PELE File Formats

IMPACT template file format

This is one of the two file formats used for templates of chemical entities, and it corresponds to residue units. The other format, the PELE Custom Template Format is used for description of inter-residue parameters, such as disulfide bonds, peptide bonds, etc.

This format originates in the IMPACT ([banks:2005]) software template file format.

It follows a FORTRAN-like fixed columns style.

For the application of these parameters in the energy function, check Energy Function.

File name

It corresponds to the residue 3-letter code, without spaces (for example, the template for calcium, CA_, the space is represented as an underscore, would be represented by file caz, where the z is for saying it corresponds to an isolated residue).

It may have an additional qualifying character, depending on its position in a chain:

  • b, for residues at the beginning of the chain.

  • e, for residues at the end of the chain.

  • z, for isolated residues.

  • no character, for mid-chain residues.

Force field

Each template includes the parameters to work with a given residue in the specified template, which is one of those allowed by PELE.

Comments

Lines with an asterisk (*) as the first character are considered comments and are ignored during processing.

Tags

The file is structured in several sections, each starting with a 4-character tag. All files have all the sections (even if empty) and the RESX section must be the first one:

  • RESX (atom specification).

  • NBON (non bonded parameters).

  • BOND (bonded parameters).

  • THET (angle parameters).

  • PHI (dihedral parameters).

  • IPHI (improper dihedral parameters).

  • END

RESX

It must appear as the first section in the file. Examples:

LYS      22    21     38     51     110
LYSB     24    23     43     57     123
 DA      32    34     59     92     165
 DAE     33    35     60     95     170
 DCB     28    29     51     81     147

The first four characters are the template name. However, not all files comply with this rule. Therefore, we may find that in one forcefield, for the _DAE residue, we actually have _DA_ written (underscores mean spaces).

To allow for wrongly written template names, spaces are not significant, and the qualifying ending character may or may not be present in this RESX first line.

After the template name, the RESX first line has 5 integers:

  • Total number of atoms in the template (also corresponds to the number of elements in the NBON section).

  • Number of elements in the BOND section.

  • Number of elements in the THET section.

  • Number of dihedral angles described in the PHI and IPHI sections.

The exact format of this initial line is:

char(5) + int(6) + int(6) + int(7) + int(7) + int(8)

  • Template Name: char(5) (0-4)

  • Number of non bond. parms.: int(6) (5-10)

  • Number of bond parms.: int(6) (11-16)

  • Number of angle parms.: int(7) (17-23)

  • Number of dihedral parms.: int(7) (24-30)

  • Number of non-null elements in the matrix of interactions: int(8) (31-38)

All numbers are right justified.

Then, for each atom in the residue, there is a line of this type:

int(5) + ' ' + int(5) + ' ' + char(1) + ' 'x3 + char(4) + ' ' + char(4) + ' ' + int(5) + ' ' + real(5.5) + ' ' + real(5.5) + ' ' + real(5.5) + ' '

  • Atom id Number: int(5) (0-4)

  • Parent Id: int(5) (6-10)

  • Location (M for backbone, S for side chain; ligand links and non-ligand links use these classification for some checks. However, protein links define its backbone atoms independently of this flag; protein residue templates have M only for N, C and CA, under whatever name is actually used for those atoms): char(1) (12)

  • Atom Type (used, for example, for penalty terms in the SGB model): char(4) (16-19).

  • Pdb Atom name: char(4) (21-24)

  • Unknown: int(5) (26-30)

  • X z-matrix: real(5.5) (32-42)

  • Y z-matrix: real(5.5) (44-54)

  • Z z-matrix: real(5.5) (56-66)

Notice that the Z-matrix is used to generate the sparse atoms.

With all integer right justified, and reals with 0 padding to fill the 5 allocated places. All atom names must have an underscore _ instead of a space.

