Generate a moltemplate file containing a definition of a Polymer molecule containing monomers located at the positions specified in "coords.raw" (a 3-column text file). Monomers will be rotated so that they point along the polymer axis direction (see "-dir-indices") with an optional helical twist added (see "-helix"). Users can specify one or more bonds connecting each monomer to the next monomer (see "-bond"). Similarly, 3-body and 4-body angular interactions between atoms in different monomers can either be generated automatically (using the standard moltemplate "Angle By Type" rules) OR generated manually (using "-angle", "-dihedral", "-improper" arguments).
genpoly_lt.py \ [-bond btype a1 a2] \ [-helix deltaphi] \ [-axis x,y,z] \ [-circular yes/no/connected] \ [-dir-indices ia ib] \ [-angle atype a1 a2 a3 i1 i2 i3] \ [-dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4] \ [-improper itype a1 a2 a3 a4 i1 i2 i3 i4] \ [-monomer-name mname] \ [-sequence sequence.txt] \ [-polymer-name pname] \ [-inherits ForceFieldObject] \ [-header "import monomer.lt"] \ [-cuts cuts.txt] \ [-box paddingX,paddingY,paddingZ] \ [-polymer-directions polarities.txt] \ < coords.raw > polymer.lt
-axis x,y,z direction of the polymer axis in the original monomer object. These three numbers (separated by commas with no spaces) define the direction that the monomer subunit is pointing in. By default, the three numbers are 1 0 0 (ie, the X axis) -helix deltaphi = Optionally, rotate each monomer around it's axis by angle deltaphi (in degrees) beforehand -circular keyword keyword must be one of these: "no" The polymer is a linear chain with the two ends not connected. "yes" The polymer is a circular loop with the two ends connected pointing in similar directions. "connected" Connect the two ends together with bonds (and angles, and dihedrals, if applicable) to make a closed loop. But do not adjust the orientation of the first and last monomers so that they point towards eachother. (Use this if you plan to simulate an "infinitely" long polymer using periodic boundary conditions, with the two ends are connected on opposite sides.) -dir-indices ia ib The program attempts to orient each monomer in a direction that the polymer is pointing. By default, the program will orient monomer i in the direction connecting the monomers before and after it (monomers i-1 and i+1). The user can override this using the -dir-indices command line argument. The ia and ib arguments are integer offsets. To point monomer i in the direction connecting it to the following monomer (i+1), use -dir-indices 0 1 (For circular polymers, the indices will be wrapped appropriately.) -bond btype a1 a2 Add a bond between successive monomers of type btype. between atoms named a1 and a2 (all three arguments are strings and omit the @bond: and $atom: prefixes in moltemplate variables) Multiple bonds between successive monomers can be added by having "-bond bt a1 a2" appear several times in the argument list. For example, double-stranded DNA can be implemented as a polymer with 2 bonds connecting separate monomers (if each "monomer corresponds to a base pair). -angle atype a1 a2 a3 i1 i2 i3 Add a 3-body angle interaction between atoms a1 a2 a3 in monomers i1 i2 and i3. (The aname atype a1, a2, a3 arguments are strings containing moltemplate variable names. The standard moltemplate prefixes "$angle:", "@angle:", and "$atom:" should be omitted. The i1, i2, i3 arguments are integer indices indicating the monomer that each atom belongs to. 0 corresponds to the current monomer 1 corresponds to the next monomer 2 corresponds to the following monomer, etc... (For circular polymers, the indices will be wrapped appropriately.) Multiple angles per monomer can be added by having: "-angle aname atype a1 a2 a3 i1 i2 i3" appear several times in the argument list. -dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4 Add a 4-body dihedral interaction between atoms a1 a2 a3 a4 in monomers i1 i2 and i3. (The dname dtype a1, a2, a3, a4, arguments are strings containing moltemplate variable names. The moltemplate prefixes "$dihedral:", "@dihedral:", and "$atom:" should be omitted The i1, i2, i3, i4 arguments are integer indices indicating the monomer that each atom belongs to. (See explanation above.) Multiple dihedrals per monomer can be added by having: "-dihedral dname dtype a1 a2 a3 a4 i1 i2 i3 i4" appear several times in the argument list. -improper itype a1 a2 a3 a4 i1 i2 i3 i4 Add a 4-body improper interaction between atoms a1 a2 a3 a4 in monomers i1 i2 and i3. (The iname itype a1, a2, a3, a4, arguments are strings containing moltemplate variable names. The moltemplate prefixes "$improper:", "@improper:", and "$atom:" should be omitted The i1, i2, i3, i4 arguments are integer indices indicating the that each atom belongs to. (See explanation above.) Multiple impropers per monomer can be added by having: "-improper iname itype a1 a2 a3 a4 i1 i2 i3 i4" appear several times in the argument list. -monomer-name name Name of the moltemplate object that will be replicated along the length of the polymer(s). ("Monomer" by default). This monomer should be defined elsewhere and ORIENTED SO THAT THE POLYMER AXIS LIES IN THE +X DIRECTION. You can use the "-header" argument to specify where the monomer(s) is defined. *Note: If you are defining heteropolymers or polymers with end-caps, then do not use the "-monomer" argument. Use the "-sequence" argument instead. You can include rotations or transformations to the monomer subunit before it is moved into position. For example, it is often useful to to use a modified version of the monomer whose initial coordinates are compressed to avoid collisions with other monomers. To do this, use something like "Monomer.scale(0.5,0.7,0.7)" instead of "Monomer". This would compress each monomer lengthwise by 0.5 and 0.7 laterally. (After minimization, each monomer should expand back to its ordinary size and shape.)