EFP parameters

How to prepare EFP parameters? There are two ways, either find existing parameters in a Parameter database or Computing parameters.

Parameter database

We have prepared and validated EFP parameters for the following systems:

• monomers from S22 and S66 sets

• amino acid parameters from doi.org/10.1021/acs.jctc.0c00758

Learn more detail about these EFP parameters on EFP parameter databases.

Computing parameters

Parameters for any molecule can be computed using MAKEFP run in the GAMESS electronic structure package.

For general information on using GAMESS please refer to the GAMESS manual.

Apart of standard .log and .dat outputs, MAKEFP run creates an additional file with an extension .efp that contains all EFP parameters of your molecule.

An example of GAMESS input file for computing EFP parameters makefp.inp.

 $contrl units=angs local=boys runtyp=makefp coord=cart icut=11 $end
 $system timlim=99999  mwords=200 $end
 $scf dirscf=.t. soscf=.f. diis=.t. conv=1.0d-06  $end
 $basis gbasis=n31 ngauss=6 ndfunc=1 diffsp=.t. $end
 $damp ifttyp(1)=2,0 iftfix(1)=1,1 thrsh=500.0 $end
 $makefp chtr=.f. disp7=.f. $end
 
 $data 
comment line
C1
N  7  1.08099635  1.08099635  1.08099635
H  1  1.89264145  1.37035655  0.59462495
H  1  1.37035655  0.59462495  1.89264145
H  1  0.59462495  1.89264145  1.37035655
 $end
 

.efp parameter file

Note

.efp file follows general GAMESS input file conventions:

• Group names starting with $ should start at the second line character.

• Lines should not exceed 72 characters; use > as a continuation sign for longer lines.

An example of .efp file nh3.efp.

The .efp file has the following structure (see also $FRAGNAME group section in GAMESS manual):

$FRAGNAME

• FRAGNAME section provides user-specified fragment name.

• The section is mandatory.

• FRAGNAME tag should match the fragment name in LibEFP, GAMESS, Q-Chem inputs. Capitalization is not important.

• FRAGNAME tag should match the name of the .efp file. For example, $nh3 fragment should be contained in nh3.efp file.

• $ in front of the FRAGNAME tag should be positioned at the second line character.

Commment line

• The section is mandatory.

COORDINATES

• COORDINATES section provides coordinates of all atoms and bond-midpoints of the fragment.

• The section is mandatory.

• Each line contains name tag, x, y, z coordinates (in Bohr), atom mass, nuclear charge.

• For atoms, the name tag is produced as A + two-digit number + atom name from the MAKEFP input, e.g., A01N.

• For bond-midpoints, the name tag is produced as BO + second atom number + first atom number, e.g., BO21.

• These name tags are used in MULTIPOLES, DIPOLES, QUADRUPOLES, OCTUPOLES, PROJECTION BASIS SET, and SCREEN and SCREEN2 sections.

• The name tags can be changed by user if needed (typically not needed, see below).

• GAMESS does not correctly assign name tags in fragments containing more than 99 atoms. Such potentials require atom and bond-midpoint renaming by user.

• The section ends with mandatory STOP line.

MONOPOLES

• MONOPOLES section contains nuclear and electronic charges of atoms and bond-midpoints of the fragment.

• Each line contains name tag, electronic charge, nuclear charge.

• Name tags should match those in COORDINATES section.

• The section is mandatory in GAMESS input and optional in LibEFP and Q-Chem inputs.

• The section can contain less atoms/bond midpoints than COORDINATES section.

• The section ends with mandatory STOP line.

DIPOLES

• DIPOLES section contains point dipoles of atoms and bond-midpoints of the fragment.

• Each line contains name tag and x, y, z values of a point dipole in atomic units.

• Name tags should match those in COORDINATES section.

• The section is optional.

• The section can contain less atoms/bond midpoints than COORDINATES section.

• Direction of the dipoles is dependent on the fragment orientation as provided by the fragment coordinates.

• The section ends with mandatory STOP line.

QUADRUPOLES

• QUADRUPOLES section contains point quadrupoles of atoms and bond-midpoints of the fragment.