Example (from lys template):

Line:    1     0 M   N    _N__     1     1.33000   116.21694   180.00000

Then, all lists of atomic bonded interactions appear (to generate the upper triangle of a boolean matrix of interactions of size \(n^2\), having, therefore, size \(n(n-1)/2\)), where bonded means the atoms form either a bond, angle or dihedral term. The first line has as many integers as rows will have the interaction matrix (one per atom), with format:

int(4) * num atoms

Example:

Lines have at most 16 integers, so if the number of atoms is greater, then additional lines appear.

Following lines will write the identifiers of atoms that are bonded (bond, angle or dihedral) to the atom corresponding to this line. Therefore, \({x=\text{line}, y \in \text{bonded}(x) | (x,y)}\) Since the last atom has no other connections in the upper triangle, then this line always has a 0 in it.

The format is a sequence of integers int(5).

Example:

Line:    3     5     6     7    10     2     4     8     9

Full example. Let the bonding/interactions matrix be:

id    1 2 3 4
      N C H O
1  N    *   *
2  C      *
3  H        *
4  O

It means the following atoms are bonded or are indirectly bonded (bond, angle or dihedral): C-N, O-N, H-C, O-H.

First line in the template would say:

Line:    2   1   1

meaning that there exist 2 relations for N, 1 for C and 1 for H in the upper triangle of the relation/bonding/interaction matrix.

Therefore, the first line has as many numbers are atoms are in the template, and for each atom it says how many numbes will appear in that atom’s line.

The following lines, one per atom, and in the same order as the atoms in the template, and each contains the numbers of those atoms to which it is directly or indirectly bonded (bond, angle or dihedral), as long as it has not already been specified in a previous atom (that is, only the upper triangle of the matrix is expressed); the line of the last atom contains a 0. For the previous case, it would be:

Line:    2   4
Line:    3
Line:    4
Line:    0

NBON

This section stores the non-bonded parameters (van der Waals and electrostatic). Original OPLS parameters are in [jorgensen:1996] (supplementary material).

See The Molecular Mechanics energy terms for details on the meaning of the parameters.

int(5) + ' ' + real(3.4) + ' ' + real(3.4) + ' ' + real(3.6) + ' ' + real(3.4) + ' ' + real(3.4) + ' ' + real(3.9) + ' ' + real(3.9)

  • Atom id: int(5) (0-4)

  • Sigma (\(\sigma_{ii}\) in OPLS, \(r_{i}\) in AMBER; units are in \(\AA{}\)): real(3.4) (6-13)

  • Epsilon (\(\epsilon_{ii}\); units are in kcal/mol): real(3.4) (15-22)

  • Charge (\(q_{i}\); units are elementary charge (atomic units)): real(3.6) (24-31)

  • Rad. Non Polar SGB (atomic radii used to calculate the surface of the molecules when obtaining SGB Born radii; it corresponds to eq. 6 of [gallicchio:2002], though not in all cases, perhaps because specific fittings done in OPLS2005; despite the name, the Born radii calculated with the surface generated by these radii can be used both for polar solvation energy in the SGB/VDGB models as for the non-polar solvation energy, as in the ACE model used in the PELE OBC solvation model): real(3.4) (33-40)

  • Rad. Non Polar Type (atomic radii used to calculate SASA in the non-polar term of the SGB and VDGBNP models; see eq. 7 of [gallicchio:2002]; it is also used to calculate the SASA metric): real(3.4) (42-49)

  • SGB Non Polar gamma (gamma parameter for the nonpolar model of [gallicchio:2002]): real(3.9) (51-63)

  • SGB Non Polar type (alpha parameter for the nonpolar model of [gallicchio:2002]): real(3.9) (65-77)

Example:

Line:    1   3.2500   0.1700  -0.5000   1.9200   1.7000   0.168599800  -5.228863800

Exceptions:

The fourth parameter (charge) may be a real(3.6). This exception is easily found because the line has a length of 80 characters instead of 78.

