epmf (c39b2)
EPMF Module of CHARMM
EPMF module implements an empirical energy term based on
an angle and distance (HBPMF) or a distance (1DPMF). 1D PMF is defined
as function of distance between two atoms(DONR and ACCP), whereas HBON PMF
is function of distance (DONR-ACCP) and cosine of angle (DONR-HYD-ACCP).
(H) (H)
| | | |
| {B} d| {A} | BLEN |
| | a | |
----(accp).......(donr)-----(atom2) (accp)........(donr)
| | | F1 / \
| | b {D} | F2 / \
| | | / \
(atom1) (atom1) (atom2)
HBON/DEFA HBON/GEOM
A sketch of Hydrogen atom construction and interactions is shown above.
Few comments on the notation.
(1) 1D PMF is function of distance between (donr) and (accp) atoms.
(2) Empirical hydrogen bonding provided by the DEFA option is applicable
only when atom2, atom1 and donr atoms are planar.Then position of the hydrogen
atom bonded to donr can estimated using the relation
_ _
-|d| | sin(B) sin(A) |
vec(d) = ----- | ----- vec(a) + ------- vec(b) |
sin(D) |_ |a| |b| _|
where A,B,D are the angles defined by (H-donr-atom2), (H-donr-atom1)
and (atom1-donr-atom2) respectively.
A more flexible way of estimating hydrogen atom is also provided by the GEOM
option which uses the bonding information: hydrogen atom-donr bond, hydrogen
atom-donr-atm1 angle and hydrogen atom-donr-atm1-atm2 dihedral.
* Syntax | Syntax of the EPMF command
* Function | Purpose of each of the command
* PMF-file | Format of PMF file
* Examples | Usage examples of the EPMF module
EPMF module implements an empirical energy term based on
an angle and distance (HBPMF) or a distance (1DPMF). 1D PMF is defined
as function of distance between two atoms(DONR and ACCP), whereas HBON PMF
is function of distance (DONR-ACCP) and cosine of angle (DONR-HYD-ACCP).
(H) (H)
| | | |
| {B} d| {A} | BLEN |
| | a | |
----(accp).......(donr)-----(atom2) (accp)........(donr)
| | | F1 / \
| | b {D} | F2 / \
| | | / \
(atom1) (atom1) (atom2)
HBON/DEFA HBON/GEOM
A sketch of Hydrogen atom construction and interactions is shown above.
Few comments on the notation.
(1) 1D PMF is function of distance between (donr) and (accp) atoms.
(2) Empirical hydrogen bonding provided by the DEFA option is applicable
only when atom2, atom1 and donr atoms are planar.Then position of the hydrogen
atom bonded to donr can estimated using the relation
_ _
-|d| | sin(B) sin(A) |
vec(d) = ----- | ----- vec(a) + ------- vec(b) |
sin(D) |_ |a| |b| _|
where A,B,D are the angles defined by (H-donr-atom2), (H-donr-atom1)
and (atom1-donr-atom2) respectively.
A more flexible way of estimating hydrogen atom is also provided by the GEOM
option which uses the bonding information: hydrogen atom-donr bond, hydrogen
atom-donr-atm1 angle and hydrogen atom-donr-atm1-atm2 dihedral.
* Syntax | Syntax of the EPMF command
* Function | Purpose of each of the command
* PMF-file | Format of PMF file
* Examples | Usage examples of the EPMF module
Top
Syntax of the EPMF Command
[SYNTAX EPMF]
EPMF [UPFR] int [CLEA]
{DIST dist-option-spec dist-PMF-spec selection-spec}
{HBON ATM1 atom-selection F1 real
ATM2 atom-selection F2 real
BLEN real hbon-option-spec hbon-PMF-spec selection-spec}
dist-option-spec ::= { PMF0 unit [PMF1 unit] [PMF2 unit] [PMF3 unit]
[PMFN unit] [PMFM unit] [PMFP unit]
[SCL0] real [SCL1] real [SCL2] real [SCL3] real
[SCLN] real [SCLP] real [SCLM] real
}
hbon-option-spec ::= { DEFA defa-specs
GEOM geom-specs
[PMF1 unit] [PMF2 unit] [PMF3 unit] PMFN unit
[SCL1] real [SCL2] real [SCL3] real [SCLN] real
[EMIN] real
}
selection-spec :: = { DONO atom-selection ACCP atom-selection}
Syntax of the EPMF Command
[SYNTAX EPMF]
EPMF [UPFR] int [CLEA]
{DIST dist-option-spec dist-PMF-spec selection-spec}
{HBON ATM1 atom-selection F1 real
ATM2 atom-selection F2 real
BLEN real hbon-option-spec hbon-PMF-spec selection-spec}
dist-option-spec ::= { PMF0 unit [PMF1 unit] [PMF2 unit] [PMF3 unit]
[PMFN unit] [PMFM unit] [PMFP unit]
[SCL0] real [SCL1] real [SCL2] real [SCL3] real
[SCLN] real [SCLP] real [SCLM] real
}
hbon-option-spec ::= { DEFA defa-specs
GEOM geom-specs
[PMF1 unit] [PMF2 unit] [PMF3 unit] PMFN unit
[SCL1] real [SCL2] real [SCL3] real [SCLN] real
[EMIN] real
}
selection-spec :: = { DONO atom-selection ACCP atom-selection}
Top
Purpose of the various EPMF variables
Variable Explanation
CLEA clears the memory allocated for EPMF module data structures.
