| 1 | ! ****************************************************************
|
|---|
| 2 | ! Trial version implementing the semi-local conformational update
|
|---|
| 3 | ! BGS (Biased Gaussian Steps). This file presently contains the
|
|---|
| 4 | ! functions initlund, bgsposs and bgs.
|
|---|
| 5 | !
|
|---|
| 6 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
|
|---|
| 7 | ! Jan H. Meinke, Sandipan Mohanty
|
|---|
| 8 | ! ****************************************************************
|
|---|
| 9 |
|
|---|
| 10 | ! Subroutine initlund: Initializes data structures used frequently
|
|---|
| 11 | ! in connection with Biased Gaussian Steps and the energy functions
|
|---|
| 12 | ! from Anders Irback's protein folding model. Calls: none.
|
|---|
| 13 | !
|
|---|
| 14 | subroutine init_lund
|
|---|
| 15 | include 'INCL.H'
|
|---|
| 16 | include 'incl_lund.h'
|
|---|
| 17 | logical bgsposs
|
|---|
| 18 | do i=1,mxrs
|
|---|
| 19 | iN(i)=-1
|
|---|
| 20 | iCa(i)=-1
|
|---|
| 21 | iC(i)=-1
|
|---|
| 22 | iphi(i)=-34
|
|---|
| 23 | ipsi(i)=-35
|
|---|
| 24 | enddo
|
|---|
| 25 | ! print *,'total number of variables = ',nvr
|
|---|
| 26 |
|
|---|
| 27 | do i=1,ntlml
|
|---|
| 28 | npprs=1
|
|---|
| 29 | do j=ivrml1(i),ivrml1(i)+nvrml(i)-1
|
|---|
| 30 | mlvr(j)=i
|
|---|
| 31 | if (nmvr(j).eq.'phi') then
|
|---|
| 32 | iphi(npprs)=j
|
|---|
| 33 | ! Now if the residue is a proline, there is no phi angle in the variable
|
|---|
| 34 | ! list in SMMP, and so iphi(j) will remain at the initial value.
|
|---|
| 35 | ! So, make sure you never use iphi(i) for proline.
|
|---|
| 36 | endif
|
|---|
| 37 | if (nmvr(j).eq.'psi'.or.nmvr(j).eq.'pst') then
|
|---|
| 38 | ipsi(npprs)=j
|
|---|
| 39 | npprs=npprs+1
|
|---|
| 40 | endif
|
|---|
| 41 | enddo
|
|---|
| 42 | do j=irsml1(i),irsml2(i)
|
|---|
| 43 | iN(j)=iatrs1(j)
|
|---|
| 44 | do k=iatrs1(j),iatrs2(j)
|
|---|
| 45 | if (nmat(k)(1:2).eq.'ca') then
|
|---|
| 46 | iCa(j)=k
|
|---|
| 47 | endif
|
|---|
| 48 | if (nmat(k)(1:1).eq.'c') then
|
|---|
| 49 | iC(j)=k
|
|---|
| 50 | endif
|
|---|
| 51 | enddo
|
|---|
| 52 | ! print *,'determined phi,psi serial for residue',j,' as '
|
|---|
| 53 | ! # ,iphi(j),ipsi(j)
|
|---|
| 54 | enddo
|
|---|
| 55 | enddo
|
|---|
| 56 | abgs=300.0
|
|---|
| 57 | bbgs=10.0
|
|---|
| 58 | bgsnvar=0
|
|---|
| 59 | do i=1,nvr
|
|---|
| 60 | if (bgsposs(i)) then
|
|---|
| 61 | bgsnvar=bgsnvar+1
|
|---|
| 62 | bgsvar(bgsnvar)=i
|
|---|
| 63 | endif
|
|---|
| 64 | enddo
|
|---|
| 65 | end
|
|---|
| 66 |
|
|---|
| 67 | ! Checks if it is possible to perform a BGS update starting at the
|
|---|
| 68 | ! variable indexed ipos. Calls: none.
