11.5 Effective Fragment Potential Method

11.5.7 fEFP Input Structure

(June 30, 2021)

A two-step script, prefefp.pl located in $QC/bin, allows users to break molecular structures from a PDB file into the capped fragments in the gamess format, such that parameters for fEFP calculations can be generated.

To use the prefefp.pl scripts you need a PDB file, a MAP file, and a directory with all your .efp parameter files. Run the following commands to: (1) obtain the N input file generating the N EFP parameters for the N capped fragments, and (2) create the EFP input file in XYZ format.

perl prefp.pl 1 <PDB file> <MAP file>
perl prefp.pl 2 <PDB file> <.efp path> <MAP file> <GMS input file name>

At the first step the script splits the biomolecule (PDB format) into N fragments generating N gamess MAKEFP input files with the help of a MAP file.

At the second step the .efp file from gamess MAKEFP is analyzed and is auto-edited using the same MAP file to create the final EFP input (XYZ format).

The MAP file is required as an input for the script. It defines groups of atoms belonging to each EFP fragment both for the MAKEFP calculation and for the consequent EFP jobs. Here is a description of the MAP file: Each fragment described using section $RESIDUE followed by closing $end In this example the Lys2 is extracted cutting through the peptidic bond, the cut bond is saturated with hydrogen atom. The explanation of each variable is given below.

$Residue
Name = lys2
PreAtoms = 14-35
NH = 14,12
CH = 34,36
PostAtoms = 14-35
Rescharge = +1
USEFP = lys2
$end

The four first lines are required for the first step of the script (gamess MAKEFP job); the next ones are necessary for the actual EFP job.
Name: Residue name
PreAtoms: Atoms which belongs to the residue for gamess MAKEFP calculation.
CH, NH, or OH: In the case of broken bonds a hydrogen atom is added so that in X-Y bond (X belongs to the Lys2 residue and Y belongs to the previous or next residue) the Y atom is replaced by H along the X-Y axis. The default equilibrium distance for the X-H bond is set to 1.08 Å for a C-H bond, to 1.00 Å for a N-H bond, and to 0.94 Å for a O-H bond. It required to specify the atom number of the X and Y atoms.
PostAtoms: Atoms which belong to the residue after removing the overlapping fragment atoms or caps when the HLA or the CLA scheme is used. This important step removes multipoles and polarizability expansion points of those atoms according to the cutoff procedure (set by default to 1.3 Å and 1.2 Å for multipoles and polarizability expansion points, respectively). Multipole expansion at duplicated points are eliminated but to maintain the net integer charge on each amino acid the monopole expansion of the caps is redistributed on the natural fragment. This method is called Expand-Remove-Redistribute. Concerning the polarizability expansion points, only one polarizability expansion point is removed when a hydrogen atom saturates the dangling bond, whereas 6 or 5 polarizability points are removed when the cap is an amine or an aldehyde, respectively.
ResCharge: The net charge of the residue after removing the overlapping fragment atoms (cfr. LA scheme).
USEFP: Name of the EFP fragment (and .efp file) to use with this fragment in the actual EFP calculation.

Note:  In the MFCC scheme, the two first letters of the concap fragment have to be ’CC’.

Note:  If the PostAtoms keyword is not present, the second script will generate an EFP job file without any modification of the parameters, which is useful for the MFCC scheme.