Summarization of Responses to Interaction Energy and Hydrophobicity



Dear Fellow Netters,
      The following is a summary to the net of responses to the query below.
 Many thanks to all those who responded. We are very grateful for the
 generosity of those who supplied the valuable information summarized below.
 Susan Yamamura
 ***************************************************************************
 QUERY
      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-0at0-cgf.chem.arizona.edu
 RESPONSES
 ONE
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 We use a program created by P. Claverie and J. Caillet in the seventies,
 this program does not fit exactly with your needs because the proteins
 are not parametrized but may be it could work with minors adaptations.
 Francois BAYARD                  |  e-mail bayard-0at0-chitheo1.univ-lyon1.fr
 UNIVERSITE CLAUDE BERNARD LYON 1 |  tel    (+33) 72 44 82 79
 43 Bd du 11 Novembre 1918        |  fax    (+33) 72 44 08 03
 F-69622 VILLEURBANNE - FRANCE    |
 --------------------------------------------------------------------------
 ======================================================================
    ***************************************************
    *                                                 *
    *      PROGRAM   PCRISTA                          *
    *                                                 *
    * INTERMOLECULAR ENERGY CALCN. IN A  CRYSTAL      *
    *      CALCULATION OF THE PACKING ENERGY          *
    * AUTHORS :   PIERRE CLAVERIE & J.CAILLET         *
    * ACTA.CRYST A31 P 448-461  1975                  *
    * ENERGY : DISPERSION  REPULSION  ELECTROST  POLAR*
    *                                                 *
    * SIMULATED ANNEALING - CALCULATION OF THE ENERGY *
    * NEAR THE SURFACE OF THE CRYSTAL                 *
    * AUTHORS:    BAYARD F.  &  DECORET C.            *
    * Mol. Cryst. Liq. Cryst. Inc. Nonlin. Opt        *
    * vol 161 pp 67-76 1988                           *
    *                                                 *
    * VERSION 1992/01 anl                             *
    * ask for registration and update at :            *
    *                                                 *
    *  UNIVERSITE CLAUDE BERNARD  LYON 1 BAT 305      *
    *  69622 VILLEURBANNE  CEDEX            FRANCE    *
    *  tel (+33) 72 44 82 79                          *
    *  e-mail bayard-0at0-chitheo1.univ-lyon1.fr           *
    *                                                 *
    *  draw (Sun Core) and file HPGL in comments      *
    ***************************************************
 Package possibilities :
 **********************
 - Computation of the energy of a crystal which is built around a
   central cell.
 - Minimization of this energy by the selective variation of the
 geometry of the cell and the Euler angles and translation of the
 molecules in the central cell (VA10A or Monte-carlo (simulated
 annealing).
 - Computation of the interaction energy between the cell near the
 surface and the bulk.
 - Computation of the approach of a ligand near the surface defined
 before (and minimisation of energy).
 The central cell is built by symetry operations applied to one
 molecule or by differents species.
 The geometry of the molecule is introduce by :
    - cristallographic coordinates
    - internal coordinates system (rho theta phi).
 Several ways to modifie this geometry are available :
    - internal rotations ( e.g. rotation of an acetyl group )
    - rotation and translation of the whole molecule :
               - rotation defined through Euler angles.
               - rotation defined through axes and angles.
 Warning : at this moment all molecules are considered fixed and their
 	  internal geometry do not change during the minimisation.
 	  the parametrization concern small organic molecules and is
 	  based on the William's parameters. A work is to be done
 	  to adjust them for proteins.
 *************************************************************************
 RESPONSE 2
 From:	SMTP%"hogue-0at0-sdisu1.den.mmc.com" 20-JUL-1992 14:31
 Date: Mon, 20 Jul 92 15:29:25 MDT
 From: hogue-0at0-sdisu1.den.mmc.com (Pat Hogue)
 Message-Id: <9207202129.AA01776-0at0-sdisu1>
 To: yamamura-0at0-cgf.chem.arizona.edu
 Subject: adsorption
 I am beginning to study adsorption of polymer chain onto inorganic substrates
 and would like to know if you come up with a program to do protein to solid
 adsorption.  I'm using the semiempirical set of programs called GEOMOS
 (QCPE 584).  I don't have any results yet.  I would appreciate a personal note
 if you can.  Pat Hogue (303) 971-3369.
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