DIST evaluates interaction energy based on 1D PMF for the
given selections The donor and the acceptor atoms are
specified by keywords DONOr and ACCEptor respectively.
HBON evaluates interaction energy based on 2D PMF for the
given selections. This option in addition to DONOr atom,
needs two other atoms (ATM1, ATM2)for estimating position of
H-atom bonded to the Donor atom. Further three additional
real arguments are needed. For DEFA option these factors are
F1 = ( -|d|/sin(D) * sin(B)/|a| ) (see the sketch
F2 = ( -|d|/sin(D) * sin(A)/|b| ) in top section)
BLEN = |d|
Note that the hydrogen atom construction for this case remains
accurate only when angles A, B and D are around 120 degrees.
To alleviate this issue, an additional robust method GEOM, which
relay on bonding features is provided. For GEOM, option F1 becomes
the equilibrium angle Hydrogen-Donor-ATM1 and F2 becomes the
equilibrium dihedral Hydrogen-Donor-ATM1-ATM2 . The BLEN option
remains the same as in previous case.
PMF0
PMF1 PMF0..N specify the PMF data file used for
PMF2 the (i, i+n(n=1..N)) residue interactions.
PMF3 See PMF-file section for the format description of
PMFN these files. PMF0, PMFP(i+1 residue) and PMFM(i-1 residue)
PMFP are valid only for DIST1
PMFM
UPFR specifies the update frequency for the (i,i+n)
donor-acceptor list. Default value is 25
SCL0
SCL1
SCL2 Scaling of PMF0..N energies. Default scaling factors are 1.0
SCL4 SCL0, SCLM and SCLP are valid only for DIST PMF
SCLN
SCLM
SCLP
EMIN specifies the minimum allowed energy of EPMF interactions defined
per residue. If the EPMF energy for particular residue becomes
less than the desired value, the subsequent EPMF calculations
for that residue is reset to ZERO. By default EMIN is set to
-10 kcal/mol
ATM1 These selections are used only for HBON PMF. The selections
ATM2 are specified by atom name, prefixed by '+', '-' or ''.
If DONO selection belongs to jth residue, than '+' indicates
ATM1/ATM2 belongs to j+1th residue, '-' ATM1/ATM2 belongs to
j-1th residue. If prefix is '', ATM1/ATM2 belong to jth
residue
atom-selection:== (» select .)
Purpose of the various EPMF variables
Variable Explanation
CLEA clears the memory allocated for EPMF module data structures.
DIST evaluates interaction energy based on 1D PMF for the
given selections The donor and the acceptor atoms are
specified by keywords DONOr and ACCEptor respectively.
HBON evaluates interaction energy based on 2D PMF for the
given selections. This option in addition to DONOr atom,
needs two other atoms (ATM1, ATM2)for estimating position of
H-atom bonded to the Donor atom. Further three additional
real arguments are needed. For DEFA option these factors are
F1 = ( -|d|/sin(D) * sin(B)/|a| ) (see the sketch
F2 = ( -|d|/sin(D) * sin(A)/|b| ) in top section)
BLEN = |d|
Note that the hydrogen atom construction for this case remains
accurate only when angles A, B and D are around 120 degrees.
To alleviate this issue, an additional robust method GEOM, which
relay on bonding features is provided. For GEOM, option F1 becomes
the equilibrium angle Hydrogen-Donor-ATM1 and F2 becomes the
equilibrium dihedral Hydrogen-Donor-ATM1-ATM2 . The BLEN option
remains the same as in previous case.
PMF0
PMF1 PMF0..N specify the PMF data file used for
PMF2 the (i, i+n(n=1..N)) residue interactions.
PMF3 See PMF-file section for the format description of
PMFN these files. PMF0, PMFP(i+1 residue) and PMFM(i-1 residue)
PMFP are valid only for DIST1
PMFM
UPFR specifies the update frequency for the (i,i+n)
donor-acceptor list. Default value is 25
SCL0
SCL1
SCL2 Scaling of PMF0..N energies. Default scaling factors are 1.0
SCL4 SCL0, SCLM and SCLP are valid only for DIST PMF
SCLN
SCLM
SCLP
EMIN specifies the minimum allowed energy of EPMF interactions defined
per residue. If the EPMF energy for particular residue becomes
less than the desired value, the subsequent EPMF calculations
for that residue is reset to ZERO. By default EMIN is set to
-10 kcal/mol
ATM1 These selections are used only for HBON PMF. The selections
ATM2 are specified by atom name, prefixed by '+', '-' or ''.
