source/cluster/wham/src-HCD-5D/readpdb.F

   1       subroutine readpdb
   2 C Read the PDB file and convert the peptide geometry into virtual-chain
   3 C geometry.
   4       implicit real*8 (a-h,o-z)
   5       include 'DIMENSIONS'
   6       include 'COMMON.FRAG'
   7       include 'COMMON.LOCAL'
   8       include 'COMMON.VAR'
   9       include 'COMMON.CHAIN'
  10       include 'COMMON.INTERACT'
  11       include 'COMMON.IOUNITS'
  12       include 'COMMON.GEO'
  13       include 'COMMON.NAMES'
  14       include 'COMMON.CONTROL'
  15       integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
  16       logical lprn /.false./,fail
  17       double precision e1(3),e2(3),e3(3)
  18       double precision dcj,efree_temp
  19       character*3 seq,res
  20       character*5 atom
  21       character*80 card
  22       double precision sccor(3,20)
  23       integer rescode
  24       integer iterter(maxres)
  25       efree_temp=0.0d0
  26       ibeg=1
  27       ishift1=0
  28       ishift=0
  29 c      write (2,*) "UNRES_PDB",unres_pdb
  30       ires=0
  31       ires_old=0
  32       iii=0
  33       lsecondary=.false.
  34       nhfrag=0
  35       nbfrag=0
  36       do
  37         read (ipdbin,'(a80)',end=10) card
  38 !       write (iout,'(a)') card
  39         if (card(:5).eq.'HELIX') then
  40           nhfrag=nhfrag+1
  41           lsecondary=.true.
  42           read(card(22:25),*) hfrag(1,nhfrag)
  43           read(card(34:37),*) hfrag(2,nhfrag)
  44         endif
  45         if (card(:5).eq.'SHEET') then
  46           nbfrag=nbfrag+1
  47           lsecondary=.true.
  48           read(card(24:26),*) bfrag(1,nbfrag)
  49           read(card(35:37),*) bfrag(2,nbfrag)
  50 !rc----------------------------------------
  51 !rc  to be corrected !!!
  52           bfrag(3,nbfrag)=bfrag(1,nbfrag)
  53           bfrag(4,nbfrag)=bfrag(2,nbfrag)
  54 !rc----------------------------------------
  55         endif
  56         if (card(:3).eq.'END') then
  57           goto 10
  58         else if (card(:3).eq.'TER') then
  59 ! End current chain
  60           ires_old=ires+2
  61           itype(ires_old-1)=ntyp1
  62           iterter(ires_old-1)=1
  63           itype(ires_old)=ntyp1
  64           ishift1=ishift1+1
  65           ibeg=2
  66 !          write (iout,*) "Chain ended",ires,ishift,ires_old
  67           if (unres_pdb) then
  68             do j=1,3
  69               dc(j,ires)=sccor(j,iii)
  70             enddo
  71           else
  72             call sccenter(ires,iii,sccor)
  73           endif
  74 c          iii=0
  75         endif
  76 ! Read free energy
  77         if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
  78 ! Fish out the ATOM cards.
  79         if (index(card(1:4),'ATOM').gt.0) then
  80           read (card(12:16),*) atom
  81 c          write (2,'(a)') card
  82 !          write (iout,*) "! ",atom," !",ires
  83 !          if (atom.eq.'CA' .or. atom.eq.'CH3') then
  84           read (card(23:26),*) ires
  85           read (card(18:20),'(a3)') res
  86 !          write (iout,*) "ires",ires,ires-ishift+ishift1,
  87 !     &      " ires_old",ires_old
  88 !          write (iout,*) "ishift",ishift," ishift1",ishift1
  89 !          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
  90           if (ires-ishift+ishift1.ne.ires_old) then
  91 ! Calculate the CM of the preceding residue.
  92 !            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
  93             if (ibeg.eq.0) then
  94 !              write (iout,*) "Calculating sidechain center iii",iii
  95               if (unres_pdb) then
  96                 do j=1,3
  97                   dc(j,ires+nres)=sccor(j,iii)
  98                 enddo
  99               else
 100                 call sccenter(ires_old,iii,sccor)
 101               endif
 102               iii=0
 103             endif
 104 ! Start new residue.
