elecont.f

   1       subroutine elecont(lprint,ncont,icont)
   2       implicit real*8 (a-h,o-z)
   3       include 'DIMENSIONS'
   4       include 'COMMON.IOUNITS'
   5       include 'COMMON.CHAIN'
   6       include 'COMMON.INTERACT'
   7       include 'COMMON.LOCAL'
   8       include 'COMMON.FFIELD'
   9       include 'COMMON.NAMES'
  10       logical lprint
  11       double precision elpp_6(2,2),elpp_3(2,2),ael6_(2,2),ael3_(2,2)
  12       double precision app_(2,2),bpp_(2,2),rpp_(2,2)
  13       integer ncont,icont(2,maxcont)
  14       double precision econt(maxcont)
  15 *
  16 * Load the constants of peptide bond - peptide bond interactions.
  17 * Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
  18 * proline) - determined by averaging ECEPP energy.
  19 *
  20 * as of 7/06/91.
  21 *
  22 c      data epp    / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
  23       data rpp_    / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
  24       data elpp_6  /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
  25       data elpp_3  / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
  26       data elcutoff /-0.3d0/,elecutoff_14 /-0.5d0/
  27       if (lprint) write (iout,'(a)')
  28      &  "Constants of electrostatic interaction energy expression."
  29       do i=1,2
  30         do j=1,2
  31         rri=rpp_(i,j)**6
  32         app_(i,j)=epp(i,j)*rri*rri
  33         bpp_(i,j)=-2.0*epp(i,j)*rri
  34         ael6_(i,j)=elpp_6(i,j)*4.2**6
  35         ael3_(i,j)=elpp_3(i,j)*4.2**3
  36         if (lprint)
  37      &  write (iout,'(2i2,4e15.4)') i,j,app_(i,j),bpp_(i,j),ael6_(i,j),
  38      &                               ael3_(i,j)
  39         enddo
  40       enddo
  41       ncont=0
  42       ees=0.0
  43       evdw=0.0
  44       do 1 i=nnt,nct-2
  45         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) goto 1
  46         xi=c(1,i)
  47         yi=c(2,i)
  48         zi=c(3,i)
  49         dxi=c(1,i+1)-c(1,i)
  50         dyi=c(2,i+1)-c(2,i)
  51         dzi=c(3,i+1)-c(3,i)
  52         xmedi=xi+0.5*dxi
  53         ymedi=yi+0.5*dyi
  54         zmedi=zi+0.5*dzi
  55           xmedi=mod(xmedi,boxxsize)
  56           if (xmedi.lt.0) xmedi=xmedi+boxxsize
  57           ymedi=mod(ymedi,boxysize)
  58           if (ymedi.lt.0) ymedi=ymedi+boxysize
  59           zmedi=mod(zmedi,boxzsize)
  60           if (zmedi.lt.0) zmedi=zmedi+boxzsize
  61         do 4 j=i+2,nct-1
  62           if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) goto 4
  63           ind=ind+1
  64           iteli=itel(i)
  65           itelj=itel(j)
  66           if (j.eq.i+2 .and. itelj.eq.2) iteli=2
  67           if (iteli.eq.2 .and. itelj.eq.2) goto 4
  68           aaa=app_(iteli,itelj)
  69           bbb=bpp_(iteli,itelj)
  70           ael6_i=ael6_(iteli,itelj)
  71           ael3_i=ael3_(iteli,itelj)
  72           dxj=c(1,j+1)-c(1,j)
  73           dyj=c(2,j+1)-c(2,j)
  74           dzj=c(3,j+1)-c(3,j)
  75           xj=c(1,j)+0.5*dxj
  76           yj=c(2,j)+0.5*dyj
  77           zj=c(3,j)+0.5*dzj
  78           xj=mod(xj,boxxsize)
  79           if (xj.lt.0) xj=xj+boxxsize
  80           yj=mod(yj,boxysize)
  81           if (yj.lt.0) yj=yj+boxysize
  82           zj=mod(zj,boxzsize)
  83           if (zj.lt.0) zj=zj+boxzsize
  84       dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
  85       xj_safe=xj
  86       yj_safe=yj
  87       zj_safe=zj
  88       isubchap=0
  89       do xshift=-1,1
  90       do yshift=-1,1
  91       do zshift=-1,1
  92           xj=xj_safe+xshift*boxxsize
  93           yj=yj_safe+yshift*boxysize
  94           zj=zj_safe+zshift*boxzsize
  95           dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
  96           if(dist_temp.lt.dist_init) then
  97             dist_init=dist_temp
  98             xj_temp=xj
  99             yj_temp=yj
 100             zj_temp=zj
 101             isubchap=1
 102           endif
 103        enddo
 104        enddo
 105        enddo
 106        if (isubchap.eq.1) then
 107           xj=xj_temp-xmedi