• Each line contains name tag and xx, yy, zz, xy, xz, yz components of a quadrupole moment tensor in atomic units. Three other elements (yx, zx, zy) are identical to xy, xz, yz respectively and are omitted.

• Name tags should match those in COORDINATES section.

• The section is optional.

• The section can contain less atoms/bond midpoints than COORDINATES section.

• Direction of the quadrupole tensor is dependent on the fragment orientation as provided by the fragment coordinates.

• The quadrupole moments are given in the Buckingham form, i.e., xx, xy, xz etc components correspond to \(a_x a_x\), \(a_x a_y\), \(a_x a_z\), respectively, where a is a vector describing particle position. Conversion to multipoles in the Cartesian form \(\Theta_{\alpha \beta} = \sum_a e_a (\frac{3}{2}a_{\alpha}a_{\beta}-\frac{1}{2}a^2\delta_{\alpha \beta})\) is conducted within LibEFP or GAMESS codes.

• The section ends with mandatory STOP line.

OCTUPOLES

• OCTUPOLES section contains point octupoles of atoms and bond-midpoints of the fragment.

• Each line contains name tag and xxx, yyy, zzz, xxy, xxz, xyy, yyz, xzz, yzz, xyz components of an octupole moment tensor in atomic units. Other elements are determined by symmetry and are omitted.

• Name tags should match those in COORDINATES section.

• The section is optional.

• The section can contain less atoms/bond midpoints than COORDINATES section.

• Direction of the quadrupole tensor is dependent on the fragment orientation as provided by the fragment coordinates.

• The octupole moments are given in the Buckingham form, e.g., xxx corresponds to \(a_x a_x a_x\), where a is a vector describing particle position. Conversion to the Cartesian form is conducted within LibEFP or GAMESS codes.

• The section ends with mandatory STOP line.

In the example below, $FRAGNAME ($nh3 in this case), COORDINATES, MONOPOLES, DIPOLES, QUADRUPOLES, OCTUPOLES sections are highlighted.

          RUNTYP=MAKEFP EFFECTIVE FRAGMENT POTENTIAL DATA FOLLOWS...
          FRAGNAMEEFP GENERATED AT Sat Dec 10 15:44:05 2022
 $nh3
EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX
 COORDINATES (BOHR)
A01N       0.0000000000   0.0000000000  -0.1190788329  14.0030700  7.0
A02H      -1.5998498006   0.6978969618   0.5515075313   1.0078250  1.0
A03H       1.4043213984   1.0365620887   0.5515075313   1.0078250  1.0
A04H       0.1955284022  -1.7344590505   0.5515075313   1.0078250  1.0
BO21      -0.7999249003   0.3489484809   0.2162143492   0.0000000  0.0
BO31       0.7021606992   0.5182810443   0.2162143492   0.0000000  0.0
BO41       0.0977642011  -0.8672295252   0.2162143492   0.0000000  0.0
 STOP
 MONOPOLES 
A01N      -7.3243188890   7.00000
A02H      -0.6687876199   1.00000
A03H      -0.6687876199   1.00000
A04H      -0.6687876199   1.00000
BO21      -0.2231060838   0.00000
BO31      -0.2231060838   0.00000
BO41      -0.2231060838   0.00000
 STOP
 DIPOLES 
A01N       -0.0000000000    0.0000000000    0.2736428914
A02H       -0.0499270117    0.0217794882    0.0113925498
A03H        0.0438250959    0.0323483164    0.0113925498
A04H        0.0061019158   -0.0541278045    0.0113925498
BO21        0.1736798191   -0.0757637486   -0.0038087063
BO31       -0.1524532405   -0.1125292612   -0.0038087063
BO41       -0.0212265786    0.1882930098   -0.0038087063
 STOP
 QUADRUPOLES 
A01N       -4.3696813753   -4.3696813753   -5.8536961016   -0.0000000000 >
            0.0000000000   -0.0000000000
A02H       -0.3443573873   -0.3486092962   -0.3462279849   -0.0022907014 >
           -0.0051656323    0.0022533859
A03H       -0.3455625134   -0.3474041701   -0.3462279849    0.0029864812 >
            0.0045343056    0.0033468758
A04H       -0.3495301245   -0.3434365589   -0.3462279849   -0.0006957799 >
            0.0006313267   -0.0056002617
BO21       -0.0599289578   -0.0799073136   -0.0952457439   -0.0107632709 >
           -0.0063071060    0.0027513271
BO31       -0.0655914587   -0.0742448128   -0.0952457439    0.0140325173 >
            0.0055362722    0.0040864505
BO41       -0.0842339906   -0.0556022808   -0.0952457439   -0.0032692464 >
            0.0007708338   -0.0068377776
 STOP
 OCTUPOLES  
A01N          0.023087929      0.065944727      0.426940863     -0.065944727 >
              0.117018335     -0.023087929      0.117018335      0.000000000 >
             -0.000000000      0.000000000
A02H         -0.063695493      0.031880814      0.012702640      0.005890173 >
             -0.001214362     -0.022890221      0.003577870     -0.022180921 >
              0.009675907      0.002581799
A03H          0.058246411      0.045627524      0.012702640      0.010472410 >
              0.000143909      0.017757080      0.002219599      0.019470041 >
              0.014371288     -0.003365997
A04H          0.009180459     -0.066850618      0.012702640     -0.027020304 >
              0.004615716      0.001401763     -0.002252207      0.002710879 >
             -0.024047194      0.000784198
BO21          0.599193840     -0.263116162      0.032938337     -0.085702140 >
              0.012148985      0.200432638      0.014924642      0.197106829 >
             -0.085983232      0.001495376
BO31         -0.526950080     -0.390068205      0.032938337     -0.128019487 >
              0.012935695     -0.174948669      0.014137933     -0.173017078 >
             -0.127707905     -0.001949582
BO41         -0.073821815      0.648677060      0.032938337      0.218228934 >
              0.015525761     -0.023905914      0.011547866     -0.024089751 >
              0.213691137      0.000454207
 STOP