 105             if (res.eq.'Cl-' .or. res.eq.'Na+') then
 106               ires=ires_old
 107               cycle
 108             else if (ibeg.eq.1) then
 109 c              write (iout,*) "BEG ires",ires
 110               ishift=ires-1
 111               if (res.ne.'GLY' .and. res.ne. 'ACE') then
 112                 ishift=ishift-1
 113                 itype(1)=ntyp1
 114               endif
 115               ires=ires-ishift+ishift1
 116               ires_old=ires
 117 !              write (iout,*) "ishift",ishift," ires",ires,&
 118 !               " ires_old",ires_old
 119               ibeg=0
 120             else if (ibeg.eq.2) then
 121 ! Start a new chain
 122               ishift=-ires_old+ires-1 !!!!!
 123               ishift1=ishift1-1    !!!!!
 124 !              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
 125               ires=ires-ishift+ishift1
 126               ires_old=ires
 127               ibeg=0
 128             else
 129               ishift=ishift-(ires-ishift+ishift1-ires_old-1)
 130               ires=ires-ishift+ishift1
 131               ires_old=ires
 132             endif
 133             if (res.eq.'ACE' .or. res.eq.'NHE') then
 134               itype(ires)=10
 135             else
 136               itype(ires)=rescode(ires,res,0)
 137             endif
 138           else
 139             ires=ires-ishift+ishift1
 140           endif
 141 !          write (iout,*) "ires_old",ires_old," ires",ires
 142           if (card(27:27).eq."A" .or. card(27:27).eq."B") then
 143 !            ishift1=ishift1+1
 144           endif
 145 !          write (2,*) "ires",ires," res ",res!," ity"!,ity
 146           if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
 147      &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
 148             read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
 149 !            write (iout,*) "backbone ",atom
 150 #ifdef DEBUG
 151             write (iout,'(2i3,2x,a,3f8.3)')
 152      &      ires,itype(ires),res,(c(j,ires),j=1,3)
 153 #endif
 154             iii=iii+1
 155             do j=1,3
 156               sccor(j,iii)=c(j,ires)
 157             enddo
 158 c            write (2,*) card(23:27),ires,itype(ires),iii
 159           else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
 160      &             atom.ne.'N' .and. atom.ne.'C' .and.
 161      &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
 162      &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
 163 !            write (iout,*) "sidechain ",atom
 164             iii=iii+1
 165             read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
 166 c            write (2,*) "iii",iii
 167           endif
 168         endif
 169       enddo
 170    10 write (iout,'(a,i5)') ' Nres: ',ires
 171 C Calculate dummy residue coordinates inside the "chain" of a multichain
 172 C system
 173       nres=ires
 174       do i=2,nres-1
 175 c        write (iout,*) i,itype(i)
 176
 177         if (itype(i).eq.ntyp1) then
 178          if (itype(i+1).eq.ntyp1) then
 179 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
 180 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
 181 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
 182 C           if (unres_pdb) then
 183 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
 184 C            call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
 185 C            if (fail) then
 186 C              e2(1)=0.0d0
 187 C              e2(2)=1.0d0
 188 C              e2(3)=0.0d0
 189 C            endif !fail
 190 C            do j=1,3
 191 C             c(j,i)=c(j,i-1)-1.9d0*e2(j)
 192 C            enddo
 193 C           else   !unres_pdb
 194            do j=1,3
 195              dcj=(c(j,i-2)-c(j,i-3))/2.0
 196              c(j,i)=c(j,i-1)+dcj
 197              c(j,nres+i)=c(j,i)
 198            enddo
 199 C          endif   !unres_pdb
 200          else     !itype(i+1).eq.ntyp1
 201 C          if (unres_pdb) then
 202 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
 203 C            call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
 204 C            if (fail) then
 205 C              e2(1)=0.0d0
 206 C              e2(2)=1.0d0
 207 C              e2(3)=0.0d0
 208 C            endif
 209 C            do j=1,3
 210 C              c(j,i)=c(j,i+1)-1.9d0*e2(j)
 211 C            enddo
 212 C          else !unres_pdb
 213            do j=1,3
 214             dcj=(c(j,i+3)-c(j,i+2))/2.0
 215             c(j,i)=c(j,i+1)-dcj
 216             c(j,nres+i)=c(j,i)
