aspenrmb (c37b1)
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
(» gbim )
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
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
(» gbim )
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, » energy .
Reading surf file: open unit 1 read memb30.surf
read saim unit 1
close unit 1
[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, » energy .
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 (» aspener ) 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.
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 (» aspener ) 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
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