|
|---|
| 69 | logical function bgsposs(ips)
|
|---|
| 70 | include 'INCL.H'
|
|---|
| 71 | include 'incl_lund.h'
|
|---|
| 72 | logical ians
|
|---|
| 73 |
|
|---|
| 74 | jv=idvr(ips)
|
|---|
| 75 | iaa=nursvr(jv)
|
|---|
| 76 | ians=.true.
|
|---|
| 77 | ! print *,'evaluating bgs possibility for ',ips,nmvr(jv)
|
|---|
| 78 | if (nmvr(jv).ne.'phi') then
|
|---|
| 79 | ! print *,'bgs not possible because variable name is ',nmvr(jv)
|
|---|
| 80 | ians=.false.
|
|---|
| 81 | else if (iaa.gt.(irsml2(mlvr(jv))-3)) then
|
|---|
| 82 | ! print *,'bgs impossible, residue too close to end'
|
|---|
| 83 | ! print *,'iaa = ',iaa,' end = ',irsml2(mlvr(jv))
|
|---|
| 84 | ians=.false.
|
|---|
| 85 | else
|
|---|
| 86 | nnonfx=0
|
|---|
| 87 | do i=iaa,iaa+3
|
|---|
| 88 | if (iphi(i).gt.0) then
|
|---|
| 89 | if (.not.fxvr(iphi(i))) then
|
|---|
| 90 | nnonfx=nnonfx+1
|
|---|
| 91 | endif
|
|---|
| 92 | endif
|
|---|
| 93 | if (.not.fxvr(ipsi(i))) then
|
|---|
| 94 | nnonfx=nnonfx+1
|
|---|
| 95 | endif
|
|---|
| 96 | enddo
|
|---|
| 97 | if (nnonfx.lt.6) then
|
|---|
| 98 | ! print *,iaa,'bgs impossible because ndof = ',nnonfx
|
|---|
| 99 | ians=.false.
|
|---|
| 100 | endif
|
|---|
| 101 | endif
|
|---|
| 102 | if (ians) then
|
|---|
| 103 | ! print *,'bgs is possible for angle ',ips,jv,nmvr(jv)
|
|---|
| 104 | endif
|
|---|
| 105 | bgsposs=ians
|
|---|
| 106 | return
|
|---|
| 107 | end
|
|---|
| 108 |
|
|---|
| 109 | ! Biased Gaussian Steps. Implements a semi-local conformational update
|
|---|
| 110 | ! which modifies the protein backbone locally in a certain range of
|
|---|
| 111 | ! amino acids. The 'down-stream' parts of the molecule outside the
|
|---|
| 112 | ! region of update get small rigid body translations and rotations.
|
|---|
| 113 | !
|
|---|
| 114 | ! Use the update sparingly. It is rather local, and is not of great
|
|---|
| 115 | ! value if we need big changes in the conformation. It is recommended
|
|---|
| 116 | ! that this update be used to refine a structure around a low energy
|
|---|
| 117 | ! candidate structure. Even at low energies, if you always
|
|---|
| 118 | ! perform BGS, the chances of coming out of that minimum are small.
|
|---|
| 119 | ! So, there is a probability bgsprob, which decides whether BGS or the
|
|---|
| 120 | ! normal single angle update is used.
|
|---|
| 121 | !
|
|---|
| 122 | ! Calls: energy, dummy (function provided as argument), addang, (rand)
|
|---|
| 123 | !