BOND

This section stores the parameters for atomic bonding (1-2 interactions).

\[E_{\text{bond}} = \sum_{\text{bonds}} K_{r}(r - r_{\text{eq}})^{2}\]
int(5) + ' ' + int(5) + ' ' + real(5.3) + ' ' + real(2.3)

  • Atom 1 Id: int(5) (0-4)

  • Atom 2 Id: int(5) (6-10)

  • Spring constant (\(K_{r}\)): real(5.3) (12-20)

  • Equilibrium distance (\(r_{\text{eq}}\)): real(2.3) (22-27)

Example:

Line:    1     3   337.000  1.449

THET

This section stores the parameters for angles formed by 3 atoms (1-3 interactions).

\[E_{\text{angle}} = \sum_{\text{angles}} K_{\theta} (\theta - \theta_{\text{eq}})^{2}\]
int(5) + ' ' + int(5) + ' ' + int(5) + ' ' + real(5.5) + real(5.5)

  • Atom 1 Id: int(5) (0-4)

  • Atom 2 Id: int(5) (6-10)

  • Atom 3 Id: int(5) (12-16)

  • Spring constant (\(K_{\theta}\)): real(5.5) (18-28)

  • Equilibrium angle (\(\theta_{\text{eq}}\); expressed in degrees in the template file, though PELE uses radians internally): real(5.5) (29-39)

If atomId1 and atomId2 are both the symbol -, then the parameters are available for 1-4 calculations.

Example:

Line:     1     3     5    63.00000  110.10000

Notice that the same angle ABC is actually defined whether atom 1 is A, atom 2 is B and atom 3 is C, than in reverse order, with atom 1 being C, atom 2 being B, and atom 3 being A.

PHI

This section stores the parameters for dihedral angles formed by 4 atoms (1-4 interactions). Since it may have several terms, each line stores the values for one of the terms.

\[E_{\text{torsion}} = \sum_{\text{angle}\, i} \sum_{j} {k_{j,1}^{i}[1 + k_{j,2} \cos (n_{j}\phi_{i})]}\]
int(5) + ' ' + int(5) + ' ' + int(5) + ' ' + int(5) + ' ' + real(3.5) + ' ' + real(2.1) + ' ' + real(1.1)

  • Atom 1 Id: int(5) (0-4)

  • Atom 2 Id: int(5) (6-10)

  • Atom 3 Id: int(5) (12-16)

  • Atom 4 Id: int(5) (18-22)

  • Constant (\(k_{j,1}\); corresponds to the \(\frac{V_{n}}{2}\) factors in each of the torsional terms of the torsion energy component for a given dihedral angle): real(3.5) (24-32)

  • Prefactor (\(k_{j,2}\), can be \(-1.0\) or \(1.0\)): real(2.1) (34-37)

  • Number of term (\(n_{j}\)): real(1.1) (39-41)

Example:

Line:    1     3     5     6   0.00000  1.0 1.0

Notice that the \(\pm 1.0\) values for the prefactor actually represent the phases of \(0^\circ{}\) or \(180^\circ{}\) degrees in other versions of the energy term formula. For the OPLS force field, it represents the sign preceding the cosine.

If one of the atom ids 2 and 3 is prefixed by a minus sign, this means that atom 1 and atom 4 should not be included in the 1-4 list for energy calculations (this usually happens if the same 1-4 atoms were already included in a different dihedral, to avoid repetition, and also when the 1-4 atoms are actually 1-3, 1-2 or the same atom, in the case of rings).

Notice that the same dihedral is defined either by atoms ABCD or atoms DCBA.

IPHI

For improper dihedral angles. Just the same format as for the dihedrals (see PHI tag).

END

This is the final tag. Nothing will be read past this tag.

PELE custom template file format

This is the other file format used for templates of chemical entities, and corresponds to the description of inter-residue parameters, such as disulfide bonds, peptide bonds or bonds between nucleic acids. Notice that the parameters provided in these files apply to the same energy terms as those parameters in the IMPACT template files.

The parameters for bonds, angles and dihedrals between atoms in different links or units appear in files using this format. These files are:

  • inter_nucleicacid_bonds: When the links are nucleic acids. Notice that the version for DNA is actually used for both DNA and RNA.

  • disulphide_bonds: When the links are cysteines forming a disulfide bond.

