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Molecular Topology

The molecular structure is specified in NMRFx using a sequence file. Here are examples. Note: when doing structure calculations more complex structures may be specified in the projects .yaml file. See the project file documentation.

Sequence Files

Simple sequence

TXT
met
ala
asn
glu
lys

Sequence starts at "5"

TXT
met 5
ala
asn
glu
lys

Sequence with breaks in numbering

TXT
met 5
ala
asn 8
glu
lys
thr
his 15
arg
thr

RNA sequence

TXT
a
u
c
g

DNA sequence

TXT
da
dt
dc
dg

Sequence with entity names

TXT
-molecule fred
-polymer chainA
-coordset mono1
met 5
ala
asn
glu
lys

Heterodimer

TXT
-molecule mymol
-polymer poly1
-coordset A
met
ala
asn
glu
-polymer poly2
-coordset A
val
asp
arg

Polymer with ATP ligand

TXT
-molecule atpBinding
-polymer chainA
-coordset A
-sdfile atp.sdf
met
ala
asn
glu
lys

Template Library

When generating a molecular structure in NMRFx by reading in a sequence file it is necessary to translate the residue names into the set of atoms and bonds that define the molecular topology. To do this, NMRFx, looks at each residue name in the sequence file, and checks to see if a file corresponding to that name with a ".prf" extension can be located.

NMRFx looks in two places for these files. First, if a local residue library directory has been set, it looks there. Local residue libraries are specified in the NMRFx Analyst GUI in the Preferences dialog (Structure section). In NMRFx Structure the location is specified in the project .yaml file as a "reslib" entry. For example:

TXT
molecule :
  reslib  :  reslib

  entities :
      - file : input/A.seq
        ptype : protein

If a local residue library is not specified, or the file is not found there, then the built-in residue library is searched.

Two special aspects of residue names can be used in the sequence file. First, residue names that are followed with ":d" are automatically changed to D-amino acids. For example, in the following:

TXT
gly
ser
ala:d
trp

The alanine residue will be D-alanine

Second, entries that have an underscore character will internally have the name set with the portion before the underscore character, but will be set from the .prf file with the full name.
For example, "glu_prot", will be read from the file glu_prot.prf (which specifies the protonated form of glutamic acid), but will have the name "glu".

PRF Files

If a residue file is found, that file is scanned to extract the topology for that residue. NMRFx works with residues using an internal coordinate system, where the molecular topology is determined by a tree-like structure starting from the first atom in the structure. To properly define the structure then, it is necessary to provide values for the valance angles, dihedral angles, bond distances and connectivity. Most of this information is defined in the ATOM and FAMILY records. The .prf files, which are derived from information originally published by Robson & Osguthorpe (J. Mol. Biol. 132:19-51) are described below. Our original use of .prf files was in our structure calculation program, PEGASUS (Johnson & Sugg, Biochem., 1992, 31,8151-8159).

TXT
LNAME Serine
SNAME ser
RCHAR S
ATOM   N      N     1.32  114.00  -120.0  -0.41570
ATOM   H      H     1.00  123.00  0.0     0.27190 middle
ATOM   H      H     1.00  123.00  0.0     0.27190 end
ATOM   H1     H1    1.08  109.00  60.0    0.27190 start
ATOM   H2     H2    1.08  109.00  60.0    0.27190 start
ATOM   H3     H3    1.08  109.00  60.0    0.27190 start
ATOM   CA     CX    1.47  123.00  180.0   -0.02490
ATOM   HA     H1    1.08  109.47  -120.0  0.08430
ATOM   CB     2C    1.53  109.47  -121.5  0.21170
ATOM   HB2    H1    1.08  109.47  -120.0  0.03520
ATOM   HB3    H1    1.08  109.47  -120.0  0.03520
ATOM   OG     OH    1.42  109.47  0.0     -0.65460
ATOM   HG     HO    1.00  110.00  0.0     0.42750
ATOM   C      C     1.53  109.47  120.0   0.59730
ATOM   O      O     1.24  121.00  180.0   -0.56790 start
ATOM   O      O     1.24  121.00  180.0   -0.56790 middle
ATOM   O      O     1.24  180.00  120.0   -0.56790 end
ATOM   OXT    OH    1.24  180.00  120.0   -0.56790 end
FAMILY   -      N      H      CA    middle
FAMILY   -      N      H      CA    end
FAMILY   -      N      H1     H2     H3    CA    start
FAMILY   N      CA     C      CB     HA
FAMILY   CA     CB     OG     HB3    HB2
FAMILY   CB     OG     HG
FAMILY   CA     C      +      =O
FAMILY   CA     C      OXT    =O  end
ANGLE     CA      PHI 1
ANGLE     CB     CHI1 2
ANGLE     OG     CHI2 6
ANGLE     C       PSI 1
ATREE  CA  CB  C
ATREE  CB  OG
ATREE  OG
ATREE  C  +
PSEUDO QB HB2 HB3
CRAD CA   4.0