SCREEN and SCREEN2

• SCREEN and SCREEN2 sections provide screening parameters to account for charge-penetration energy between QM and EFP regions (SCREEN) and between EFP fragments (SCREEN2).

• Both sections are optional.

• Each line contains name tag and \(\alpha\) and \(\beta\) parameters that effectively screen EFP electronic charges.

  For QM-EFP interactions (SCREEN): \(q_A \rightarrow _A(1-\alpha \exp(-\beta (r_A-r_e)^2))\), where \(r_e\) is position of an electron.

  For EFP-EFP interactions (SCREEN2): \(q_A \rightarrow _A(1-\alpha \exp(-\beta (r_A-r_B)))\), where \(r_B\) is position of another charge.

  \(\alpha\) parameters in both cases are typically set to 1.

• SCREEN and SCREEN2 sections are typically found in the very end of .efp file, even though exact placement of sections can be varied by user.

• Name tags should match those in COORDINATES section.

• Sections can contain less atoms/bond midpoints than COORDINATES section.

• Each section ends with mandatory STOP line.

SCREEN2      (FROM VDWSCL=   0.700)
 A01N       1.000000000   1.624352412
 A02H       1.000000000   2.785518573
 A03H       1.000000000   3.110587808
 A04H       1.000000000   3.098409474
 BO21       1.000000000   6.053889393
 BO31       1.000000000  10.000000000
 BO41       1.000000000  10.000000000
STOP
SCREEN       (FROM VDWSCL=   0.700)
 A01N       1.000000000   0.760652041
 A02H       1.000000000   1.018858487
 A03H       1.000000000   1.057200085
 A04H       1.000000000   1.054696149
 BO21       1.000000000  10.088209433
 BO31       1.000000000  10.000000000
 BO41       1.000000000  10.000000000
STOP
 $END

POLARIZABLE POINTS

• POLARIZABLE POINTS section provides coordinates and values of anisotropic polarizability tensors for computing polarization energy.

• The section is optional.