  • inter_residue_bonds: When the links are aminoacids.

This format allows comments, marked with a # symbol. Anything appearing after the hash mark, will be considered a comment and ignored together with the hash mark.

Contrary to the IMPACT format, each record has a label which indicates its meaning, so though the files are usually organized by sections, the format process line by line independently of the others.

The six labels recognized by this format are:

  • NAME

  • ATOID

  • BOND

  • ANGL

  • TORS

  • ITOR

Sample file contents:

#-----------------------------------
# Peptide Bond
#-----------------------------------
NAME PEPTIDE_BOND

#-----------------------------------
# ATOM IDS
#-----------------------------------
ATOID  1 _O___
ATOID  2 _C___
# ...

#-----------------------------------
# GEOMETRY
#-----------------------------------

BOND   C     N  * 490.000   1.335

ANGL   CA    C     N  *  70.000 116.600
ANGL   O     C     N  *  80.000 122.900
ANGL   C     N  *  CA *  50.000 121.900
ANGL   C     N  *  H  *  35.000 119.800
ANGL   C     N  *  CD *  50.000 121.900

TORS   O     C     N  *  H  *  2.4500 -1.0 2
TORS   O     C     N  *  CA *  3.0445 -1.0 2
TORS   C     N  *  CA *  CB *  0.2595  1.0 1
# ...

ITOR   CA    N  *  C     O     10.500 -1.0 2
ITOR   CA *  C     N  *  H  *  1.0000 -1.0 2  #?????????????
ITOR   CA *  C     N  *  CD *  1.0000 -1.0 2  #??????? or (1)

NAME

There should be a single record of this type. It includes a single element, which is the name of the template, and should match one of these:

  • PEPTIDE_BOND

  • DISULPHIDE_BOND

  • PHOSPHODIESTER_BOND

Example:

Line:NAME PEPTIDE_BOND

ATOID

This record enumerates the atoms considered in the template.

The format of this record is:

"ATOID " + int(2) + char(5)

  • Atom id number: int(2) (6-7)

  • Atom name/type: Spaces in the atom name are identified by underscores. Atom names are actually 4-character long, with a final character to mark whether the atom belongs to the first link in the two-link structure (marked with a space, codified as an underscore) or if it belongs to the second (marked with an asterisk *). char(5) (9-13)

Notice that since these templates are used for parameterizing bonds between residues or units, an asterisk is used to differentiate atoms of the second unit from those of the first unit.

Example:

Line:ATOID  1 _O___

BOND

This record identifies the bonds formed between atoms in the template.

The format of this record is:

"BOND  " + char(5) + ' ' + char(5) + ' ' + real(7) + ' ' + real(7)

  • Atom 1 Id: char(5) (6-10)

  • Atom 2 Id: char(5) (12-16)

  • Spring constant (\(K_{r}\)): real(7) (18-24)

  • Equilibrium distance (\(r_{\text{eq}}\)): real(7) (26-32)

Notice that atom names show spaces as such, instead of using underscores.

Example:

Line:BOND   C     N  * 490.000   1.335

ANGL

This records identifies the angles formed between three atoms in the template.

The format of this record is:

"ANGL  " + char(5) + ' ' + char(5) + ' ' + char(5) + ' ' + real(7) + ' ' + real(7)

  • Atom 1 Id: char(5) (6-10)

  • Atom 2 Id: char(5) (12-16)

  • Atom 3 Id: char(5) (18-22)

  • Spring constant (\(K_{\theta}\)): real(7) (24-30)

  • Equilibrium distance (\(\theta_{\text{eq}}\); expressed in degrees in the template file, though PELE uses radians internally): real(7) (32-38)

Notice that the same angle is defined by atoms ABC as for the same atoms in reverse order (CBA).

Example:

Line:ANGL   CA    C     N  *  70.000 116.600

TORS

This record identifies the dihedral angles formed between four atoms in the template.