If DONO selection belongs to jth residue, than '+' indicates
ATM1/ATM2 belongs to j+1th residue, '-' ATM1/ATM2 belongs to
j-1th residue. If prefix is '', ATM1/ATM2 belong to jth
residue
atom-selection:== (» select .)
Top
PMF-File
The PMF-file must contain either two(1D PMF/DIST) or three(HBOND) columns.
The last column always correspond to energy and other column(s) are the grid
points of PMF co-ordinate(s). In addition to data, the PMF-file must contain
a header section describing type of PMF, maximum and minimum values of grid
points and number of X/Y entries in the file.
For 1D PMF the header section of PMF-file must be
<XMAX> <XBINS> <XMIN> <XPTS>
4.50 0.1 0.00
0.00 0.00
0.1 0.05
...
...
...
4.49 0.95
4.50 1.00
For HBOND PMF the header section is
<XMAX> <XBINS> <XMIN> <YPTS>
<YMAX> <YBINS> <YMIN> <XPTS>
4.50 0.1 3.00 21
1.0 0.05 0.00 16
3.00 0.00 0.00
3.00 0.05 -0.15
...
...
...
4.50 0.95 0.15
4.50 1.00 0.00
PMF-File
The PMF-file must contain either two(1D PMF/DIST) or three(HBOND) columns.
The last column always correspond to energy and other column(s) are the grid
points of PMF co-ordinate(s). In addition to data, the PMF-file must contain
a header section describing type of PMF, maximum and minimum values of grid
points and number of X/Y entries in the file.
For 1D PMF the header section of PMF-file must be
<XMAX> <XBINS> <XMIN> <XPTS>
4.50 0.1 0.00
0.00 0.00
0.1 0.05
...
...
...
4.49 0.95
4.50 1.00
For HBOND PMF the header section is
<XMAX> <XBINS> <XMIN> <YPTS>
<YMAX> <YBINS> <YMIN> <XPTS>
4.50 0.1 3.00 21
1.0 0.05 0.00 16
3.00 0.00 0.00
3.00 0.05 -0.15
...
...
...
4.50 0.95 0.15
4.50 1.00 0.00
Top
Examples
Example (1)
EPMF DIST PMF3 19 PMFN 23 DONO select type (OE* .or. OD*) end ACCP select
ND .or. NE* end
A simple distance based PMF to mimick salt bridges for some polar and charged
residues. The PMF data for i+/-3 interactions are read from unit 13 and i+/-n
from unit 23
Example (2)
EPMF HBON defa atm1 CA f1 -.6736 atm2 -C f2 -.7627 blen .997 -
PMF1 13 PMFN 17 DONO select type N end ACCP select type O end
This example calculates putative hydrogen bond interactions between backbone O
and N atoms. Position of hydrogen is estimated using DEFA option of HBOND
potential. Additional atoms CA (ith residue) , -C (i-1th residue) and
corresponding factors F1,F2,BLEN are needed for estimation of position of
hydrogen atom bonded to N of (ith residue). Also needed are the PMF data files
given by unit 13 (for i+/-3) and unit 17 ( for i+/-n, where n>3).
Example (3)
EPMF HBON geom atm1 CA atm2 -C f1 116.0 f2 180.0 blen 0.997 -
PMF1 13 PMFN 17 DONO select type N end ACCP select type O end
Same as Example(2), but using GEOM option of HBON for estimating Hydrogen
atom position.
Application of DIST and HBON PMFs in context of PRIMO force field is given as
test case of charmm c36a451 version.
Examples
Example (1)
EPMF DIST PMF3 19 PMFN 23 DONO select type (OE* .or. OD*) end ACCP select
ND .or. NE* end
A simple distance based PMF to mimick salt bridges for some polar and charged
residues. The PMF data for i+/-3 interactions are read from unit 13 and i+/-n
from unit 23
Example (2)
EPMF HBON defa atm1 CA f1 -.6736 atm2 -C f2 -.7627 blen .997 -
PMF1 13 PMFN 17 DONO select type N end ACCP select type O end
This example calculates putative hydrogen bond interactions between backbone O
and N atoms. Position of hydrogen is estimated using DEFA option of HBOND
potential. Additional atoms CA (ith residue) , -C (i-1th residue) and
corresponding factors F1,F2,BLEN are needed for estimation of position of
hydrogen atom bonded to N of (ith residue). Also needed are the PMF data files
given by unit 13 (for i+/-3) and unit 17 ( for i+/-n, where n>3).
Example (3)
EPMF HBON geom atm1 CA atm2 -C f1 116.0 f2 180.0 blen 0.997 -
PMF1 13 PMFN 17 DONO select type N end ACCP select type O end
Same as Example(2), but using GEOM option of HBON for estimating Hydrogen
atom position.
Application of DIST and HBON PMFs in context of PRIMO force field is given as
test case of charmm c36a451 version.