* -header 'some text' This is a way to insert text at the beginning of the file. It was intended as a way to tell moltemplate to import files containing definitions of the monomer subunits you will need. For example: -header 'import "FILE_WHICH_DEFINES_Monomer.lt"' -sequence sequence.txt If you are building a heteropolymer, this argument allows you to specify the sequence of monomers in the polymer. You can also use this argument to add *end-caps* (ie custom monomer types) to the ends of your polymer, and orient them in the forward and backward directions. See example below. The "sequence.txt" file contains the sequence of monomers you want in your polymer(s). Each line of this file should be the name of a moltemplate object for the monomer subunit you want at that location. The number of lines in this file should match the sum of all of the lengths of the polymers (which equals the number of lines in the coordinate file). Each type of monomer listed must be a moltemplate object which contains atoms whose $atom (atom-ID) variables match the a1,a2 atoms mentioned in the -bond, -angle, -dihedral, and -improper arguments (if applicable). (In the butane example below, it would be the carbon atom in the backbone.) As before, you can include coordinate transforms in each monomer's name. Here is an example for butane: --- sequences.txt --- CH3 CH2 CH2 CH3.rot(180,0,0,1) ----- The CH2 and CH3 moltemplate objects are presumably defined elsewhere and ORIENTED WITH THE POLYMER AXIS ALONG THE +X DIRECTION. The ".rot(180,0,0,1)" makes sure the final CH3 monomer is oriented in the -X (opposite) direction. (Additional movement and rotation commands will be added to align each monomer with the direction of the curve.) If you are using the "-cuts" argument to create multiple polymers, then this file would resemble the file above, with the sequence of multiple such polymers appended together. It would include additional "CH3" and "CH3.rot(180,0,0,1) end-cap monomers at places which are before and after the integers specified using the "-cuts" argument. -polymer-name name Name of the moltemplate object that will be created. (By default "Polymer") -inherits ForceFieldObject "ForceFieldObject" is the name of a moltemplate object which defines any rules for creating angles, dihedrals, impropers which you want to be generated automatically. Hopefully this is object was defined somewhere in the file that you imported using the "-header" argument. -cuts cut_locations.txt Cut the polymer in several places along its length. This is useful if your goal is to create many polymers of different lengths instead of one long polymer. This will simply cut the polymer N times along its length. The file "cut_locations.txt" is a text file containing a list of positive integers (one per line) indicating where you would like the polymer to be cut. For each integer, i, which appears in this file, a cut is made between monomers i-1 and i (Indexing begins at 0, so a value of 1 corresponds to a cut between the first and second monomers.) A separate polymer object will be created for each polymer, and an integer suffix will be added to the name, to distinguish them from each other. (Each of these polymers will be part of a larger object defined by this program. Instantiating that object will create all of the individual polymers.) **NOTE** To put *end-caps* at the ends of each polymer (ie. to change the monomer type at the ends of each polymer), you *must* use the "-sequence" argument. You must supply a text file with the monomers you want to put at the beginning and ending of each polymer listed at the appropriate place in this file. (You also have the option to apply different rotations to the monomers at either end of each polymer to orient them in the forward and backward directions.) See the description of the *-sequence* argument for details. -box paddingX,paddingY,paddingZ This will cause the program to attempt to estimate the size of the smallest rectangular box which encloses all of the coordinates in the coordinate file. The user must supply 3 comma-separated numbers (no spaces) which indicate how much extra room is needed in the x,y,z directions, at both ends. -polymer-directions polarities.txt Change the order that coordinates are read from the file. This is specified once per polymer. You must supply a file containing one line per polymer. (Unless you used the -cuts argument this file will have only line.) Each line must contain either "1" or "-1". A value of "1" indicates that you want to read the coordinates for that polymer in the order they appear in the coordinate file. (IE. the normal behavior.) A value of -1 will cause the coordinates for that polymer to be reversed after reading. (In other words, read the coordinates from the corresponding portion of the file in reverse order. This feature is probably not useful to most users.)
- Make a simple polymer, adding "@bond:Backbone" type bonds between "$atom:c2" from each monomer with "$atom:c1" from the next monomer.
genpoly_lt.py -bond Backbone c2 c1 < crds.raw > poly.lt
- Make a circular twisted double-stranded DNA model, treating each base-pair as a monomer, and connecting each base-pair monomer with 2 bonds with the next base-pair. This is done using 2 "-bond" commands connecting the "O3p_a" atom with the "P_a" atom (in strand A), and the "P_b" atom with the "O3p_b" atom (from the opposite strand, B).
genpoly_lt.py -circular yes -helix 34.2857 \ -header 'import "basepair.lt" #<--defines "BasePair"' \ -monomer-name "BasePair" \ -polymer-name "Plasmid" \ -bond Backbone O3p_a P_a \ -bond Backbone P_b O3p_b \ < dna_basepair_CM_coords.raw \ > chromosome.lt
If you want to control the sequence of the polymer, replace the "-monomer-name" argument with "-sequence sequence.txt".