The format of this record is:

"TORS  " + char(5) + ' ' + char(5) + ' ' + char(5) + ' ' + char(5) + ' ' + real() + ' ' + real() + ' ' + int()

  • Atom 1 Id: char(5) (6-10)

  • Atom 2 Id: char(5) (12-16)

  • Atom 3 Id: char(5) (18-22)

  • Atom 4 Id: char(5) (24-28)

  • Constant (\(k_{j,1}\)): real

  • Prefactor (\(k_{j,2}\), can be \(-1.0\) or \(1.0\)): real

  • Number of term (\(n_{j}\)): int

Notice that the \(\pm 1.0\) values for the prefactor actually represent the phases of \(0^\circ{}\) or \(180^\circ{}\) degrees in other versions of the energy term formula.

In this case, all dihedral angles define real 1-4 interactions between the end atoms, so there is no need to use prefix - as to mark the atoms not to be included in the 1-4 list.

Notice that the same dihedral is defined either by atoms ABCD or atoms DCBA.

Example:

Line:TORS   O     C     N  *  H  *  2.4500 -1.0 2

ITOR

For improper dihedral angles. Just the same format as for the dihedrals, except the ITOR label is used to identify these records.

Example:

Line:ITOR   CA    N  *  C     O     10.500 -1.0 2

Non-ligand rotamer library file

A rotamer library file lists rotamers for a given link side chain. Notice that this format only allows for single side chain links, differently from what can happen with a ligand link.

These files are stored in directory Data/RotamerLibs/, and each rotamer library file has the uppercase name of the residue, followed by the suffix .side. For example, the aspartic acid rotamer library file is Data/RotamerLibs/ASP.side. Notice the existence of special rotamer libraries that start with FRE; these represent all possible angle values for a given resolution and for a single dihedral. More information about these files at the end of this section.

An example file:

* SER  1  27  10.0  1
_OG_
POLARH  _HG_  1
   6
  -6
  18
   7
  -7
  17
  -5
 -17
   5
   8
   4
  16
  -8
  -4
 -16
 -10
   2
 -14
  -2
  13
  15
   1
 -12
  10
  12
  -1
 -11

Another example with multiple atoms in the side chain:

* ASP   2 233  10.0  0
_CG_
_OD1
  -7  -1
  -6  -3
  -6  -4
  -8  -2
...
 -11  -1
   7   6
  -1  -8
   4   2
   7  -1
  -8  -9
   2   9
 -10   8
   8   8

Header

The first line is the header. It has several fields separated by blanks. The fields are, in order:

  • A star (‘*’) character.

  • The name of the link.

  • The number of angles that define each rotamer.

  • The number of rotamers included in the file. It must match the number of lines defining rotamers in this file.

  • The resolution of the rotamer library, in degrees, for both the core side chain and the polar part.

  • Whether this side chain has a polar part at the end (either 1 or 0).

Atom names

After the header line, appear all atoms to apply the rotamer angles. For all dihedral angles of the side chain (chi1, chi2, etc.), being A-B-C-D the atoms defining that dihedral (see the Gold Book entry for torsion angle: http://goldbook.iupac.org/T06406.html), it is the D atoms those that appear in this list. The names correspond to the PELE convention, and have spaces substituted by underscore characters.

Polar line

If the link’s side chain has a polar part, then it follows this line, with the next items (separated by blanks):

  • The POLARH string.

  • The name of the polar atom (PELE convention, spaces substituted by underscore).

  • iper: Limits the range covered by the dihedral angle. When the polar atom has other symmetric siblings, it suffices with sampling only for a smaller range. For example, lysine zeta nitrogen has 3 hydrogens attached. Due to symmetry, it suffices with sampling the first hydrogen for dihedral angles between -60 and +60; sampling outside that range will position HZ1 at a different place, but it would be equivalent to either HZ2 or HZ3 position in one of the values sampled in the restricted set. The values allowed for iper are: 0 (it covers [-180, 180)), 1 ([-90, 90)) and 2 ([-60, 60)).

