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Adaptive Poisson-Boltzmann Solver (APBS)

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Atomic Solvation Parameter Model with Implicit Membrane

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Atomic Solvation Parameter Based Energy

Purpose: calculate solvation free energy and forces based on the exposed surface area of each atom using Atomic Solvation Parameters.

Please report problems to brbrooks@helix.nih.gov

REFERENCES:

    1. Wesson and D. Eisenberg, 19??.

Syntax

Syntax: The ASP specifications 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 *note Skipe (chmdoc/energy.doc).


Reading surf file:  open unit 1 read vap_to_wat_kd.surf
                    read surf unit 1
                    close unit 1

Structure

This module computes solvation energies and forces based on the surface area model proposed by Wesson and Eisenberg, i.e., E_solv = Sum (Gamma_i * ASA_i + Eref_i), where Gamma_i is a parameter describing the free energy cost of burying atom i (in units of cal/mol/A^2), ASA_i is the surface area of atom i with radius RvdW_i and probe radius Rprobe and Eref_i is a reference solvation energy. The analytic expressions for atomic surface areas and corresponding cartesian derivitives are used in these calculations.

The values of the required parameters are read from a “surf” file which has the following syntax:

* file:  vap_to_wat_kd.surf
*
!   Note:  These are asp's from Wolfendon water to vapor numbers,
!                     adjusted for standard state by Kyte and Doolittle.
!                    They are in units of cal/(mol*A**2).
!                    Table of ASP's
!
   1.400000 ! the probe radius
!
! residue-type  atom-name  asp-value  radius  reference-area  swap-pairs
      ANY           H*        00.0     -1.0       0.0  ! ignore hydrogens

      ANY           C         04.0      1.90      0.00
      ANY          OT1      -112.0      1.40      0.00           OT2
      ANY          OT2      -112.0      1.40      0.00           OT1
      ANY           N       -112.0      1.70      0.00
                 .
                 .
                 .
                 .
       TRP          CZ2        04.0     1.90      0.00
       TRP          CZ3        04.0     1.90      0.00
       TRP          CH2        04.0     1.90      0.00
       ASN          OD1       -112.0    1.40      0.00
       ASP          OD1       -112.0    1.40      0.00           OD2
       ASP          OD2       -166.0    1.40      0.00           OD1

END

Note

  • 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 then one line the LAST line is used.
  • This file is free field format.

Examples

To set up energy calculations/simulations/minimizations with the ASP potential, the following call is expected to be adequate in most situations:

open unit 1 read form name vap_to_wat_kd.surf
read surf unit 1
close unit 1

When you do an energy calculation, dynamics or minimization with ASP, 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>        0    -44.02560      7.74091      6.01738
ENER INTERN>        0.00000      0.04160      0.00000      0.00000      0.04556
ENER EXTERN>        5.95140    -42.32325      0.00000     -7.74091      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------

and the same during minimization and dynamics.

see also: test cases c27test/aspenr.inp