|
|---|
| 124 |
|
|---|
| 125 | integer function bgs(eol1,dummy)
|
|---|
| 126 | include 'INCL.H'
|
|---|
| 127 | include 'incl_lund.h'
|
|---|
| 128 | external dummy
|
|---|
| 129 | dimension xiv(8,3),bv(8,3),rv(3,3),dv(3,8,3)
|
|---|
| 130 | dimension ab(8), A(8,8),p(8),ppsi(8)
|
|---|
| 131 | double precision ovr(mxvr)
|
|---|
| 132 | ! Initialize
|
|---|
| 133 | ! print *,'using BGS on angle ',nmvr(idvr(ivar))
|
|---|
| 134 | if (bgsnvar.eq.0) then
|
|---|
| 135 | bgs=0
|
|---|
| 136 | goto 171
|
|---|
| 137 | endif
|
|---|
| 138 | ivar=1+grnd()*bgsnvar
|
|---|
| 139 | do i=1,8
|
|---|
| 140 | iph(i)=-50000
|
|---|
| 141 | dph(i)=0
|
|---|
| 142 | enddo
|
|---|
| 143 | nph=0
|
|---|
| 144 | jv=idvr(ivar)
|
|---|
| 145 | ia=nursvr(jv)
|
|---|
| 146 | ! Get BGS matrices based on coordinates of atoms in 4 amino acids
|
|---|
| 147 | do i=1,4
|
|---|
| 148 | icurraa=ia+i-1
|
|---|
| 149 | if (iphi(icurraa).gt.0.and..not.fxvr(iphi(icurraa))) then
|
|---|
| 150 | nph=nph+1
|
|---|
| 151 | xiv(nph,1)=xat(iCa(icurraa))
|
|---|
| 152 | xiv(nph,2)=yat(iCa(icurraa))
|
|---|
| 153 | xiv(nph,3)=zat(iCa(icurraa))
|
|---|
| 154 | bv(nph,1)=xiv(nph,1)-xat(iN(icurraa))
|
|---|
| 155 | bv(nph,2)=xiv(nph,2)-yat(iN(icurraa))
|
|---|
| 156 | bv(nph,3)=xiv(nph,3)-zat(iN(icurraa))
|
|---|
| 157 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
|
|---|
| 158 | & +bv(nph,3)*bv(nph,3)
|
|---|
| 159 | iph(nph)=iphi(icurraa)
|
|---|
| 160 | endif
|
|---|
| 161 | if (.not.fxvr(ipsi(icurraa))) then
|
|---|
| 162 | nph=nph+1
|
|---|
| 163 | xiv(nph,1)=xat(iC(icurraa))
|
|---|
| 164 | xiv(nph,2)=yat(iC(icurraa))
|
|---|
| 165 | xiv(nph,3)=zat(iC(icurraa))
|
|---|
| 166 | bv(nph,1)=xiv(nph,1)-xat(iCa(icurraa))
|
|---|
| 167 | bv(nph,2)=xiv(nph,2)-yat(iCa(icurraa))
|
|---|
| 168 | bv(nph,3)=xiv(nph,3)-zat(iCa(icurraa))
|
|---|
| 169 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
|
|---|
| 170 | & +bv(nph,3)*bv(nph,3)
|
|---|
| 171 | iph(nph)=ipsi(icurraa)
|
|---|
| 172 | endif
|
|---|
| 173 | enddo
|
|---|
| 174 | rv(1,1)=xat(iCa(ia+3))
|
|---|
| 175 | rv(1,2)=yat(iCa(ia+3))
|
|---|
| 176 | rv(1,3)=zat(iCa(ia+3))
|
|---|
| 177 | rv(2,1)=xat(iC(ia+3))
|
|---|
| 178 | rv(2,2)=yat(iC(ia+3))
|
|---|
| 179 | rv(2,3)=zat(iC(ia+3))
|
|---|
| 180 | rv(3,1)=xat(iC(ia+3)+1)
|
|---|
| 181 | rv(3,2)=yat(iC(ia+3)+1)
|
|---|
| 182 | rv(3,3)=zat(iC(ia+3)+1)
|
|---|
| 183 |
|
|---|
| 184 | do i=1,3
|
|---|
