Long Range and Short Range Potentials

DATA File for Long Range and Short Range Interactions

INFORMATION

This file contains the long range and short range interactions.

(Residue types : 1. Glycine, 2. Alanine, 3. Valine, 4. Isoleucine, 5. Leucine, 6. Serine, 7. Threonine, 8. Aspartate, 9. Asparagine, 10. Glutamate, 11. Glutamine, 12 Lysine, 13. Arginine, 14. Cysteine, 15. Methionine, 16. Phenylalanine, 17. Tyrosine, 18. Trptophan, 19. Histidine, 20. Proline, 21. Cysteine-Cysteine)

Long Range Interactions

The tabulated values are Eab(r) = Exx(r) + deltaEab(r), in RT units, for bins of size 0.4 Angstroms, starting from 2.0 +- 0.2 Angstroms. (For pairs not observed, the potential is set equal to 15 RT, as an upper bound, so as to avoid overflow)

Short Range Interactions

Singlet energies

Torsional energies are given for the range [-180¡, 180¡], at intervals of 30¡, starting from f+ = f- = -180¡. Bond angle (q) energies are given in [60, 170¡], at intervals of 10¡. All energies are in units of RT. 10 RT is set as an upper bound, to avoid overflow.

Doublet energies Results are listed in matrix form for each type of residue.Torsional angles vary in the range [-180, 180], at intervals of 30; bond angles in [60, 180], at intervals of 10 degrees, such that the (1,2) element of E(q,f+),for example, corresponds to q = 60 and f+ = -150 degrees. All energies are in RT units. A value of 6.0 RT is assigned to pairs not observed. EA(f+,f-)/RT

A Fourtan code to read the potentials:

subroutine readenergies(enss,ensb,enbb,efixr,efirx,etheta,
:edoub,edoub2,edoub3)

real enss(21,21,400),ensb(21,400),enbb(400)
real efixr(21,13),efirx(21,13),etheta(21,13)
real edoub(21,13,13),edoub2(21,13,13),edoub3(21,13,13)

c READING DATAFILES

open (unit=1,file='../../energies.dat')
do 6644 i=1,21
do 6644 j=1,21
do 6647 mmm=1,28
6647read(1,*) ik,jk,enss(i,j,mmm+5)
do 5748 mmm=34,400
5748enss(i,j,mmm)=0.
do 6651 mmm=1,5
6651enss(i,j,mmm)=15.
6644continue
do 6645 i=1,21
do 6649 mmm=1,28
6649read(1,*) ik,ensb(i,mmm+5)
do 6548 mmm=34,400
6548ensb(i,mmm)=0.
do 6652 mmm=1,5
6652ensb(i,mmm)=15.
6645continue

do 6646 mmm=1,28
6646 read(1,*) ik,enbb(mmm+5)
do 6650 mmm=34,400
6650enbb(mmm)=0.
do 6654 mmm=1,5
6654enbb(mmm)=15.
do 69 ij=1,21 do 69 k=1,13
read(1,*) ik,efirx(ij,k),efixr(ij,k),etheta(ij,k)
69continue
do 7731 ij=1,21
do 7731 k=1,13
do 7731 m=1,13
read(1,*)iik,kk,mk,edoub(ij,k,m),edoub2(ij,k,m),edoub3(ij,k,m)
7731write(202,*)edoub3(ij,k,m),ij,k,m

c Here at the end of this read file the following variables are found:

c 1. enss(jres1,jres2,mmm) for s-s interactions between jres1&jres2
c 2. ensb(jres1,mmm) for s-b interactions between jres1& backbone
c 3. enbb(mmm) for b-b interactions (backbone & backbone)
c mmm=6 refers to dist=2.0+-0.2, mmm=7 for dist=2.4+-0.2 Angstroms, etc.
c 1. efirx(jres,mmm) (fi+) mmm=1 refers to {-195, -165]
c 2. efixr(jres,mmm) (fi-) mmm=1 refers to {-195, -165]
c 3. etheta(jres,mmm) (the) mmm=1 refers to {-65, -55]
c 4. edoub(jres,mm,mm') extra (mm, mm') -> (fi+, fi-)
c 5. edoub2(jres,mm,mm') extra (mm, mm') -> (theta, fi-)
c 6. edoub2(jres,mm,mm') extra (mm, mm') -> (theta, fi+)

close(1)
return
end

File Format

The first 3 columns from 1 1 12.6265 to 21 21 1.5545 give the long range side-chain side chain interactions.

Following 2 columns from 1 20.0 to 21 0.180 give the long range side chain-backbone interactions.

The two columns 22 7.626 to 22 0.0 give the long range backbone-backbone interactions.

Following 4 columns starting from 1 0.6337238 0.1423162 5.286160

to 21 1.542229 0.7519877 10.00000 give the short range singlet energies

and 6 columns starting from 1 1 1 -0.380727 10.000000 10.000000
to 21 13 13 -0.380727 10.000000 10.000000 give the short range doublet energies.