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 firstname.lastname@example.org REFERENCES: M. Wesson and D. Eisenberg, 19??. * Menu: * Syntax:: Syntax of ASP input * Structure:: Structure of the .surf file containing ASP data * Examples:: Usage examples of the ASP module
Syntax [SYNTAX ASP functions] 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 (energy.doc). Reading surf file: open unit 1 read vap_to_wat_kd.surf read surf unit 1 close unit 1
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 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 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
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute