Gromacs

Genvsites

    Table of contents
    1. 1. Status report (1 Oct 2007)

    This program should read and write topology files and coordinate files, and modify them. The program could be called a multi-scaling program, as it should read coordinates and topology files and add or remove vsites in them. In addition the program could change between atomistic and coarse-grained representations of molecules.

    Daniel Larsson (Uppsala, Sweden) is working on this one. Erik Marklund (Uppsala, Sweden) is joining Daniel in his efforts.

    I worked on this project for a while, and not much has happened. I start to think that this should all go into tpbconv anyway. - Erik M

    Status report (1 Oct 2007)

    - Erik Marklund

    The new genvsites program will read a generic vsite data file listing which virtual site constructions can be made for all residues. The idea here is to have a force field independent way of describing and creating the virtual sites. Thus, no explicit atom types are allowed in the vsite data file, only atom names. To make the vsite data easier to read and maipulate, it is to contain no geometrical data. Instead, ideal geometries and, when needed, center of mass and moment of inertia, are to be calculated from crystallographic data contained in the file refi_aa.dat. The latter contains little information about hydrogens, which may lead to some force field dependence when making hydrogen coordinates.

    Proposed format of vsite data file:

    [ RES1 ]
    Anchor {M}{S|P} (VStype) Atoms {(VStype) Atoms ...}
    

    And this is how it works:

    ; [ RES ]     Specifies what residue any vsite records that follow belong to.
    ; 'Anchor'    The heavy atom to which the vsite is bonded, e.g. the Cbeta in
    ;             alanine, or the Cdelta in lysine.
    ; 'M'         Generate Dummy masses. Virtual sites will be based upon them.
    ;             Optional.
    ; 'S'         Symmetry. It means that COM will lie on the rotaion axis,
    ;             and that there is no point in trying to put the dummy masses
    ;             in the plane spanned by the rotation axis and the anchor-COM
    ;             vectors. Instead, the in-plane atoms are explicitly given in the
    ;             record, and the dummy masses will be placed in the plane defined
    ;             by the rotation axis and the first atom of vstype 2, 3, 3fd or
    ;             3fad.
    ;             Implies 'M'.
    ;             Optional.
    ; 'P'         Planar. Assume/enforce planarity.
    ;             Implies 'M'.
    ;             Optional.
    ; '(VStype)'  Sets the vstype for the trailing atoms.
    ; 'Atoms'     A list of atoms to be turned into virtual sites of the type
    ;             specified by the last '(VStype)' encountered.
    ; Linebreaks terminate a vsite record.
    ; Lines starting with ';' are ignored, as are empty lines.  
    

    It should be noted that some things are implicit from these simple (?) vsite decriptions. For instance, when dummy masses are generated, all virtual sites will be determined from the positions of the anchor and the masses. When no masses are generated the heavy atoms determining the positions of the virtual sites are implicit from the connectivity of the anchor, e.g. the three periferal carbons in tert-butanol are used to construct the hydrogen bonded to the middle carbon. The vsite record would looke something like this:

    C2 (4fd) H21
    

    Example:

    [ TRP ]
    CB M P (3) HB1 HB2 CG CD1 HD1 CD2 NE1 HE1 CE2 CE3 HE3 CZ2 HZ2 CZ3 HZ3 CH2 HH2
    [ LEU ]
    CB M S (3out) HD13 HD12 (3) HD11 CG1
    CB M S (3out) HD23 HD22 (3) HD21 CG2
    

    In the example above, the file begins with a tryptophan directive. It tells the program (or reader) to interpret succeeding lines as tryptohan data, until EOF or another directive is encountered. The next line is a vsite record starting with the anchor CB, an 'M' to generate dummy masses, and a 'P' to enforce/assume planarity. Since the ring system of tryptophan lies in the same plane as the rotation axis, the whole group can be described as virtual sites of type 3, the heavy atoms being the anchor and the dummy masses. The program will generate the geomoety of the ring system from the crystallographic data found in refi_aa.dat. From the geomety it will then calculate center of mass and moment of inertia of the group, position dummy masses accordingly and finally generate vsite parameters.

    The next directive tells the program to interpret any succeeding lines as vsite constructions for leucine. The first vsite record following the directive is a recipie for one of the methyl groups attached to the beta carbon of leucine, hence the 'CB'. 'M' prompts for dummy mass generation and 'S' means that the group has a symmetry that makes its center of mass lie on the rotation axis. The symmetry means that the rotation axis and the center of mass does not define a plane, and that the orientation of the dummy masses therefore is undefined. Thus, the first in-plane atom (HD11) will determine the orientation of the dummy masses. After the symmetry flag there is a VStype tag (3out) and a list of atoms that are to be turned into virtual sites of named type. Another VStype tag (3) later on in the same record followed by another list of atoms mean that some atoms lie in the plane of the two dummy masses and the rotation axis, and that they can be descibed a vsites of type 3. The last line is nearly identical to the first methyl construction.

    Note that the vsite data in the example above is not in any way exhaustive for Trp or Leu. There are more vsite constructions that can be done for named residues.

    Page last modified 21:07, 26 May 2010 by erikm?