c42b1

aspenrmb

Atomic Solvation Parameter Model with Implicit Membrane Purpose: ASPENRMB is an extended version of ASPENR that includes the effect of Implicit Membrane (IM) in surface area caculations. ASPENRMB can be used to calculate solvation free energy and forces based on the solvent accessible Surface Area (SA) of each atom, using Atomic Solvation Parameters (ASP). Gsolv = Sum ( Gamma_i * ASA_i + Gref_i ) See also aspener.doc The combined use of the GBIM and ASPENRMB modules permits calculation of the solvation energy in the frames of the GBSA\IM model(Spassov et al., 2002) Gsolv = Gpol + Gnp where the polar contribution Gpol is calculated using the GBIM module (See gbim.doc) and the non-polar (hydrophobic) energy term is approximated by: N Gnp = Sum ( Gamma_i * ASA_i + Gref_i ) i=1 Gamma_i is a parameter describing the SA contribution of atom i to the non-polar energy term; ASA_i is the surface area of atom i with radius RvdW_i, Gref_i is a reference solvation energy. The most popular GBSA models use uniform ASP parameters, i.e., Gamma_i = const. Please report problems to vss@accelrys.com REFERENCES: V.Z. Spassov, L. Yan and S. Szalma. Introducing an Implicit Membrane in Generalized Born / Solvent Accessibility Continuum Solvent Models. J. Phys. Chem. B, 106,8726-8738 (2002). * Syntax / Syntax of ASPENRMB input * Structure / Structure of the .surf file containing ASP data * Examples / Usage examples of the ASPENRMB module
Top [SYNTAX ASPENRMB functions] The ASP / Implicit Membrane specifications are similar to ASPENR and can be specified any time prior to an energy calculation and can be input either through reading a file or parsed directly off the command line - although the file route is more usual. Once turned on, the ASP energy term is in place during the course of the CHARMM run, i.e., it cannot be turned off except using the skipe command, see Skipe . Reading surf file: open unit 1 read memb30.surf read saim unit 1 close unit 1
Top The extended ASPENR module permits the effect of an Implicit Membrane to be included in the computation of solvation energies and forces based on the surface area models, such as that proposed by Wesson and Eisenberg (see aspener.doc) or only for the non-polar contribution to solvation energy, as in GBSA/IM models. The values of the required parameters are read from a "surf" file which has the following syntax: * file: memb30.surf ! Note: Uniform asp's for solvent accessible surface area non-polar energy term ! They are in units of cal/(mol*A**2). ! 1.40 30. 0. z ! probe radius, membrane thickness, ! membrane midplane at Z = 0, membrane normal along Z axis ! residue-type atom-name asp-value radius reference-area swap-pairs ANY C 25.0 2.1 0.0 ANY O 25.0 1.6 0.0 ANY N 25.0 1.6 0.0 ANY H 25.0 0.8 0.0 ..................................................... GLU OE1 25.0 1.6 0.0 GLU OE2 25.0 1.6 0.0 END Notes: - ANY refers to any residue type - A negative radius causes the atom to be ignored (such as hydrogens,...) - Atom name can use CHARMM wildcard rules (not residue names). - These commands ar eprocessed sequentially. If an atom is matched by more than one line the LAST line is used. - This file is free field format. - If the membrane parameters are omitted or membrane thickness is set to zero, the calculations are carried out without a membrane in the model.
Top Examples The energy calculations/simulations/minimizations with the ASP / IM potential are activated using the following call: open unit 1 read form name test.surf read saim unit 1 close unit 1 When you do an energy calculation, dynamics or minimization with ASPENRMB, you get columns in the log file printout with energy terms for ASP, e.g., ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER PBEQ: PBnp PBelec GBEnr ---------- --------- --------- --------- --------- --------- ENER> 0 -67.45895 23.21501 0.92593 ENER INTERN> 0.16626 1.60325 0.00000 1.76170 0.09019 ENER EXTERN> -6.94067 -40.92466 0.00000 5.60539 0.00000 ENER PBEQ> 0.00000 0.00000 -28.82040 ---------- --------- --------- --------- --------- --------- and the same during minimization and dynamics. see also: test cases c31test/gbsaim.inp