• The group contains a set of two-line entries each containing:

  • first line: polarizable point tag, x, y, z coordinates of the point (in Bohr)

  • second line: XX, YY, ZZ, XY, XZ, YZ, YX, ZX, ZY elements of the polarizability tensor

• The section ends with mandatory STOP line.

• Coordinates of the polarizability points and orientations of polarizability tensors are given with respect to the fragment coordinate frame as given in COORDINATES.

• Typically coordinates of polarizability points are centroids of the localized molecular orbitals, but other choices (e.g., atom positions) are possible.

DYNAMIC POLARIZABLE POINTS

• DYNAMIC POLARIZABLE POINTS section provides coordinates and values of anisotropic dynamic polarizability tensors for computing dispersion energy.

• The section is optional.

• The group contains twelve entries each similar to the POLARIZABLE POINTS section, i.e., each containing multiple sets of two-line entries:

  • first line: polarizable point tag, x, y, z coordinates of the point (in Bohr)

  • second line: XX, YY, ZZ, XY, XZ, YZ, YX, ZX, ZY elements of the dynamic polarizability tensor

  Each of these 12 sets contains time-dependent (dynamic) polarizabilities computed at given values of imaginary frequencies. Coordinates of polarizability points remain the same between all twelve sets.

• The section ends with mandatory STOP line.

• Coordinates of the dynamic polarizability points and orientations of tensors are given with respect to the fragment coordinate frame as given in COORDINATES.

• Typically coordinates of dynamic polarizability points are centroids of the localized molecular orbitals, but other choices (e.g., atom positions) are possible.

• Only first three elements (XX, YY, ZZ) of the tensors are used in calculation of the \(\frac{C_6}{R^6}\) dispersion energy (the one implemented in LibEFP).

 POLARIZABLE POINTS
CT1  -0.9650292512   0.4209713827   0.3161330289
    3.5468464622    1.3266142599    1.1332988876   -1.1962568619 >
   -1.3009405693    0.5675525723   -1.1964374523   -1.2419548605 >
    0.5417403247
CT2   0.1179427138  -1.0462255382   0.3161330290
    0.8455408832    4.0280072355    1.1332988881   -0.3633659575 >
    0.1590054944   -1.4102796405   -0.3633872275    0.1518165472 >
   -1.3464346223
CT3   0.8470865372   0.6252541554   0.3161330294
    2.9174983534    1.9558680889    1.1332988894    1.5595878449 >
    1.1419350762    0.8427270687    1.5595626025    1.0901383149 >
    0.8046942983
CT4   0.0000000002   0.0000000001  -0.7882271310
    1.7193643981    1.7192501115    5.9821499943    0.0000068731 >
   -0.0000000013   -0.0000000005    0.0001243872   -0.0000000017 >
   -0.0000000007
 STOP
 DYNAMIC POLARIZABLE POINTS
CT  1  -0.9650292512   0.4209713827   0.3161330289 -- FOR W= 0.002792I A.U.
    3.5468331653    1.3264064658    1.1333208209   -1.1962472920 >
   -1.3009786346    0.5675214234   -1.1962472920   -1.2420029348 >
    0.5417946573
CT  2   0.1179427138  -1.0462255382   0.3161330290
    0.8455325960    4.0277070350    1.1333208213   -0.3633493178 >
    0.1590013479   -1.4104412593   -0.3633493178    0.1517935310 >
   -1.3465034222
CT  3   0.8470865372   0.6252541554   0.3161330294
    2.9174936840    1.9557459444    1.1333208227    1.5595966112 >
    1.1419772880    0.8429198365    1.5595966112    1.0902094055 >
    0.8047087656
CT  4   0.0000000002   0.0000000001  -0.7882271310
    1.7193402431    1.7193402433    5.9814558166   -0.0000000014 >
   -0.0000000013   -0.0000000005   -0.0000000014   -0.0000000017 >
   -0.0000000007
CT  1  -0.9650292512   0.4209713827   0.3161330289 -- FOR W= 0.015107I A.U.
    3.5447871587    1.3259797791    1.1325371132   -1.1953748890 >
   -1.3000577587    0.5671197128   -1.1953748890   -1.2404763132 >
    0.5411287044
CT  2   0.1179427138  -1.0462255382   0.3161330290
    0.8454566025    4.0253103351    1.1325371136   -0.3630843332 >
    0.1588888015   -1.4094429021   -0.3630843332    0.1516069523 >
   -1.3448483526
CT  3   0.8470865372   0.6252541554   0.3161330294
    2.9159066440    1.9548602909    1.1325371150    1.5584592236 >
    1.1411689585    0.8423231898    1.5584592236    1.0888693625 >
    0.8037196489
CT  4   0.0000000002   0.0000000001  -0.7882271310
    1.7180716243    1.7180716245    5.9699691089   -0.0000000014 >
   -0.0000000013   -0.0000000005   -0.0000000014   -0.0000000017 >
   -0.0000000007
CT  1  -0.9650292512   0.4209713827   0.3161330289 -- FOR W= 0.039002I A.U.
    3.5328436557    1.3234825327    1.1279950490   -1.1902857505 >
   -1.2946847903    0.5647758814   -1.1902857505   -1.2316469988 >
    0.5372771230
CT  2   0.1179427138  -1.0462255382   0.3161330290
    0.8450051152    4.0113210731    1.1279950494   -0.3615385534 >
    0.1582321349   -1.4036178593   -0.3615385534    0.1505278625 >
   -1.3352761514
CT  3   0.8470865372   0.6252541554   0.3161330294
    2.9066405104    1.9496856753    1.1279950508    1.5518243053 >
    1.1364526567    0.8388419784    1.5518243053    1.0811191380 >
    0.7979990291
CT  4   0.0000000002   0.0000000001  -0.7882271310
    1.7106813261    1.7106813262    5.9037030573   -0.0000000014 >
   -0.0000000013   -0.0000000005   -0.0000000014   -0.0000000017 >
   -0.0000000007

