From ntw@iris141.biosym.com Thu Apr 15 04:18:26 1993 Date: Thu, 15 Apr 93 11:18:26 -0700 From: ntw@biosym.com (Noppawan Whitledge ) Message-Id: <9304151818.AA18277@iris141.biosym.com> To: chemistry@ccl.net Subject: RMS comparison -- Discover (Biosym) TO: JIE YUAN - RMS comparison There was a bug in Discover 2.8 about the template file. However, it has been fixed in the 2.9 release. This problem should go away if the customer uses Discover 2.9. =================================================================== Noppawan T. Whitledge, Ph.D. Biosym Technologies, Inc. Phone: (619) 546-5509 9685 Scranton Road Fax: (619) 458-0431 San Diego, CA 92121-2777 e-mail: ntw@biosym.com =================================================================== From venugopa@UMDNJ.EDU Thu Apr 15 13:57:25 1993 Message-Id: <199304152157.AA18107@oscsunb.ccl.net> Date: Thu, 15 Apr 93 17:57:25 -0400 From: Manju Venugopal To: chemistry@ccl.net Subject: pKa/bohr-effect/charges/proteins Hi I am looking for some information on the change in the pKa of Lys. Its pKa is 10.8 when free, but in proteins it is in the range 10-10.2. Has anybody come across cases where the pKa of Lys or any other amino acid is observed to be much higher than expected? (Bohr effect) For example for Lys present in fibrous peptide that I am studying, even by pH 12.9 it still has partial positive charge exisiting on it, because here it is involved in inter-chain ion-pair formation. What is the pKa value of Lys in Globular proteins? Is anybody out there involved in looking at the role of charges, ion-pairs and their electrostatic interactions in proteins? Are there any reviews or references available on these topics? Please respond directly to me and i will be happy to sum up the responses and forward them to whosoever will be interested. Manju venugopa@umdnj.rwja.edu Thanks in advance From AHOLDER@VAX1.UMKC.EDU Mon Apr 15 11:24:58 1993 Date: 15 Apr 1993 17:24:58 -0600 (CST) From: Andy Holder Subject: Fluorine and semiempirical methods To: CHEMISTRY@ccl.net Message-Id: <01GX1QF6A6SI9885BC@VAX1.UMKC.EDU> Someone posted a few days ago about a fluoroether problem using AM1. The F parameters have always been a problem and the fluoroether problem has been especially ticklish. This is basically due to a limitation in the theoretical model underlying these methods: the valence orbitals are single-valence. This strictly limits the flexibility of these orbitals in terms of their ability to adjust to situations of high charge such as those found in compounds containing fluorine atoms. (Ex.: A highly positively charged atom in a split valence ab initio basis set can weight more heavily the smaller segment of the orbital in deriving the wavefunction. This mimics the contraction of the orb- ital when the atoms becoming positively charged.) In any case, the values for the mentioned molecule do not seem too out-of-line in this case, especially for the C-F bonds. The AM1 results and SAM1 results are listed below. Andy Holder ----------------------------------------------------------------- SUMMARY OF AM1 CALCULATION 15-APR-93 AMPAC Version 4.0 Presented by: Semichem, Inc. 12715 West 66th Terrace Shawnee, KS 66216 (913) 268-3271 (913) 268-3445 (fax) C 2 O F 6 perfluorodimethylether ajh 4/15/93 GRADIENT (COMPONENT) TEST WAS SATISFIED IN BFGS OR DFP SCF FIELD WAS ACHIEVED HEAT OF FORMATION = -380.396929 KCAL ELECTRONIC ENERGY = -11233.094548 EV CORE-CORE REPULSION = 7742.806537 EV GRADIENT NORM = 0.095309 DIPOLE = 0.410145 DEBYE NO. OF FILLED LEVELS = 28 IONISATION POTENTIAL = 14.686671 EV MOLECULAR WEIGHT = 154.012 COMPUTATION TIME = 53.66 SECONDS FINAL GEOMETRY OBTAINED CHARGE AM1 PRECISE GRAD T=3500 BONDS perfluorodimethylether ajh 4/15/93 C 0.000000 0 0.000000 0 0.000000 0 0 0 0 0.5643 O 1.405188 1 0.000000 0 0.000000 0 1 0 0 -0.3663 C 1.405176 1 121.302039 1 0.000000 0 2 1 0 0.5643 F 1.351240 1 104.555776 1 -178.814637 1 1 2 3 -0.1065 F 1.353739 1 111.032749 1 118.962493 1 1 2 4 -0.1375 F 1.353716 1 110.875855 1 -118.860417 1 1 2 4 -0.1371 F 1.351240 1 104.561097 1 -179.430934 1 3 2 1 -0.1065 F 1.353727 1 110.980597 1 118.949703 1 3 2 7 -0.1374 F 1.353738 1 110.927172 1 -118.875489 1 3 2 7 -0.1372 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 ----------------------------------------------------------------- SUMMARY OF SAM1 CALCULATION 15-APR-93 AMPAC Version 4.0 Presented by: Semichem, Inc. 12715 West 66th Terrace Shawnee, KS 66216 (913) 268-3271 (913) 268-3445 (fax) C 2 O F 6 perfluorodimethylether ajh 4/15/93 GRADIENT (COMPONENT) TEST WAS SATISFIED IN BFGS OR DFP SCF FIELD WAS ACHIEVED HEAT OF FORMATION = -373.750354 KCAL ELECTRONIC ENERGY = -10766.654753 EV CORE-CORE REPULSION = 7400.208133 EV GRADIENT NORM = 0.148629 DIPOLE = 0.224593 DEBYE NO. OF FILLED LEVELS = 28 IONISATION POTENTIAL = 14.100089 EV MOLECULAR WEIGHT = 154.012 COMPUTATION TIME = 40.41 SECONDS FINAL GEOMETRY OBTAINED CHARGE SAM1 PRECISE GRAD T=3500 BONDS perfluorodimethylether ajh 4/15/93 C 0.000000 0 0.000000 0 0.000000 0 0 0 0 0.6047 O 1.453171 1 0.000000 0 0.000000 0 1 0 0 -0.3003 C 1.453167 1 108.205747 1 0.000000 0 2 1 0 0.6047 F 1.330351 1 107.794147 1 179.992164 1 1 2 3 -0.1292 F 1.342578 1 109.326704 1 120.247260 1 1 2 4 -0.1627 F 1.342591 1 109.330522 1 -120.246174 1 1 2 4 -0.1627 F 1.330351 1 107.793755 1 179.989909 1 3 2 1 -0.1292 F 1.342584 1 109.332584 1 120.245723 1 3 2 7 -0.1627 F 1.342584 1 109.327408 1 -120.247768 1 3 2 7 -0.1627 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=