 108           yj=yj_temp-ymedi
 109           zj=zj_temp-zmedi
 110        else
 111           xj=xj_safe-xmedi
 112           yj=yj_safe-ymedi
 113           zj=zj_safe-zmedi
 114        endif
 115           rij=xj*xj+yj*yj+zj*zj
 116             sss=sscale(sqrt(rij))
 117             sssgrad=sscagrad(sqrt(rij))
 118           rrmij=1.0/(xj*xj+yj*yj+zj*zj)
 119           rmij=sqrt(rrmij)
 120           r3ij=rrmij*rmij
 121           r6ij=r3ij*r3ij
 122           vrmij=vblinv*rmij
 123           cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
 124           cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
 125           cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
 126           fac=cosa-3.0*cosb*cosg
 127           ev1=aaa*r6ij*r6ij
 128           ev2=bbb*r6ij
 129           fac3=ael6_i*r6ij
 130           fac4=ael3_i*r3ij
 131           evdwij=ev1+ev2
 132           el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
 133           el2=fac4*fac
 134           eesij=el1+el2
 135           if (j.gt.i+2 .and. eesij.le.elcutoff .or.
 136      &        j.eq.i+2 .and. eesij.le.elecutoff_14) then
 137              ncont=ncont+1
 138              icont(1,ncont)=i
 139              icont(2,ncont)=j
 140              econt(ncont)=eesij
 141           endif
 142           ees=ees+eesij
 143           evdw=evdw+evdwij*sss
 144     4   continue
 145     1 continue
 146       if (lprint) then
 147         write (iout,*) 'Total average electrostatic energy: ',ees
 148         write (iout,*) 'VDW energy between peptide-group centers: ',evdw
 149         write (iout,*)
 150         write (iout,*) 'Electrostatic contacts before pruning: '
 151         do i=1,ncont
 152           i1=icont(1,i)
 153           i2=icont(2,i)
 154           it1=itype(i1)
 155           it2=itype(i2)
 156           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)')
 157      &     i,restyp(it1),i1,restyp(it2),i2,econt(i)
 158         enddo
 159       endif
 160 c For given residues keep only the contacts with the greatest energy.
 161       i=0
 162       do while (i.lt.ncont)
 163         i=i+1
 164         ene=econt(i)
 165         ic1=icont(1,i)
 166         ic2=icont(2,i)
 167         j=i
 168         do while (j.lt.ncont)
 169           j=j+1
 170           if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or.
 171      &        ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
 172 c            write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
 173 c     &       " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
 174             if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
 175               if (ic1.eq.icont(1,j)) then
 176                 do k=1,ncont
 177                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)
 178      &               .and. iabs(icont(1,k)-ic1).le.2 .and.
 179      &               econt(k).lt.econt(j) ) goto 21
 180                 enddo
 181               else if (ic2.eq.icont(2,j) ) then
 182                 do k=1,ncont
 183                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)
 184      &               .and. iabs(icont(2,k)-ic2).le.2 .and.
 185      &               econt(k).lt.econt(j) ) goto 21
 186                 enddo
 187               endif
 188 c Remove ith contact
 189               do k=i+1,ncont
 190                 icont(1,k-1)=icont(1,k)
 191                 icont(2,k-1)=icont(2,k)
 192                 econt(k-1)=econt(k)
 193               enddo
 194               i=i-1
 195               ncont=ncont-1
 196 c              write (iout,*) "ncont",ncont
 197 c              do k=1,ncont
 198 c                write (iout,*) icont(1,k),icont(2,k)
 199 c              enddo
 200               goto 20
 201             else if (econt(j).gt.ene .and. ic2.ne.ic1+2)
 202      &      then
 203               if (ic1.eq.icont(1,j)) then
 204                 do k=1,ncont
 205                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2
 206      &               .and. iabs(icont(1,k)-icont(1,j)).le.2 .and.