| 185 | do j=1,nph
|
|---|
| 186 | dv(i,j,1)=(1.0/ab(j))*(bv(j,2)*(rv(i,3)-xiv(j,3))-
|
|---|
| 187 | & bv(j,3)*(rv(i,2)-xiv(j,2)))
|
|---|
| 188 | dv(i,j,2)=(-1.0/ab(j))*(bv(j,1)*(rv(i,3)-xiv(j,3))-
|
|---|
| 189 | & bv(j,3)*(rv(i,1)-xiv(j,1)))
|
|---|
| 190 | dv(i,j,3)=(1.0/ab(j))*(bv(j,1)*(rv(i,2)-xiv(j,2))-
|
|---|
| 191 | & bv(j,2)*(rv(i,1)-xiv(j,1)))
|
|---|
| 192 | enddo
|
|---|
| 193 | enddo
|
|---|
| 194 | do i=1,nph
|
|---|
| 195 | do j=i,nph
|
|---|
| 196 | A(i,j)=0
|
|---|
| 197 | do k=1,3
|
|---|
| 198 | do l=1,3
|
|---|
| 199 | A(i,j)=A(i,j)+dv(k,i,l)*(dv(k,j,l))
|
|---|
| 200 | enddo
|
|---|
| 201 | enddo
|
|---|
| 202 | A(i,j)=bbgs*A(i,j)
|
|---|
| 203 | if (i.eq.j) then
|
|---|
| 204 | A(i,j)=A(i,j)+1
|
|---|
| 205 | endif
|
|---|
| 206 | A(i,j)=0.5*abgs*A(i,j)
|
|---|
| 207 | enddo
|
|---|
| 208 | enddo
|
|---|
| 209 | do i=1,nph
|
|---|
| 210 | do j=i,nph
|
|---|
| 211 | sum=A(i,j)
|
|---|
| 212 | do k=i-1,1,-1
|
|---|
| 213 | sum=sum-A(i,k)*A(j,k)
|
|---|
| 214 | enddo
|
|---|
| 215 | if (i.eq.j) then
|
|---|
| 216 | p(i)=sqrt(sum)
|
|---|
| 217 | else
|
|---|
| 218 | A(j,i)=sum/p(i)
|
|---|
| 219 | endif
|
|---|
| 220 | enddo
|
|---|
| 221 | enddo
|
|---|
| 222 | ! Generate 8 Gaussian distributed small random angles
|
|---|
| 223 | do i=1,8,2
|
|---|
| 224 | r1=grnd()
|
|---|
| 225 | ! In the rare event that this random number is 0, just take the next
|
|---|
| 226 | if (r1.le.0) r1=grnd()
|
|---|
| 227 | r1=sqrt(-log(r1))
|
|---|
| 228 | r2=grnd()
|
|---|
| 229 | ppsi(i)=r1*cos(pi2*r2)
|
|---|
| 230 | ppsi(i+1)=r1*sin(pi2*r2)
|
|---|
| 231 | enddo
|
|---|
| 232 | do i=1,nph
|
|---|
| 233 | dph(i)=0
|
|---|
| 234 | enddo
|
|---|
| 235 | ! Solve lower triangular matrix to get dphi proposals
|
|---|
| 236 | do i=nph,1,-1
|
|---|
| 237 | sum=ppsi(i)
|
|---|
| 238 | do k=i+1,nph
|
|---|
| 239 | sum=sum-A(k,i)*dph(k)
|
|---|
| 240 | enddo
|
|---|
| 241 | dph(i)=sum/p(i)
|
|---|
| 242 | enddo
|
|---|
| 243 | ! Calculate intrinsic (non-Boltzmann) weight for forward process
|
|---|
| 244 | ! print *,'calculating intrinsic weight for forward process'
|
|---|
| 245 | sum=0
|
|---|
| 246 | do i=1,nph
|
|---|
| 247 | sum=sum+ppsi(i)*ppsi(i)
|
|---|
| 248 | enddo
|
|---|
| 249 | wfw=exp(-sum)
|
|---|
| 250 | do i=1,nph
|
|---|
| 251 | wfw=wfw*p(i)
|
|---|
| 252 | enddo
|
|---|
| 253 |
|
|---|
| 254 | ! Reconstruct chain and calculate new energy
|
|---|