 217            enddo
 218 C          endif !unres_pdb
 219          endif !itype(i+1).eq.ntyp1
 220         endif  !itype.eq.ntyp1
 221       enddo
 222 C Calculate the CM of the last side chain.
 223       call sccenter(ires,iii,sccor)
 224       nsup=nres
 225       nstart_sup=1
 226       if (itype(nres).ne.10) then
 227         nres=nres+1
 228         itype(nres)=ntyp1
 229         do j=1,3
 230           dcj=(c(j,nres-2)-c(j,nres-3))/2.0
 231           c(j,nres)=c(j,nres-1)+dcj
 232           c(j,2*nres)=c(j,nres)
 233         enddo
 234       endif
 235       do i=2,nres-1
 236         do j=1,3
 237           c(j,i+nres)=dc(j,i)
 238         enddo
 239       enddo
 240       do j=1,3
 241         c(j,nres+1)=c(j,1)
 242         c(j,2*nres)=c(j,nres)
 243       enddo
 244       if (itype(1).eq.ntyp1) then
 245         nsup=nsup-1
 246         nstart_sup=2
 247         do j=1,3
 248           dcj=(c(j,4)-c(j,3))/2.0
 249           c(j,1)=c(j,2)-dcj
 250           c(j,nres+1)=c(j,1)
 251         enddo
 252       endif
 253 C Calculate internal coordinates.
 254       if (lprn) then
 255       write (iout,'(/a)')
 256      &  "Cartesian coordinates of the reference structure"
 257       write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
 258      & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
 259       do ires=1,nres
 260         write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
 261      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
 262      &    (c(j,ires+nres),j=1,3)
 263       enddo
 264       endif
 265 C Calculate internal coordinates.
 266        write (iout,'(a)')
 267      &   "Backbone and SC coordinates as read from the PDB"
 268        do ires=1,nres
 269         write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
 270      &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
 271      &    (c(j,nres+ires),j=1,3)
 272        enddo
 273       call int_from_cart(.true.,.false.)
 274       call sc_loc_geom(.false.)
 275       do i=1,nres
 276         thetaref(i)=theta(i)
 277         phiref(i)=phi(i)
 278       enddo
 279       do i=1,nres-1
 280         do j=1,3
 281           dc(j,i)=c(j,i+1)-c(j,i)
 282           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
 283         enddo
 284       enddo
 285       do i=2,nres-1
 286         do j=1,3
 287           dc(j,i+nres)=c(j,i+nres)-c(j,i)
 288           dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
 289         enddo
 290 c        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
 291 c     &   vbld_inv(i+nres)
 292       enddo
 293 c      call chainbuild
 294 C Copy the coordinates to reference coordinates
 295       do i=1,2*nres
 296         do j=1,3
 297           cref(j,i)=c(j,i)
 298         enddo
 299       enddo
 300
 301
 302       do j=1,nbfrag
 303         do i=1,4
 304          bfrag(i,j)=bfrag(i,j)-ishift
 305         enddo
 306       enddo
 307
 308       do j=1,nhfrag
 309         do i=1,2
 310          hfrag(i,j)=hfrag(i,j)-ishift
 311         enddo
 312       enddo
 313       ishift_pdb=ishift
 314       return
 315       end
 316 c---------------------------------------------------------------------------
 317       subroutine int_from_cart(lside,lprn)
 318       implicit real*8 (a-h,o-z)
 319       include 'DIMENSIONS'
 320       include 'COMMON.LOCAL'
 321       include 'COMMON.VAR'
 322       include 'COMMON.CHAIN'
 323       include 'COMMON.INTERACT'
 324       include 'COMMON.IOUNITS'
 325       include 'COMMON.GEO'
 326       include 'COMMON.NAMES'
 327       character*3 seq,res
 328 c      character*5 atom
 329       character*80 card
 330       dimension sccor(3,20)
 331       integer rescode
 332       logical lside,lprn
 333        if (lprn) then
 334         write (iout,'(/a)')
 335      &  'Internal coordinates calculated from crystal structure.'