 207      &               econt(k).lt.econt(i) ) goto 21
 208                 enddo
 209               else if (ic2.eq.icont(2,j) ) then
 210                 do k=1,ncont
 211                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1
 212      &               .and. iabs(icont(2,k)-icont(2,j)).le.2 .and.
 213      &               econt(k).lt.econt(i) ) goto 21
 214                 enddo
 215               endif
 216 c Remove jth contact
 217               do k=j+1,ncont
 218                 icont(1,k-1)=icont(1,k)
 219                 icont(2,k-1)=icont(2,k)
 220                 econt(k-1)=econt(k)
 221               enddo
 222               ncont=ncont-1
 223 c              write (iout,*) "ncont",ncont
 224 c              do k=1,ncont
 225 c                write (iout,*) icont(1,k),icont(2,k)
 226 c              enddo
 227               j=j-1
 228             endif
 229           endif
 230    21     continue
 231         enddo
 232    20   continue
 233       enddo
 234       if (lprint) then
 235         write (iout,*)
 236         write (iout,*) 'Electrostatic contacts after pruning: '
 237         do i=1,ncont
 238           i1=icont(1,i)
 239           i2=icont(2,i)
 240           it1=itype(i1)
 241           it2=itype(i2)
 242           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)')
 243      &     i,restyp(it1),i1,restyp(it2),i2,econt(i)
 244         enddo
 245       endif
 246       return
 247       end
 248 c--------------------------------------------
 249       subroutine secondary2(lprint)
 250       implicit real*8 (a-h,o-z)
 251       include 'DIMENSIONS'
 252       include 'COMMON.CHAIN'
 253       include 'COMMON.IOUNITS'
 254       include 'COMMON.DISTFIT'
 255       include 'COMMON.VAR'
 256       include 'COMMON.GEO'
 257       include 'COMMON.CONTROL'
 258       integer ncont,icont(2,maxcont),isec(maxres,4),nsec(maxres)
 259       logical lprint,not_done,freeres
 260       double precision p1,p2
 261       external freeres
 262
 263 cc????      if(.not.dccart) call chainbuild
 264 cd      call write_pdb(99,'sec structure',0d0)
 265       ncont=0
 266       nbfrag=0
 267       nhfrag=0
 268       do i=1,nres
 269         isec(i,1)=0
 270         isec(i,2)=0
 271         nsec(i)=0
 272       enddo
 273
 274       call elecont(lprint,ncont,icont)
 275
 276 c finding parallel beta
 277 cd      write (iout,*) '------- looking for parallel beta -----------'
 278       nbeta=0
 279       nstrand=0
 280       do i=1,ncont
 281         i1=icont(1,i)
 282         j1=icont(2,i)
 283         if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
 284           ii1=i1
 285           jj1=j1
 286 cd          write (iout,*) i1,j1
 287           not_done=.true.
 288           do while (not_done)
 289            i1=i1+1
 290            j1=j1+1
 291             do j=1,ncont
 292               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and.
 293      &             freeres(i1,j1,nsec,isec)) goto 5
 294             enddo
 295             not_done=.false.
