aspenr (c46b2)
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:
M. Wesson and D. Eisenberg, 19??.
* Syntax | Syntax of ASP input
* Structure | Structure of the .surf file containing ASP data
* Examples | Usage examples of the ASP module
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:
M. Wesson and D. Eisenberg, 19??.
* Syntax | Syntax of ASP input
* Structure | Structure of the .surf file containing ASP data
* Examples | Usage examples of the ASP module
Top
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 » energy
Reading surf file: open unit 1 read vap_to_wat_kd.surf
read surf unit 1
close unit 1
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 » energy
Reading surf file: open unit 1 read vap_to_wat_kd.surf
read surf unit 1
close unit 1
Top
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.
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.
Top
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
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