 336         if (lside) then
 337           write (iout,'(8a)') '  Res  ','       dvb','     Theta',
 338      & '     Gamma','    Dsc_id','       Dsc','     Alpha',
 339      & '     Beta '
 340         else
 341           write (iout,'(4a)') '  Res  ','       dvb','     Theta',
 342      & '     Gamma'
 343         endif
 344        endif
 345       do i=1,nres-1
 346         iti=itype(i)
 347         if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
 348           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
 349 ctest          stop
 350         endif
 351         vbld(i+1)=dist(i,i+1)
 352         vbld_inv(i+1)=1.0d0/vbld(i+1)
 353         if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
 354         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
 355       enddo
 356 c      if (unres_pdb) then
 357 c        if (itype(1).eq.ntyp1) then
 358 c          theta(3)=90.0d0*deg2rad
 359 c          phi(4)=180.0d0*deg2rad
 360 c          vbld(2)=3.8d0
 361 c          vbld_inv(2)=1.0d0/vbld(2)
 362 c        endif
 363 c        if (itype(nres).eq.ntyp1) then
 364 c          theta(nres)=90.0d0*deg2rad
 365 c          phi(nres)=180.0d0*deg2rad
 366 c          vbld(nres)=3.8d0
 367 c          vbld_inv(nres)=1.0d0/vbld(2)
 368 c        endif
 369 c      endif
 370       if (lside) then
 371         do i=2,nres-1
 372           do j=1,3
 373             c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
 374      &     +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
 375           enddo
 376           iti=itype(i)
 377           di=dist(i,nres+i)
 378 C 10/03/12 Adam: Correction for zero SC-SC bond length
 379           if (itype(i).ne.10 .and. itype(i).ne.ntyp1. and. di.eq.0.0d0)
 380      &     di=dsc(itype(i))
 381           vbld(i+nres)=di
 382           if (itype(i).ne.10) then
 383             vbld_inv(i+nres)=1.0d0/di
 384           else
 385             vbld_inv(i+nres)=0.0d0
 386           endif
 387           if (iti.ne.10) then
 388             alph(i)=alpha(nres+i,i,maxres2)
 389             omeg(i)=beta(nres+i,i,maxres2,i+1)
 390           endif
 391            if (lprn)
 392      &     write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
 393      &     rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
 394      &     rad2deg*alph(i),rad2deg*omeg(i)
 395         enddo
 396       else if (lprn) then
 397         do i=2,nres
 398           iti=itype(i)
 399           write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
 400      &     rad2deg*theta(i),rad2deg*phi(i)
 401         enddo
 402       endif
 403       return
 404       end
 405 c-------------------------------------------------------------------------------
 406       subroutine sc_loc_geom(lprn)
 407       implicit real*8 (a-h,o-z)
 408       include 'DIMENSIONS'
 409       include 'COMMON.LOCAL'
 410       include 'COMMON.VAR'
 411       include 'COMMON.CHAIN'
 412       include 'COMMON.INTERACT'
 413       include 'COMMON.IOUNITS'
 414       include 'COMMON.GEO'
 415       include 'COMMON.NAMES'
 416       include 'COMMON.CONTROL'
 417       double precision x_prime(3),y_prime(3),z_prime(3)
 418       logical lprn
 419       do i=1,nres-1
 420         do j=1,3
 421           dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
 422         enddo
 423       enddo
 424       do i=2,nres-1
 425         if (itype(i).ne.10) then
 426           do j=1,3
 427             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
 428           enddo
 429         else
 430           do j=1,3
 431             dc_norm(j,i+nres)=0.0d0
 432           enddo
 433         endif
 434       enddo
 435       do i=2,nres-1
 436         costtab(i+1) =dcos(theta(i+1))
 437         sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
 438         cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
 439         sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
 440         cosfac2=0.5d0/(1.0d0+costtab(i+1))
 441         cosfac=dsqrt(cosfac2)
 442         sinfac2=0.5d0/(1.0d0-costtab(i+1))
 443         sinfac=dsqrt(sinfac2)
 444         it=itype(i)
 445         if (it.ne.10) then
 446 c
 447 C  Compute the axes of tghe local cartesian coordinates system; store in
 448 c   x_prime, y_prime and z_prime
 449 c
 450         do j=1,3
 451           x_prime(j) = 0.00
 452           y_prime(j) = 0.00
 453           z_prime(j) = 0.00
 454         enddo
 455         do j = 1,3
 456           x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
 457           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
 458         enddo
 459         call vecpr(x_prime,y_prime,z_prime)