PROJECTION BASIS SET

• PROJECTION BASIS SET section contains information on the basis set used in calculation of the exchange-repulsion energy and overlap-based electrostatic and dispersion dampings.

• The section is optional.

• Basis set information for all atoms of the fragment is given, separated by empty lines.

• The first line for each atom entry contains atom name tag that should match one from the COORDINATES section, x, y, z coordinates of the atom (in Bohr), and a number corresponding to the atom nuclear charge minus the number of electrons in core orbitals. For example, 5 = 7-2 for N, 4 = 6-2 for C, 1 = 1-0 for H etc. The following information on basis functions is given in the GAMESS basis set format.

• The section ends with mandatory STOP line.

 PROJECTION BASIS SET
A01N         0.0000000000   0.0000000000  -0.1190788329    5.0
   S          6
     1      4173.5114600000     0.67899792
     2       627.4579110000     1.25043140
     3       142.9020930000     2.02035647
     4        40.2343293000     2.64421231
     5        12.8202129000     2.26500482
     6         4.3904370100     0.77918790
   L          3
     7        11.6263618604    -0.51587465     2.06805186
     8         2.7162798073    -0.25502307     1.61001139
     9         0.7722183966     0.67273451     0.76449036
   L          1
    10         0.2120314975     0.22269495     0.20508815
   L          1
    11         0.0639000000     0.09058071     0.04579480
   D          1
    12         0.8000000000     1.11382493
  
A02H        -1.5998498006   0.6978969618   0.5515075313    1.0
   S          3
    13        18.7311369600     0.21493545
    14         2.8253943648     0.36457120
    15         0.6401216923     0.41505143
   S          1
    16         0.1612777588     0.18138065
  
A03H         1.4043213984   1.0365620887   0.5515075313    1.0
   S          3
    17        18.7311369600     0.21493545
    18         2.8253943648     0.36457120
    19         0.6401216923     0.41505143
   S          1
    20         0.1612777588     0.18138065
  
A04H         0.1955284022  -1.7344590505   0.5515075313    1.0
   S          3
    21        18.7311369600     0.21493545
    22         2.8253943648     0.36457120
    23         0.6401216923     0.41505143
   S          1
    24         0.1612777588     0.18138065
  
 STOP

MULTIPLICITY

• MULTIPLICITY section provides multiplicity of the fragment used in computing exchange-repulsion energy and overlap-based electrostatic and dispersion dampings.