 296   5         continue
 297 cd            write (iout,*) i1,j1,not_done
 298           enddo
 299           j1=j1-1
 300           i1=i1-1
 301           if (i1-ii1.gt.1) then
 302             ii1=max0(ii1-1,1)
 303             jj1=max0(jj1-1,1)
 304             nbeta=nbeta+1
 305             if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',
 306      &               nbeta,ii1,i1,jj1,j1
 307
 308             nbfrag=nbfrag+1
 309             bfrag(1,nbfrag)=ii1+1
 310             bfrag(2,nbfrag)=i1+1
 311             bfrag(3,nbfrag)=jj1+1
 312             bfrag(4,nbfrag)=min0(j1+1,nres)
 313
 314             do ij=ii1,i1
 315              nsec(ij)=nsec(ij)+1
 316              isec(ij,nsec(ij))=nbeta
 317             enddo
 318             do ij=jj1,j1
 319              nsec(ij)=nsec(ij)+1
 320              isec(ij,nsec(ij))=nbeta
 321             enddo
 322
 323            if(lprint) then
 324             nstrand=nstrand+1
 325             if (nbeta.le.9) then
 326               write(12,'(a18,i1,a9,i3,a2,i3,a1)')
 327      &          "DefPropRes 'strand",nstrand,
 328      &          "' 'num = ",ii1-1,"..",i1-1,"'"
 329             else
 330               write(12,'(a18,i2,a9,i3,a2,i3,a1)')
 331      &          "DefPropRes 'strand",nstrand,
 332      &          "' 'num = ",ii1-1,"..",i1-1,"'"
 333             endif
 334             nstrand=nstrand+1
 335             if (nbeta.le.9) then
 336               write(12,'(a18,i1,a9,i3,a2,i3,a1)')
 337      &          "DefPropRes 'strand",nstrand,
 338      &          "' 'num = ",jj1-1,"..",j1-1,"'"
 339             else
 340               write(12,'(a18,i2,a9,i3,a2,i3,a1)')
 341      &          "DefPropRes 'strand",nstrand,
 342      &          "' 'num = ",jj1-1,"..",j1-1,"'"
 343             endif
 344               write(12,'(a8,4i4)')
 345      &          "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
 346            endif
 347           endif
 348         endif
 349       enddo
 350
 351 c finding alpha or 310 helix
 352
 353       nhelix=0
 354       do i=1,ncont
 355         i1=icont(1,i)
 356         j1=icont(2,i)
 357         p1=phi(i1+2)*rad2deg
 358         p2=0.0
 359         if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
 360
 361
 362         if (j1.eq.i1+3 .and.
 363      &       ((p1.ge.10.and.p1.le.80).or.i1.le.2).and.
 364      &       ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
 365 cd          if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
 366 co          if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
 367           ii1=i1
 368           jj1=j1
 369           if (nsec(ii1).eq.0) then
 370             not_done=.true.
 371           else
 372             not_done=.false.
 373           endif
 374           do while (not_done)
 375             i1=i1+1
 376             j1=j1+1
 377             do j=1,ncont
 378               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
 379             enddo
 380             not_done=.false.
 381   10        continue
 382             p1=phi(i1+2)*rad2deg
 383             p2=phi(j1+2)*rad2deg
 384             if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80)
 385      &                              not_done=.false.
 386 cd           write (iout,*) i1,j1,not_done,p1,p2
 387           enddo
 388           j1=j1+1
 389           if (j1-ii1.gt.5) then
 390             nhelix=nhelix+1
 391 cd            write (iout,*)'helix',nhelix,ii1,j1
 392
 393             nhfrag=nhfrag+1
 394             hfrag(1,nhfrag)=ii1
 395             hfrag(2,nhfrag)=j1
 396
 397             do ij=ii1,j1
 398              nsec(ij)=-1
 399             enddo
 400            if (lprint) then
 401             write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
 402             if (nhelix.le.9) then
 403               write(12,'(a17,i1,a9,i3,a2,i3,a1)')
 404      &          "DefPropRes 'helix",nhelix,
 405      &          "' 'num = ",ii1-1,"..",j1-2,"'"
 406             else
 407               write(12,'(a17,i2,a9,i3,a2,i3,a1)')
 408      &          "DefPropRes 'helix",nhelix,
 409      &          "' 'num = ",ii1-1,"..",j1-2,"'"
 410             endif
 411            endif
 412           endif
 413         endif
 414       enddo
 415
 416       if (nhelix.gt.0.and.lprint) then
 417         write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
 418         do i=2,nhelix
 419          if (nhelix.le.9) then
 420           write(12,'(a8,i1,$)') " | helix",i
 421          else
 422           write(12,'(a8,i2,$)') " | helix",i
 423          endif
 424         enddo
 425         write(12,'(a1)') "'"
 426       endif
 427
 428
 429 c finding antiparallel beta
 430 cd      write (iout,*) '--------- looking for antiparallel beta ---------'
 431
 432       do i=1,ncont
 433         i1=icont(1,i)
 434         j1=icont(2,i)
 435         if (freeres(i1,j1,nsec,isec)) then
 436           ii1=i1
 437           jj1=j1
 438 cd          write (iout,*) i1,j1
 439
 440           not_done=.true.