Currently, the only residues with a polar dihedral angle are:

  • ASH: POLARH _HD2 1

  • ASQ: POLARH _O2P 3

  • BMT: POLARH _HG1 1

  • CYS: POLARH _HG_ 1

  • DCY: POLARH _HG_ 1

  • DLY: POLARH 1HZ_ 3

  • DTH: POLARH _HG1 1

  • DTY: POLARH _HH_ 1

  • GLH: POLARH _HE2 1

  • LYS: POLARH _HZ1 3

  • OMY: POLARH _CH_ 1

  • PTR: POLARH _O2P 3

  • SEP: POLARH _O2P 3

  • SER: POLARH _HG_ 1

  • THR: POLARH _HG1 1

  • TPO: POLARH _O2P 3

  • TYR: POLARH _HH_ 1

Non polar rotamers

One line per rotamer; exactly the same number as the number of rotamers stated in the header. Each line consists of rotamer angle values (as many as the number of angles defined in the rotamer), with each value in a 4-character field, right justified.

Each rotamer angle value is stored as an integer factor of the rotamer library resolution.

Free rotamer libraries

The allowed full-sampling rotamers for a single dihedral are stored in the following files:

  • FREE_5.side

  • FREE10.side

  • FREE15.side

  • FREE20.side

  • FREE30.side

  • FREE40.side

  • FREE45.side

  • FREE60.side

  • FREE90.side

  • FRE120.side

  • FRE180.side

For example, for a sampling every 60 degrees, the file FREE60.side is:

* FREE60  1  6  60.0  0
ATM1
-3
-2
-1
0
1
2

Notice however that these files are not currently used and, instead, any real resolution that is a result of dividing 180 among 1..17 is allowed, plus number 5. This is because, internally, the polar library of iper 1 for the given resolution is chosen.

Ligand rotamer library file

Ligand rotamer library files are under Data/LigandRotamerLibs/, and are named as the link name in uppercase, plus the suffix .rot.assign. For example, benzamidine ligand rotamer library file is Data/ligandRotamerLibs/BEN.rot.assign.

All lines must end with an ampersand character (&), and blank lines (which cannot be the first one) are ignored.

This is an example for one ligand:

rot assign res INH &
   sidelib FREE10 _C16 _C6_ &
   sidelib FREE10 _C6_ _C22 &
   sidelib FREE10 _C22 _O5_ &
     newgrp &
   sidelib FREE10 _C14 _O3_ &
     newgrp &
   sidelib FREE10 _C16 _O4_ &

Header

This line, which must be the first one, is ignored. It has the format:

rot assign res BEN &

which basically means: assign the following rotameric information to residue BEN.

Group definition

Each side chain is defined in a group definition block. The first side chain does not need any keyword to mark the group. All the following side chains must begin with the newgrp keyword, as this:

newgrp &

Whether the first side chain or any other side chain, a group definition is formed by dihedral angle rotameric descriptions in lines tagged with the keyword sidelib:

sidelib FREE10 _C16 _C6_ &

The first value is the name of a full-sampling rotamer library for that dihedral angle, and must match with those available in Data/RotamberLibs/. Currently, you can express resolutions of 5 (FREE_5), 10 (FREE10), 15 (FREE15), 20 (FREE20), 30 (FREE30), 40 (FREE40), 45 (FREE45), 60 (FREE60), 120 (FRE120) and 180 (FRE180) degrees. Notice that all names have exactly 6 characters. Actually, you can express any desired integer resolution, and the one closest (and not bigger) from any of the following will be chosen; in any case, the smallest resolution allowed is 5.

  • 180 (2 possible values for the whole range [-180, 180)).

  • 90 (4 values).

  • 60 (6 values).

  • 45 (8 values).

  • 36 (10 values).

  • 30 (12 values).

  • 25.7143 (14 values).

  • 22.5 (16 values).

  • 20 (18 values).

  • 18 (20 values).

  • 16.3636 (22 values).

  • 15 (24 values).

  • 13.8462 (26 values).

  • 12.8571 (28 values).

  • 12 (30 values).

  • 11.25 (32 values).