• The section is optional.

• LibEFP works only with multiplicity 1 (closed shell fragments).

• The section ends with mandatory STOP line.

PROJECTION WAVEFUNCTION

• PROJECTION WAVEFUNCTION section provides localized wave function of the fragment used in computing exchange-repulsion energy and overlap-based electrostatic and dispersion dampings.

• The section is optional.

• Format: first line contains PROJECTION WAVEFUNCTION keyword, \(N_{loc}\)- number of the localized occupied orbitals (core orbitals are excluded), \(N_{basis}\) size of the basis set. The following lines provide orbital coefficients for each orbital. Each line contains orbital number, line number for the given orbital, five orbital coefficients not separated by comma. These entries are format sensitive!

• The number of orbital entries should match \(N_{loc}\) (the first number in the first line).

• The number of orbital coefficients for each orbital should match \(N_{basis}\) (the second number in the first line).

• Note: the section does not require STOP line.

FOCK MATRIX ELEMENTS

• FOCK MATRIX ELEMENTS section provides elements of the Fock matrix of the fragment in the localized basis. It is used in computing exchange-repulsion energy and overlap-based electrostatic and dispersion dampings.

• The section is optional.

• The Fock matrix is given in the lower triangular form, i.e., the matrix \(\begin{pmatrix} a_{11} & a_{12} & a_{13}\\ a_{21} & a_{22} & a_{23}\\ a_{31} & a_{32} & a_{33} \end{pmatrix}\) is provided as \(a_{11}\), \(a_{21}\), \(a_{22}\), \(a_{31}\), \(a_{32}\), \(a_{33}\).

• The size of the matrix is \(N_{loc} \times N_{loc}\), i.e. \(N_{loc} * (N_{loc}-1)\) values is expected.

• Note: the section does not require STOP line.

LMO CENTROIDS

• LMO CENTROIDS section provides coordinates of the localized molecular orbital centroids. Those are used in computing exchange-repulsion energy and overlap-based electrostatic and dispersion dampings.

• The section is optional.

• Each line contains a centroid tag name and x, y, z coordinates (in Bohr) of the centroid, with respect to the fragment reference frame as given in COORDINATES section.

• The number of centroids should match \(N_{loc}\) (the number of the localized occupied orbitals) in PROJECTION WAVEFUNCTION section.

• The section ends with mandatory STOP line.

 MULTIPLICITY    1
 STOP
 PROJECTION WAVEFUNCTION      4     25
 1  1-9.71883850E-02 1.96133060E-01-3.58609534E-01 1.56435001E-01 1.53489937E-01
 1  2 2.06117088E-01-2.07887556E-01 9.06860717E-02 1.17293141E-01 3.01362608E-02
 1  3-3.44148857E-03 1.50126869E-03 2.40265023E-02 1.77629851E-02-6.23523419E-03
 1  4 4.04858946E-03-1.49290754E-02-2.86240183E-02 1.24865568E-02 3.16057922E-01
 1  5 1.12446012E-01-2.46559058E-02-6.91992834E-02-2.46559059E-02-6.91992835E-02
 2  1-9.71883850E-02 1.96133060E-01 4.38280823E-02-3.88782467E-01 1.53489937E-01
 2  2 2.06117088E-01 2.54073359E-02-2.25378940E-01 1.17293141E-01 3.01362609E-02
 2  3 4.20607457E-04-3.73105088E-03 2.40265023E-02-1.14324859E-02 2.29602368E-02
 2  4 4.04858947E-03-4.53457194E-03 3.49833373E-03-3.10324054E-02-2.46559057E-02
 2  5-6.91992834E-02-2.46559060E-02-6.91992835E-02 3.16057922E-01 1.12446012E-01
 3  1 9.71883850E-02-1.96133060E-01-3.14781452E-01-2.32347466E-01-1.53489937E-01
 3  2-2.06117088E-01-1.82480220E-01-1.34692869E-01-1.17293141E-01-3.01362609E-02
 3  3-3.02088111E-03-2.22978218E-03-2.40265024E-02-1.09611272E-02-5.66623710E-04
 3  4-4.04858949E-03-1.94636473E-02-2.51256845E-02-1.85458486E-02 2.46559058E-02
 3  5 6.91992835E-02-3.16057922E-01-1.12446012E-01 2.46559056E-02 6.91992834E-02
 4  1-1.20039612E-01 2.75355932E-01 2.14576633E-10 8.82155725E-11-4.95490080E-01
 4  2 3.25364386E-01 1.24391037E-10 5.11389632E-11-4.15288097E-01-1.58914633E-02
 4  3 2.05923981E-12 8.46583416E-13-9.61820864E-02 1.74055845E-02 1.74055845E-02
 4  4-2.53742792E-02 1.20606819E-11 1.71273903E-11 7.04131910E-12-1.44489768E-02
 4  5-8.28234255E-03-1.44489766E-02-8.28234243E-03-1.44489767E-02-8.28234252E-03
 FOCK MATRIX ELEMENTS
   -0.7883193745   -0.1439922994   -0.7883193745    0.1439922995 >
    0.1439922995   -0.7883193746   -0.1315378524   -0.1315378524 >
    0.1315378526   -0.5045574870
 LMO CENTROIDS
CT1  -0.9650292512   0.4209713827   0.3161330289
CT2   0.1179427138  -1.0462255382   0.3161330290
CT3   0.8470865372   0.6252541554   0.3161330294
CT4   0.0000000002   0.0000000001  -0.7882271310
 STOP