| 255 | ! print *,'going to assign changes to the chain'
|
|---|
| 256 | ovr = vlvr
|
|---|
| 257 | do i=1,nph
|
|---|
| 258 | vlvr(iph(i))=addang(vlvr(iph(i)),dph(i))
|
|---|
| 259 | enddo
|
|---|
| 260 | enw = energy()
|
|---|
| 261 | ! Calculate weight for reverse process for detail balance
|
|---|
| 262 | ! print *,'proceeding to calculate weight for the reverse process'
|
|---|
| 263 | nph=0
|
|---|
| 264 | do i=1,4
|
|---|
| 265 | icurraa=ia+i-1
|
|---|
| 266 | if (iphi(icurraa).gt.0.and..not.fxvr(iphi(icurraa))) then
|
|---|
| 267 | nph=nph+1
|
|---|
| 268 | xiv(nph,1)=xat(iCa(icurraa))
|
|---|
| 269 | xiv(nph,2)=yat(iCa(icurraa))
|
|---|
| 270 | xiv(nph,3)=zat(iCa(icurraa))
|
|---|
| 271 | bv(nph,1)=xiv(nph,1)-xat(iN(icurraa))
|
|---|
| 272 | bv(nph,2)=xiv(nph,2)-yat(iN(icurraa))
|
|---|
| 273 | bv(nph,3)=xiv(nph,3)-zat(iN(icurraa))
|
|---|
| 274 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
|
|---|
| 275 | & +bv(nph,3)*bv(nph,3)
|
|---|
| 276 | iph(nph)=iphi(icurraa)
|
|---|
| 277 | endif
|
|---|
| 278 | if (.not.fxvr(ipsi(icurraa))) then
|
|---|
| 279 | nph=nph+1
|
|---|
| 280 | xiv(nph,1)=xat(iC(icurraa))
|
|---|
| 281 | xiv(nph,2)=yat(iC(icurraa))
|
|---|
| 282 | xiv(nph,3)=zat(iC(icurraa))
|
|---|
| 283 | bv(nph,1)=xiv(nph,1)-xat(iCa(icurraa))
|
|---|
| 284 | bv(nph,2)=xiv(nph,2)-yat(iCa(icurraa))
|
|---|
| 285 | bv(nph,3)=xiv(nph,3)-zat(iCa(icurraa))
|
|---|
| 286 | ab(nph)=bv(nph,1)*bv(nph,1)+bv(nph,2)*bv(nph,2)
|
|---|
| 287 | & +bv(nph,3)*bv(nph,3)
|
|---|
| 288 | iph(nph)=ipsi(icurraa)
|
|---|
| 289 | endif
|
|---|
| 290 | enddo
|
|---|
| 291 | rv(1,1)=xat(iCa(ia+3))
|
|---|
| 292 | rv(1,2)=yat(iCa(ia+3))
|
|---|
| 293 | rv(1,3)=zat(iCa(ia+3))
|
|---|
| 294 | rv(2,1)=xat(iC(ia+3))
|
|---|
| 295 | rv(2,2)=yat(iC(ia+3))
|
|---|
| 296 | rv(2,3)=zat(iC(ia+3))
|
|---|
| 297 | rv(3,1)=xat(iC(ia+3)+1)
|
|---|
| 298 | rv(3,2)=yat(iC(ia+3)+1)
|
|---|
| 299 | rv(3,3)=zat(iC(ia+3)+1)
|
|---|
| 300 |
|
|---|
| 301 | do i=1,3
|
|---|
| 302 | do j=1,nph
|
|---|
| 303 | dv(i,j,1)=(1.0/ab(j))*(bv(j,2)*(rv(i,3)-xiv(j,3))-
|
|---|
| 304 | & bv(j,3)*(rv(i,2)-xiv(j,2)))
|
|---|
| 305 | dv(i,j,2)=(-1.0/ab(j))*(bv(j,1)*(rv(i,3)-xiv(j,3))-
|
|---|
| 306 | & bv(j,3)*(rv(i,1)-xiv(j,1)))
|
|---|
| 307 | dv(i,j,3)=(1.0/ab(j))*(bv(j,1)*(rv(i,2)-xiv(j,2))-
|
|---|
| 308 | & bv(j,2)*(rv(i,1)-xiv(j,1)))
|
|---|
| 309 | enddo
|
|---|
| 310 | enddo
|
|---|
| 311 | do i=1,nph
|
|---|
| 312 | do j=i,nph
