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The
ParmTop
module defines a class (Amber) to generate a
parmtop file for AMBER. This class is incomplete,
it must be tailored for each type of model. Yammp
provides more flexibility than is permitted by
AMBER; not all model inforrmation can be translated
for AMBER.
The
ParmTop
module is located in Yup.Tools. Thus, the required
import statement is some variant of:
from
Yup.Tools.ParmTop import
Amber.
This
imports the Amber class which has three methods and
a constructor function.
To
generate parmtop files: create a class based on
this class, write a method setparameters()
specifically for your model type. Initialize your
class with the Model object that represents your
model, then apply the writecoords() method to write
out a coordinate file and the writeparmtop() method
to write out the parmtop file.
The
constructor function requires one
argument.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
__init__
|
1
|
The
Amber object
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|
Argument
|
Type
|
Preset
Value
|
|
m
|
Model
object
|
-
|
The
m argument must contain a Model object. The
force field of this model will be translated to a
parmtop file. At this time, the following force
field terms are recognized and
translated.
Multiple
instances of each term (permissible in YUP) are
concatenated for the conversion.
The
setparameters()
method sets properties that are specific to each
model type. Therefore, you must override this
method.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
setparameters
|
0
|
None
|
The
following attributes must be set:
|
Attribute
|
Contents
|
|
ANAME
|
list
of atom names
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|
ATYPE
|
list
of atom type names
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|
ITYPE
|
list
of atom type index
|
|
NRESD
|
list
of residue labels
|
|
IRESD
|
list
of residue pointers
|
|
PNONB
|
list
of non-bond force parameter pairs:
A12 and B6
constants for VanderWaalsX or
Ks and d0 for
SoftSphereX
|
|
NumTy
|
number
of exclusion atom types
|
|
NumPa
|
length
of the PNONB
list
|
|
NumRs
|
length
of the NRESD
list
|
You
must observe AMBER rules with regards to names,
numeric ranges, index base (0 or 1) and so on. The
ParmTop utility will translate the data from Yup
with little or no checking.
The
writecoords()
method writes out the coordinate file.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
setparameters
|
1
|
None
|
|
Argument
|
Type
|
Preset
Value
|
|
prefix
|
string
|
-
|
The
prefix argument must contain a non-empty
string. The coordinates will be written to a file
named 'prefix.inpcrd'
The
writeparmtop()
method writes out the parmtop file.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
writeparmtop
|
1
|
None
|
|
Argument
|
Type
|
Preset
Value
|
|
prefix
|
string
|
-
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The
prefix argument must contain a non-empty
string. The parmtop file will be named
'prefix.prmtop'
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