 460 c
 461 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
 462 C to local coordinate system. Store in xx, yy, zz.
 463 c
 464         xx=0.0d0
 465         yy=0.0d0
 466         zz=0.0d0
 467         do j = 1,3
 468           xx = xx + x_prime(j)*dc_norm(j,i+nres)
 469           yy = yy + y_prime(j)*dc_norm(j,i+nres)
 470           zz = zz + z_prime(j)*dc_norm(j,i+nres)
 471         enddo
 472
 473         xxref(i)=xx
 474         yyref(i)=yy
 475         zzref(i)=zz
 476         else
 477         xxref(i)=0.0d0
 478         yyref(i)=0.0d0
 479         zzref(i)=0.0d0
 480         endif
 481       enddo
 482       if (lprn) then
 483         do i=2,nres
 484           iti=itype(i)
 485           write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
 486      &      yyref(i),zzref(i)
 487         enddo
 488       endif
 489       return
 490       end
 491 c---------------------------------------------------------------------------
 492       subroutine sccenter(ires,nscat,sccor)
 493       implicit real*8 (a-h,o-z)
 494       include 'DIMENSIONS'
 495       include 'COMMON.CHAIN'
 496       dimension sccor(3,20)
 497       do j=1,3
 498         sccmj=0.0D0
 499         do i=1,nscat
 500           sccmj=sccmj+sccor(j,i)
 501         enddo
 502         dc(j,ires)=sccmj/nscat
 503       enddo
 504       return
 505       end
 506 c---------------------------------------------------------------------------
 507       subroutine bond_regular
 508       implicit none
 509       include 'DIMENSIONS'
 510       include 'COMMON.VAR'
 511       include 'COMMON.LOCAL'
 512       include 'COMMON.INTERACT'
 513       include 'COMMON.CHAIN'
 514       integer i,i1,i2
 515       do i=1,nres-1
 516        vbld(i+1)=vbl
 517        vbld_inv(i+1)=vblinv
 518        vbld(i+1+nres)=dsc(iabs(itype(i+1)))
 519        vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
 520 c       print *,vbld(i+1),vbld(i+1+nres)
 521       enddo
 522 c Adam 2/26/20 Alter virtual bonds for non-blocking end groups of each chain
 523       do i=1,nchain
 524         i1=chain_border(1,i)
 525         i2=chain_border(2,i)
 526         if (i1.gt.1) then
 527           vbld(i1)=vbld(i1)/2
 528           vbld_inv(i1)=vbld_inv(i1)*2
 529         endif
 530         if (i2.lt.nres) then
 531           vbld(i2+1)=vbld(i2+1)/2
 532           vbld_inv(i2+1)=vbld_inv(i2+1)*2
 533         endif
 534       enddo
 535       return
 536       end
 537 c---------------------------------------------------------------------------
 538       subroutine readpdb_template(k)
 539 C Read the PDB file with gaps for read_constr_homology with read2sigma
 540 C and convert the peptide geometry into virtual-chain geometry.
 541       implicit real*8 (a-h,o-z)
 542       include 'DIMENSIONS'
 543       include 'COMMON.LOCAL'
 544       include 'COMMON.VAR'
 545       include 'COMMON.CHAIN'
 546       include 'COMMON.INTERACT'
 547       include 'COMMON.IOUNITS'
 548       include 'COMMON.GEO'
 549       include 'COMMON.NAMES'
 550       include 'COMMON.CONTROL'
 551       integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
 552       logical lprn /.false./,fail
 553       double precision e1(3),e2(3),e3(3)
 554       double precision dcj,efree_temp
 555       character*3 seq,res
 556       character*5 atom
 557       character*80 card
 558       double precision sccor(3,20)
 559       integer rescode,iterter(maxres)
 560       do i=1,maxres
 561          iterter(i)=0
 562       enddo
 563       ibeg=1
 564       ishift1=0
 565       ishift=0
 566 c      write (2,*) "UNRES_PDB",unres_pdb
 567       ires=0
 568       ires_old=0
 569       iii=0
 570       lsecondary=.false.
 571       nhfrag=0
 572       nbfrag=0
 573       do
 574         read (ipdbin,'(a80)',end=10) card
 575         if (card(:3).eq.'END') then
 576           goto 10
 577         else if (card(:3).eq.'TER') then
 578 C End current chain
 579           ires_old=ires+2
 580           itype(ires_old-1)=ntyp1
 581           iterter(ires_old-1)=1
 582           itype(ires_old)=ntyp1
 583           iterter(ires_old)=1
 584           ibeg=2
 585 c          write (iout,*) "Chain ended",ires,ishift,ires_old
 586           if (unres_pdb) then
 587             do j=1,3
 588               dc(j,ires)=sccor(j,iii)
 589             enddo
 590           else
 591             call sccenter(ires,iii,sccor)