Additional .efp parameters

POLAB

• POLAB is a keyword specifying a short-range polarization damping parameter for the fragment.

• The section is optional.

• This section is not included in the .efp as prepared by the MAKEFP run and should be added manually if needed.

• The section format is: POLAB value, followed by the mandatory STOP line, where value is the user-specified value of the parameter.

• Default value is 0.6.

Some wisdom on a choice of the POLAB parameter:

• polab = 0.6 (default) - works well for the majority of neutral solvents;

• polab = 0.3 might improve stability of BioEFP calculations in proteins, especially relevant for charged amino acids;

• polab = 0.1 was shown to work safely for anions like F-, Cl-, etc;

• polab = 0.1 might be useful for large aromatics like porphyrins and chlorophylls (their polarizabilities are huge and orbital localization schemes often struggle, resulting in very large ~100 a.u. polarizabilities on some sites);

• polab = 0.03 for Li+, Na+ and Mg2+.

MM_CHARGE

• MM_CHARGE provides atomic charges, typically matching partial charges in classical MM calculations.

• Each line contains name tag and partial charge.

• Name tags should match those in COORDINATES section.

• The section is optional.

• This section is not included in the .efp as prepared by the MAKEFP run and should be added manually if needed.

• The section ends with mandatory STOP line.

MM_LJ

• MM_LJ provides atomic Lennard-Jones parameters as in classical MM calculations.

• Each line contains name tag, \(\sigma\), and \(\epsilon\).

• Name tags should match those in COORDINATES section.

• The section is optional.

• This section is not included in the .efp as prepared by the MAKEFP run and should be added manually if needed.

• The section ends with mandatory STOP line.

• GROMACS units are assumed: \(\sigma\) in nm, \(\epsilon\) in kJ/mol.

Currently, the Lennard-Jones energy is computed as

\[E_{ij} = 4*\epsilon_{ij}*( (\frac{\sigma_{ij}}{r})^{12} - (\frac{\sigma_{ij}}{r})^6 )\]

using the following comboination rules

\[ \begin{align}\begin{aligned}\sigma_{ij} = 0.5 * (\sigma_i + \sigma_j)\\\epsilon_{ij} = \sqrt{\epsilon_i * \epsilon_j}\end{aligned}\end{align} \]

MM_CHARGE
A01O     -0.834
A02H      0.417 
A03H      0.417
STOP
MM_LJ  
A01O    0.315057422683  0.6363864   
A02H    0.040001352445  0.1924640
A03H    0.040001352445  0.1924640
STOP