  • 10.5882 (34 values).

  • 10 (36 values).

  • 5 (72 values).

Then, the two atoms that define the central bond appear, using PELE notation (with spaces replaced by underscores). Given that a dihedral (or torsion) angle (see the IUPAC Gold Book entry http://goldbook.iupac.org/T06406.html) is defined by atoms A-B-C-D, these atoms must be B and C, and in that order.

As in the example shown above, if a given side chain (as copied below) has several dihedral angles, all of them must be shown:

sidelib FREE10 _C16 _C6_ &
sidelib FREE10 _C6_ _C22 &
sidelib FREE10 _C22 _O5_ &

In this example, the side chain has three dihedral angles, all of them consecutive (since each one shares one atom with the previous dihedral angle).

Conformation library file

Conformation library files are under Data/Conformations, and are named as the link name in uppercase, plus the suffix .conformation. For example, a theoretical conformation library file for benzamidine would be Data/Conformations/BEN.conformation.

Conformation libraries are composed by a global header, followed by a collection header, atom offsets and collection ending. A conformation library may have one or more collections, and is terminated by a single END line.

This is an example for a conformation library with 2 collections and 4 atoms per collection:

* CONFORMATIONS LIBRARY FILE
* File generated with peleffy-1.0.0+164.g06140f6
* File: PELEPipelineSanja/6Y81-LIG/CLUSTERS/CL7/cluster7.min.imaged.pdb
LIG 4 2
_N2_ 2.970000 -3.750000 -2.780000
_H2_ 2.610000 -2.910000 -3.340000
_H3_ 2.840000 -4.590000 -3.410000
_H4_ 2.330000 -3.880000 -2.040000
ENDCONFORMATION
* File: PELEPipelineSanja/6Y81-LIG/CLUSTERS/CL2/cluster2.min.imaged.pdb
LIG 4 2
_N2_ -5.330000 -2.690000 -2.210000
_H2_ -5.240000 -1.790000 -2.740000
_H3_ -4.380000 -3.100000 -2.250000
_H4_ -6.030000 -3.220000 -2.760000
ENDCONFORMATION
END

Collection header

After the global header there are one or more collections, composed by a collection header, body and end tag. The collection header consists of two lines. The first line starts with a * and contains the path to the pdb file that defines the conformation contained by the collection. The second line contains three space-separated fields: the link name, the number of atoms and the number of collections in the conformation library. The format of this header is like this:

* File: PELEPipelineSanja/6Y81-LIG/CLUSTERS/CL7/cluster7.min.imaged.pdb
LIG 4 2

Collection body

The collection body contains the atom coordinates, one per line. Each line contains four space separated fields. The first corresponds to the PDB atom names of the atom, with spaces indicated by underscores. The three remaining values are the coordinates. An example of an atom line can be found below:

_H3_ -4.380000 -3.100000 -2.250000

Collection end

After all the atoms coordinates have been specified, the collection is terminated by the use of ENDCONFORMATION tag, as shown below:

ENDCONFORMATION

Global end

After a ENDCONFORMATION there can be a collection header for a new collection, or and END tag. This tag marks the end of the conformation library, as shown below:

END

Elements Parameters file

This file is Data/Atoms/elements_parameters.txt.

It has a line per chemical element. Each line contains 3 fields, separated by spaces:

  • Element symbol, in uppercase.

  • Atomic number.

  • Atomic mass.

Sample contents:

H    1   1.008
HE   2   4.00
LI   3   6.94
BE   4   9.01
B    5   10.81
C    6   12.01
N    7   14.01
O    8   16.00
F    9   19.00

Solvent parameters for SGB

See file Data/SGB/solventParamsList.txt.

This file is simply a summary of the parameters used, and is not actually read by PELE. Instead, the parameters set in the NBON section of the IMPACT templates (IMPACT template file format), are used.

Solvent penalty terms

See file Data/SGB/penaltyTerms.

First line of the file shows the number of atom pairs to apply the penalty term.

Then, for each line, there are 9 fields:

  • atom name i

  • residue name i. It may be ANY.

