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calc_dihedral_table.py
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Created
Fri, Sep 13, 01:16
Size
2 KB
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text/x-python
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Sun, Sep 15, 01:16 (2 d)
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blob
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20736403
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rLAMMPS lammps
calc_dihedral_table.py
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#!/usr/bin/env python
# Calculate a table of dihedral angle interactions used in the alpha-helix
# and beta-sheet regions of the frustrated protein model described in
# provided in figure 8 of the supplemental materials section of:
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
# Note that the "A" and "B" parameters were incorrectly reported to be
# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon.
# The phiA and phiB values were 57.29577951308232 degrees (1 rad)
# and 180 degrees, respectively. Both expA and expB were 6.0.
#
# To generate the table used for the alpha-helix (1 degree resolution) use this:
# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
# To generate the table used for the beta-sheets (1 degree resolution) use this:
# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
#
# (If you're curious as to why I set the location of the minima at phi_alpha
# to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
# I think the correct value turns out to be something closer to 50 degrees.)
from
math
import
*
import
sys
# The previous version included the repulsive core term
def
U
(
phi
,
A
,
phiA
,
expA
,
B
,
phiB
,
expB
,
use_radians
=
False
):
conv_units
=
pi
/
180.0
if
use_radians
:
conv_units
=
1.0
termA
=
pow
(
cos
(
0.5
*
(
phi
-
phiA
)
*
conv_units
),
expA
)
termB
=
pow
(
cos
(
0.5
*
(
phi
-
phiB
)
*
conv_units
),
expB
)
return
-
A
*
termA
-
B
*
termB
# The previous version included the repulsive core term
def
F
(
phi
,
A
,
phiA
,
expA
,
B
,
phiB
,
expB
,
use_radians
=
False
):
conv_units
=
pi
/
180.0
if
use_radians
:
conv_units
=
1.0
termA
=
(
0.5
*
sin
(
0.5
*
(
phi
-
phiA
)
*
conv_units
)
*
expA
*
pow
(
cos
(
0.5
*
(
phi
-
phiA
)
*
conv_units
),
expA
-
1.0
))
termB
=
(
0.5
*
sin
(
0.5
*
(
phi
-
phiB
)
*
conv_units
)
*
expB
*
pow
(
cos
(
0.5
*
(
phi
-
phiB
)
*
conv_units
),
expB
-
1.0
))
return
-
conv_units
*
(
A
*
termA
+
B
*
termB
)
if
len
(
sys
.
argv
)
!=
10
:
sys
.
stderr
.
write
(
"Error: expected 9 arguments:
\n
"
"
\n
"
"Usage: "
+
sys
.
argv
[
0
]
+
" A phiA expA B phiB expB phiMin phiMax N
\n\n
"
)
sys
.
exit
(
-
1
)
A
=
float
(
sys
.
argv
[
1
])
phiA
=
float
(
sys
.
argv
[
2
])
expA
=
float
(
sys
.
argv
[
3
])
B
=
float
(
sys
.
argv
[
4
])
phiB
=
float
(
sys
.
argv
[
5
])
expB
=
float
(
sys
.
argv
[
6
])
phi_min
=
float
(
sys
.
argv
[
7
])
phi_max
=
float
(
sys
.
argv
[
8
])
N
=
int
(
sys
.
argv
[
9
])
for
i
in
range
(
0
,
N
):
phi
=
phi_min
+
i
*
(
phi_max
-
phi_min
)
/
(
N
-
1
)
U_phi
=
U
(
phi
,
A
,
phiA
,
expA
,
B
,
phiB
,
expB
,
use_radians
=
False
)
F_phi
=
F
(
phi
,
A
,
phiA
,
expA
,
B
,
phiB
,
expB
,
use_radians
=
False
)
print
(
str
(
i
+
1
)
+
' '
+
str
(
phi
)
+
' '
+
str
(
U_phi
)
+
' '
+
str
(
F_phi
))
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