LNAME

: Full name of residue. Unused at present.

SNAME

: Short name of residue. Unused at present.

RCHAR

: Single letter name of residue. Unused at present.

ATOM

: Properties of the atoms in the residue. There should be one line for each atom. The line is composed of at least 8 fields separated by white space (spaces or tabs).

TXT
1.  Atom name

2.  Atom type, these are currently specified as atom types as used in the AMBER force field 
    The type is used for getting atomic number and non-bond contact parameters 
    when doing structure calculations.

3.  Bond length, from this atom to the previous atom in the tree
    structure of the residue (as defined in the FAMILY lines).

4.  Valance Angle, between this atom, its parent, and grandparent,
    as defined in the tree structure of the molecule.

5.  Torsion Angle, between this atom, its parent, grandparent, and
    great grandparent (as defined in the tree structure of the
    molecule). The angle for the first "child" atom bonded to a
    given parent, as defined in the FAMILY lines, is an absolute
    torsion angle. The angles for subsequent atoms are relative to
    the previously defined dihedral.

6.  Charges.  These are currently taken from AMBER parameter files.

7.  Position specifiers.  These optional flags specify atoms that are only present 
    when the residue is at a particular position in the sequence.  Atoms without 
    a specifier are always present.
       * start: only present for first residue
       * middle: only present for residues that are not the first or last residue
       * end: only present for last residue

FAMILY

: Defines the tree structure of the residue. Each line can be considered of the form

TXT
"**FAMILY parentAtom thisAtom childAtom1 childAtom2...**".

For example, a line like, "**FAMILY N CA C CB HA**", implies that
the atom **CA**, is bonded to the **N** atom (the parent of **CA**
is **N**), and it has three children, C, CB and HA. If the parent is
specified as "-", then it is a connector atom in the previous
residue. If a child is specified as "+", then it is the connector
atom in the subsequent residue. Child atom names preceded with a
"-", like**-CD2** imply that this child atom will actually be
defined in the tree structure in some other FAMILY entry in the
structure, but that there should be a bond drawn between this child
atom and the main atom of this FAMILY line. This is used to define
bonds that close rings.

ANGLE

: Each rotatable bond in the residue has an ANGLE entry.

TXT
1.  The rotatable bond is that between the specified atom and its
    parent.

2.  The name of the angle (PHI, PSI, CHI etc.)

3.  A number indicating an entry in the file irp.def, which gives
    energy parameters for the intrinsic rotation potential for this
    atom. Only used in structure calculations.

ATREE

: One entry for each rotatable bond. The order in which they are specified gives the tree of rotation groups.

PSEUDO

: Mapping of actual atoms in structure to pseudo atom names, "PSEUDO pseudoAtomName atom1 atom2 ...". The pseudo atom position would be at the geometric mean of all the actual atoms that are listed. At present this is only used when reading in constraint files using pseudo atom names (like CYANA .upl files) and is used to translate the pseudo atom name into the set of actual atoms stored in the molecular structure.

CRAD

: This specifies the name of an atom near the center of the residue and the approximate radius of a sphere around the central atom that would encompass all atoms of the residue. Used for accelerating calculation of non-bond contact list. Unused at present in NMRFx.

PDB or Mol Files

Residue files can also be specified with .pdb or .mol files if they are located in local residue libraries. Residue files stored as .pdb or .mol files do not have information, as the .prf files do, on how to make connections to the preceding and succeeding residues. The sequence file should contain -entry and -exit lines before the residue name. For example,

TXT
leu
-entry C1
-exit C8
phq

These lines specify the names of atoms in the residue that are used to make the connection to the adjacent residues. Note: this is an experimental feature, and may be subject to changes and require bug fixes. Please contact us for more information.

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