  • atom name j

  • residue name j. It may be ANY.

  • \(V_{\text{max}}\).

  • \(a_{0}\)

  • \(a_{1}\)

  • \(\text{cutoff}^{L}\) (lower cutoff).

  • \(\text{cutoff}^{H}\) (higher cutoff).

Normal modes file format (NMD)

This file is used to enter pre-calculated normal modes (whether ANM modes, or PCA modes, or modes from any other model that fit into the ANM pahse of a PELE simulation, see ANM Block in Pele++ control file).

The input file must be in NMD format, like the files produced by ProDy: http://prody.csb.pitt.edu/manual/reference/dynamics/nmdfile.html. This format has been slightly restricted in the way that, for each mode line, you must provide a scaling factor, and this factor is the square root of the eigenvalue (PELE will compute the actual eigenvalue from this).

For PELE, the following lines in the NMD file are compulsory:

  • atomnames: a single record line, with the list of atom names to be used as nodes.

  • resnames: a single record line, with the names of the residues corresponding to the atoms in atomnames.

  • chainids: a single record line, with the chain ids corresponding to the atoms in atomnames.

  • resids: a single record line, with the residue ids corresponding to the atoms in atomnames.

  • coordinates: a single record line, with three times as many coordinate numbers as atoms in atomnames (coordinates x, y, z). This is needed to compute the number of atoms, according to the NMD format specification.

  • mode: multiple lines, containing the normal modes to apply. These lines may contain an initial integer value as the normal mode index. Then, after the optional index, and before the actual normal mode vectorial components, comes the square root of the eigenvalue corresponding to that normal mode.

Example

The following NMD file contains the normal modes for a hexapeptide. Exact coordinate values are irrelevant, except for the actual number of coordinates, that determine the number of atoms to consider in the normal mode model. All mode lines start with the square root of the eigenvalue for that normal mode, and then are followed by the normal mode vector coordinates. Notice that lines nmwiz_load and name are ignored.

nmwiz_load non_sense_text
name irrelevant
atomnames  CA   CA   CA   CA   CA   CA
resnames GLY ILE LEU TYR GLY PHE
resids 2 1 3 5 6 4
chainids A A A A A A
coordinates 69 70 71 12 13 14 90 91 92 207 208 209 270 271 272 147 148 149
mode 0.00273518 0.182563 -0.236628 -0.187276 0.138854 -0.21912 -0.0174999 -0.29117 0.385916 0.199129 -0.123327 0.113394 0.0693217 0.331322 -0.366597 -0.249164 -0.238242 0.323036 0.18549
mode 0.017155 -0.320418 0.354319 0.0588638 0.244408 -0.216638 0.0623719 0.0449705 -0.106396 -0.0868696 -0.409482 0.438541 0.138569 0.284328 -0.200384 0.0247522 0.156194 -0.269443 -0.197687
mode 0.0224504 0.20756 -0.236233 -0.0466123 -0.292223 0.272561 0.0356318 0.389414 -0.449831 -0.146309 -0.278234 0.304692 0.136053 0.123756 -0.151396 -0.139509 -0.150271 0.260207 0.160746
mode 0.185988 0.139822 -0.0557512 -0.112711 0.111934 -0.0180165 0.427796 -0.169039 -0.0480346 -0.272187 -0.0752528 -0.0711941 -0.348889 0.318833 0.0217976 0.504157 -0.326297 0.171199 -0.198165
mode 0.439333 -0.0382877 -0.0911297 -0.281036 0.0502785 -0.0421324 0.406383 -0.23339 0.0198441 -0.371058 0.385763 0.163819 0.539233 -0.0728528 0.0129334 -0.251376 -0.0915114 -0.063334 -0.0421465
mode 1.07997 0.263504 0.13792 0.602361 -0.0294801 -0.00625519 -0.292769 -0.0963889 -0.146163 -0.100595 0.199072 0.0275307 0.229903 0.0258018 0.000911341 0.00357145 -0.362509 -0.013944 -0.442471