| 1 | ! *********************************************************************
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| 2 | ! This file contains eyrccr, init_abgn, eyentr, eyabgn
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| 3 | !
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| 4 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 5 | ! Jan H. Meinke, Sandipan Mohanty
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| 6 | !
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| 7 | ! Corrections to ECEPP energy terms due to R. A. Abagyan et al.
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| 8 | !
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| 9 | ! Two terms are calculated: eyrccr and eyentr, representing respectively
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| 10 | ! c a term to slightly shift the backbone dihedral angle preferences in
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| 11 | ! the ECEPP potential slightly away from the helix region, and another
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| 12 | ! term to estimate the side-chain entropy from a given configuration.
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| 13 | !
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| 14 | !
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| 15 | ! *********************************************************************
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| 16 | real*8 function eyrccr(nml)
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| 17 | include 'INCL.H'
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| 18 | double precision et, rsscl
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| 19 |
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| 20 | integer nml, istres, indres, i, ipsi, in, ica, ic, mlvr, iphi
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| 21 |
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| 22 | dimension iN(mxrs),iCa(mxrs),iC(mxrs),mlvr(mxvr)
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| 23 | dimension iphi(mxrs),ipsi(mxrs)
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| 24 | common /lundds/iN,iCa,iC,mlvr,iphi,ipsi
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| 25 | character mynm*4
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| 26 |
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| 27 | if (nml.eq.0) then
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| 28 | istres=irsml1(1)
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| 29 | indres=irsml2(ntlml)
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| 30 | else
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| 31 | istres=irsml1(nml)
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| 32 | indres=irsml2(nml)
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| 33 | endif
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| 34 | et=0.0
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| 35 | ! print *,'***********'
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| 36 | do i=istres,indres
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| 37 | mynm=seq(i)
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| 38 | call tolost(mynm)
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| 39 | if ((mynm.eq.'val').or.(mynm.eq.'ile').or.
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| 40 | & (mynm.eq.'thr')) then
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| 41 | rsscl=1.0
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| 42 | else
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| 43 | rsscl=0.5
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| 44 | endif
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| 45 | et=et+rsscl*(1.0-sin(vlvr(ipsi(i))))
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| 46 | ! print *,' contribution = ',rsscl*(1.0-sin(vlvr(ipsi(i))))
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| 47 | ! print *,'obtained using scale ',rsscl,' and angle ',
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| 48 | ! # vlvr(ipsi(i))
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| 49 | enddo
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| 50 | ! print *,'abagyan dihedral term = ',et
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| 51 | ! print *,'***********'
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| 52 | eyrccr=et
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| 53 | return
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| 54 | end
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| 55 |
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| 56 | subroutine init_abgn
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| 57 | include 'INCL.H'
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| 58 | ! dimension rsstrg(mxrs)
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| 59 | ! common /abgncor/rsstrg
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| 60 | double precision xarea, estrg
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| 61 |
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| 62 | integer i, istres, indres, imytyp, j
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| 63 |
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| 64 | dimension xarea(nrsty),estrg(nrsty)
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| 65 | character mynm*4
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| 66 | ! print *,'Initialization of Abagyan entropic term'
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| 67 | ! Maximum accessible surface areas for different residue types
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| 68 | data (xarea(i),i=1,nrsty)/
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| 69 | ! 1 2 3 4 5
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| 70 | & 117.417 , 244.686 , 245.582 , 146.467 , 144.485 ,
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| 71 | ! 6 7 8 9 10
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| 72 | & 144.192 , 142.805 , 147.568 , 183.103 , 177.094 ,
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| 73 | ! 11 12 13 14 15
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| 74 | & 186.293 , 83.782 , 187.864 , 187.864 , 187.864 ,
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| 75 | ! 16 17 18 19 20
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| 76 | & 187.864 , 160.887 , 161.741 , 184.644 , 179.334 ,
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| 77 | ! 21 22 23 24 25
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| 78 | & 209.276 , 209.276 , 203.148 , 208.902 , 153.124 ,
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| 79 | ! 26 27 28 29 30
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| 80 | & 153.973 , 153.037 , 158.695 , 157.504 , 157.504 ,
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| 81 | ! 31 32 33 34 35
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| 82 | & 119.786 , 146.488 , 238.641 , 223.299 , 160.283 /
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| 83 | ! Entropic contribution for maximally exposed residue
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| 84 | data (estrg(i),i=1,nrsty)/
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| 85 | ! 1ala 2arg 3arg+ 4asn 5asp
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| 86 | & 0.0 , 2.13 , 2.13 , 0.81 , 0.61 ,