|
|---|
| 313 | A(i,j)=0
|
|---|
| 314 | do k=1,3
|
|---|
| 315 | do l=1,3
|
|---|
| 316 | A(i,j)=A(i,j)+dv(k,i,l)*(dv(k,j,l))
|
|---|
| 317 | enddo
|
|---|
| 318 | enddo
|
|---|
| 319 | A(i,j)=bbgs*A(i,j)
|
|---|
| 320 | if (i.eq.j) then
|
|---|
| 321 | A(i,j)=A(i,j)+1
|
|---|
| 322 | endif
|
|---|
| 323 | A(i,j)=0.5*abgs*A(i,j)
|
|---|
| 324 | enddo
|
|---|
| 325 | enddo
|
|---|
| 326 | do i=1,nph
|
|---|
| 327 | do j=i,nph
|
|---|
| 328 | sum=A(i,j)
|
|---|
| 329 | do k=i-1,1,-1
|
|---|
| 330 | sum=sum-A(i,k)*A(j,k)
|
|---|
| 331 | enddo
|
|---|
| 332 | if (i.eq.j) then
|
|---|
| 333 | p(i)=sqrt(sum)
|
|---|
| 334 | else
|
|---|
| 335 | A(j,i)=sum/p(i)
|
|---|
| 336 | endif
|
|---|
| 337 | enddo
|
|---|
| 338 | enddo
|
|---|
| 339 | do i=1,nph
|
|---|
| 340 | ppsi(i)=p(i)*dph(i)
|
|---|
| 341 | do j=i+1,nph
|
|---|
| 342 | ppsi(i)=ppsi(i)+A(j,i)*dph(j)
|
|---|
| 343 | enddo
|
|---|
| 344 | enddo
|
|---|
| 345 | sum=0
|
|---|
| 346 | do i=1,nph
|
|---|
| 347 | sum=sum+ppsi(i)*ppsi(i)
|
|---|
| 348 | enddo
|
|---|
| 349 | wbw=exp(-sum)
|
|---|
| 350 | do i=1,nph
|
|---|
| 351 | wbw=wbw*p(i)
|
|---|
| 352 | enddo
|
|---|
| 353 | ! Acceptance condition (includes additional weight)
|
|---|
| 354 | rd=grnd()
|
|---|
| 355 | ! print *,'generated selection random number ',rd
|
|---|
| 356 | ! print *,'wfw/wbw = ',wfw/wbw
|
|---|
| 357 | rd=-log(rd*wfw/wbw)
|
|---|
| 358 | ! print *,'modified rd = ',rd
|
|---|
| 359 | ! print *,'before calculating energy change'
|
|---|
| 360 | delta = dummy(enw)-dummy(eol1)
|
|---|
| 361 | ! print *,'delta = ',delta
|
|---|
| 362 | ! call outpdb(0,'after.pdb')
|
|---|
| 363 | ! print *,'after outpdb for after.pdb'
|
|---|
| 364 | ! do i=1,nph
|
|---|
| 365 | ! print *,'BGS>',i,iph(i),vlvr(iph(i)),dph(i)
|
|---|
| 366 | ! enddo
|
|---|
| 367 | if (rd.ge.delta) then
|
|---|
| 368 | ! accept
|
|---|
| 369 | eol1=enw
|
|---|
| 370 | bgs=1
|
|---|
| 371 | ! print *,'BGS move accepted'
|
|---|
| 372 | else
|
|---|
| 373 | ! reject
|
|---|
| 374 | vlvr = ovr
|
|---|
| 375 | ! enw=energy()
|
|---|
| 376 | ! if (abs(enw-eol1).gt.0.000001) then
|
|---|
| 377 | ! write(*,*) 'rejected bgs move: energy change :',eol1,enw
|
|---|
| 378 | ! endif
|
|---|
| 379 | ! write(*,*) 'rejected bgs move: ',eol1,enw,wfw,wbw,rd
|
|---|
| 380 | bgs=0
|
|---|
| 381 | endif
|
|---|
| 382 | 171 continue
|
|---|
| 383 | return
|
|---|
| 384 | end
|
|---|
| 385 |
|
|---|
