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tbgl
tools
mrdna
Commits
dbaaef73
Commit
dbaaef73
authored
Aug 11, 2017
by
cmaffeo2
Browse files
Unscaled bases are now fixed during initial minimization, should be more robust
parent
62412139
Changes
2
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Inline
Side-by-side
CanonicalNucleotideAtoms.py
View file @
dbaaef73
...
...
@@ -33,6 +33,7 @@ class CanonicalNucleotide():
for
k1
,
k2
in
zip
((
'name'
,
'type'
),(
'f1'
,
'f2'
)):
self
.
props
[
k1
]
=
[
str
(
x
,
'utf-8'
)
for
x
in
d
[
k2
]]
self
.
props
[
'beta'
]
=
np
.
ones
(
len
(
d
[
'f1'
]))
# self.props['name'] = [str(x) for x in d['f1']]
# self.props['type'] = [str(x) for x in d['f2']]
...
...
@@ -82,6 +83,7 @@ class CanonicalNucleotide():
rvec
=
scale
*
(
rvec
-
r0
)
+
r0
for
k
,
r
in
zip
((
'x'
,
'y'
,
'z'
),
rvec
):
c
.
props
[
k
][
i
]
=
r
c
.
props
[
"beta"
][
i
]
=
0
else
:
if
self
.
sequence
in
(
"A"
,
"G"
):
i0
=
self
.
index
(
"N9"
)
-
1
...
...
@@ -94,6 +96,7 @@ class CanonicalNucleotide():
rvec
=
scale
*
(
rvec
-
r0
)
+
r0
for
k
,
r
in
zip
((
'x'
,
'y'
,
'z'
),
rvec
):
c
.
props
[
k
][
i
]
=
r
c
.
props
[
"beta"
][
i
]
=
0
return
c
...
...
atomicModel.py
View file @
dbaaef73
...
...
@@ -1409,7 +1409,14 @@ cellBasisVector3 0 0 1000
if {$nLast == 0} {
temperature 300
minimize 4800
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile $prefix.pdb
fixedAtomsCol B
minimize 2400
fixedAtoms off
minimize 2400
} else {
bincoordinates output/$prefix-$nLast.restart.coor
binvelocities output/$prefix-$nLast.restart.vel
...
...
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