 441           do while (not_done)
 442            i1=i1+1
 443            j1=j1-1
 444             do j=1,ncont
 445               if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and.
 446      &             freeres(i1,j1,nsec,isec)) goto 6
 447             enddo
 448             not_done=.false.
 449   6         continue
 450 cd            write (iout,*) i1,j1,not_done
 451           enddo
 452           i1=i1-1
 453           j1=j1+1
 454           if (i1-ii1.gt.1) then
 455
 456             nbfrag=nbfrag+1
 457             bfrag(1,nbfrag)=ii1
 458             bfrag(2,nbfrag)=min0(i1+1,nres)
 459             bfrag(3,nbfrag)=min0(jj1+1,nres)
 460             bfrag(4,nbfrag)=j1
 461
 462             nbeta=nbeta+1
 463             iii1=max0(ii1-1,1)
 464             do ij=iii1,i1
 465              nsec(ij)=nsec(ij)+1
 466              if (nsec(ij).le.2) then
 467               isec(ij,nsec(ij))=nbeta
 468              endif
 469             enddo
 470             jjj1=max0(j1-1,1)
 471             do ij=jjj1,jj1
 472              nsec(ij)=nsec(ij)+1
 473              if (nsec(ij).le.2 .and. nsec(ij).gt.0) then
 474               isec(ij,nsec(ij))=nbeta
 475              endif
 476             enddo
 477
 478
 479            if (lprint) then
 480             write (iout,'(a,i3,4i4)')'antiparallel beta',
 481      &                   nbeta,ii1-1,i1,jj1,j1-1
 482             nstrand=nstrand+1
 483             if (nstrand.le.9) then
 484               write(12,'(a18,i1,a9,i3,a2,i3,a1)')
 485      &          "DefPropRes 'strand",nstrand,
 486      &          "' 'num = ",ii1-2,"..",i1-1,"'"
 487             else
 488               write(12,'(a18,i2,a9,i3,a2,i3,a1)')
 489      &          "DefPropRes 'strand",nstrand,
 490      &          "' 'num = ",ii1-2,"..",i1-1,"'"
 491             endif
 492             nstrand=nstrand+1
 493             if (nstrand.le.9) then
 494               write(12,'(a18,i1,a9,i3,a2,i3,a1)')
 495      &          "DefPropRes 'strand",nstrand,
 496      &          "' 'num = ",j1-2,"..",jj1-1,"'"
 497             else
 498               write(12,'(a18,i2,a9,i3,a2,i3,a1)')
 499      &          "DefPropRes 'strand",nstrand,
 500      &          "' 'num = ",j1-2,"..",jj1-1,"'"
 501             endif
 502               write(12,'(a8,4i4)')
 503      &          "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
 504            endif
 505           endif
 506         endif
 507       enddo
 508
 509       if (nstrand.gt.0.and.lprint) then
 510         write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
 511         do i=2,nstrand
 512          if (i.le.9) then
 513           write(12,'(a9,i1,$)') " | strand",i
 514          else
 515           write(12,'(a9,i2,$)') " | strand",i
 516          endif
 517         enddo
 518         write(12,'(a1)') "'"
 519       endif
 520
 521
 522
 523       if (lprint) then
 524        write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
 525        write(12,'(a20)') "XMacStand ribbon.mac"
 526
 527
 528        write(iout,*) 'UNRES seq:'
 529        do j=1,nbfrag
 530         write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
 531        enddo
 532
 533        do j=1,nhfrag
 534         write(iout,*) 'helix ',(hfrag(i,j),i=1,2)
 535        enddo
 536       endif
 537
 538       return
 539       end
 540 c-------------------------------------------------
 541       logical function freeres(i,j,nsec,isec)
 542       implicit real*8 (a-h,o-z)
 543       include 'DIMENSIONS'
 544       integer isec(maxres,4),nsec(maxres)
 545       freeres=.false.
 546
 547       if (nsec(i).lt.0.or.nsec(j).lt.0) return
 548       if (nsec(i).gt.1.or.nsec(j).gt.1) return
 549       do k=1,nsec(i)
 550         do l=1,nsec(j)
 551           if (isec(i,k).eq.isec(j,l)) return
 552         enddo
 553       enddo
 554       freeres=.true.
 555       return
 556       end
 557