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| 87 | ! 6asp- 7cys 8cyss 9gln 10glu
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| 88 | & 0.61 , 1.14 , 1.14 , 2.02 , 1.65 ,
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| 89 | ! 11glu- 12gly 13his 14hise 15hisd
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| 90 | & 1.65 , 0.0 , 0.99 , 0.99 , 0.99 ,
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| 91 | ! 16his+ 17hyp 18hypu 19ile 20leu
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| 92 | & 0.99 , 0.99 , 0.99 , 0.75 , 0.75 ,
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| 93 | ! 21lys 22lys+ 23met 24phe 25cpro
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| 94 | & 2.21 , 2.21 , 1.53 , 0.58 , 0.0 ,
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| 95 | ! 26pro 27cpru 28prou 29pron 30pro+
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| 96 | & 0.0 , 0.0 , 0.0 , 0.0 , 0.0 ,
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| 97 | ! 31ser 32thr 33trp 34tyr 35val
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| 98 | & 1.19 , 1.12 , 0.97 , 0.99 , 0.50 /
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| 99 | do i=1,mxrs
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| 100 | rsstrg(i)=0.0
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| 101 | enddo
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| 102 | istres=irsml1(1)
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| 103 | indres=irsml2(ntlml)
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| 104 | do i=istres,indres
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| 105 | imytyp=0
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| 106 | mynm=seq(i)
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| 107 | call tolost(mynm)
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| 108 | do j=1,nrsty
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| 109 | if (rsnmcd(j).eq.mynm) imytyp=j
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| 110 | ! print *,'comparing ',mynm,' with ',rsnmcd(j),imytyp
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| 111 | enddo
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| 112 | if (imytyp.eq.0) then
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| 113 | print *, 'Unknown residue type ',seq(i)
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| 114 | print *, 'Abagyan term strength set to 0'
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| 115 | rsstrg(i)=0.0
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| 116 | else
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| 117 | rsstrg(i)=estrg(imytyp)/xarea(imytyp)
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| 118 | endif
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| 119 | ! print *,'residue ',i,seq(i),' type ',imytyp
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| 120 | ! print *, 'strength for residue ',i,seq(i),' is ',rsstrg(i)
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| 121 | enddo
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| 122 | print *, 'initialized Abagyan corrections to ECEPP force field'
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| 123 | end
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| 124 |
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| 125 | real*8 function eyentr(nml)
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| 126 | include 'INCL.H'
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| 127 | ! dimension rsstrg(mxrs)
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| 128 | ! common /abgncor/rsstrg
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| 129 | ! common/ressurf/surfres(mxrs)
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| 130 | ! common/bet/beta
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| 131 | double precision eentr, aars, strh
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| 132 |
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| 133 | integer nml, istres, indres, i
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| 134 |
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| 135 | eentr=0
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| 136 | if (nml.eq.0) then
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| 137 | istres=irsml1(1)
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| 138 | indres=irsml2(ntlml)
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| 139 | else
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| 140 | istres=irsml1(nml)
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| 141 | indres=irsml2(nml)
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| 142 | endif
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| 143 | ! print *,'residue range ',istres,indres
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| 144 | ! print *,'for molecule ',nml
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| 145 | do i=istres, indres
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| 146 | aars=surfres(i)
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| 147 | strh=rsstrg(i)
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| 148 | ! The maximal burial entropies were estimated at temperature 300k
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| 149 | ! The values in the array estrg are k_B * T (=300k) * Entropy
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| 150 | ! Presently we need it at temperature 1/beta, so we need to
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| 151 | ! multiply the strengths in estrg with (1/beta)/(300 kelvin)
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| 152 | ! 300 kelvin is approximately 0.59576607 kcal/mol.
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| 153 | eentr=eentr+aars*strh/(0.59576607*beta)
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| 154 | ! print *,'contribution = ',aars*strh/(0.59576607*beta)
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| 155 | ! print *,'residue, exposed area = ',i,aars
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| 156 | ! print *,'strength = ',strh,' for residue index = ',i
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| 157 | ! print *,'beta = ',beta
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| 158 | enddo
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| 159 | ! print *,'abagyan entropic term = ',eentr
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| 160 | eyentr=eentr
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| 161 | return
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| 162 | end
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| 163 |
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| 164 | real*8 function eyabgn(nml)
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| 165 | include 'INCL.H'
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| 166 | double precision eyrccr, eyentr
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| 167 |
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| 168 | integer nml
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| 169 |
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| 170 | eyabgn=eyrccr(nml)+eyentr(nml)
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| 171 | ! print *,'Abagyan term = ',eyabgn
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| 172 | return
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| 173 | end
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