill, NC 27599-3290 Fax: +1-919-9622388 ===============================================================================