 592           endif
 593         endif
 594 C Fish out the ATOM cards.
 595         if (index(card(1:4),'ATOM').gt.0) then
 596           read (card(12:16),*) atom
 597 c          write (iout,*) "! ",atom," !",ires
 598 c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
 599           read (card(23:26),*) ires
 600           read (card(18:20),'(a3)') res
 601 c          write (iout,*) "ires",ires,ires-ishift+ishift1,
 602 c     &      " ires_old",ires_old
 603 c          write (iout,*) "ishift",ishift," ishift1",ishift1
 604 c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
 605           if (ires-ishift+ishift1.ne.ires_old) then
 606 C Calculate the CM of the preceding residue.
 607             if (ibeg.eq.0) then
 608               if (unres_pdb) then
 609                 do j=1,3
 610                   dc(j,ires)=sccor(j,iii)
 611                 enddo
 612               else
 613                 call sccenter(ires_old,iii,sccor)
 614               endif
 615               iii=0
 616             endif
 617 C Start new residue.
 618             if (res.eq.'Cl-' .or. res.eq.'Na+') then
 619               ires=ires_old
 620               cycle
 621             else if (ibeg.eq.1) then
 622 c              write (iout,*) "BEG ires",ires
 623               ishift=ires-1
 624               if (res.ne.'GLY' .and. res.ne. 'ACE') then
 625                 ishift=ishift-1
 626                 itype(1)=ntyp1
 627               endif
 628               ires=ires-ishift+ishift1
 629               ires_old=ires
 630 c              write (iout,*) "ishift",ishift," ires",ires,
 631 c     &         " ires_old",ires_old
 632 c              write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
 633               ibeg=0
 634             else if (ibeg.eq.2) then
 635 c Start a new chain
 636               ishift=-ires_old+ires-1
 637               ires=ires_old+1
 638 c              write (iout,*) "New chain started",ires,ishift
 639               ibeg=0
 640             else
 641               ishift=ishift-(ires-ishift+ishift1-ires_old-1)
 642               ires=ires-ishift+ishift1
 643               ires_old=ires
 644             endif
 645             if (res.eq.'ACE' .or. res.eq.'NHE') then
 646               itype(ires)=10
 647             else
 648               itype(ires)=rescode(ires,res,0)
 649             endif
 650           else
 651             ires=ires-ishift+ishift1
 652           endif
 653 c          write (iout,*) "ires_old",ires_old," ires",ires
 654 c          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
 655 c            ishift1=ishift1+1
 656 c          endif
 657 c          write (2,*) "ires",ires," res ",res," ity",ity
 658           if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
 659      &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
 660             read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
 661 c            write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
 662 #ifdef DEBUG
 663             write (iout,'(2i3,2x,a,3f8.3)')
 664      &      ires,itype(ires),res,(c(j,ires),j=1,3)
 665 #endif
 666             iii=iii+1
 667             do j=1,3
 668               sccor(j,iii)=c(j,ires)
 669             enddo
 670             if (ishift.ne.0) then
 671               ires_ca=ires+ishift-ishift1
 672             else
 673               ires_ca=ires
 674             endif
 675 c            write (*,*) card(23:27),ires,itype(ires)
 676           else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
 677      &             atom.ne.'N' .and. atom.ne.'C' .and.
 678      &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
 679      &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
 680 c            write (iout,*) "sidechain ",atom
 681             iii=iii+1
 682             read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
 683           endif
 684         endif
 685       enddo
 686    10 write (iout,'(a,i5)') ' Nres: ',ires
 687 C Calculate dummy residue coordinates inside the "chain" of a multichain
 688 C system
 689       nres=ires
 690       do i=2,nres-1
 691 c        write (iout,*) i,itype(i),itype(i+1)
 692         if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
 693          if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
 694 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
 695 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
 696 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
 697            if (unres_pdb) then
 698 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
 699             call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
 700             if (fail) then
 701               e2(1)=0.0d0
 702               e2(2)=1.0d0
 703               e2(3)=0.0d0
 704             endif !fail
 705             do j=1,3
 706              c(j,i)=c(j,i-1)-1.9d0*e2(j)
 707             enddo
 708            else   !unres_pdb
 709            do j=1,3
 710              dcj=(c(j,i-2)-c(j,i-3))/2.0
 711             if (dcj.eq.0) dcj=1.23591524223
 712              c(j,i)=c(j,i-1)+dcj
 713              c(j,nres+i)=c(j,i)
 714            enddo
 715           endif   !unres_pdb
 716          else     !itype(i+1).eq.ntyp1
 717           if (unres_pdb) then
 718 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
 719             call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
 720             if (fail) then
 721               e2(1)=0.0d0
 722               e2(2)=1.0d0
 723               e2(3)=0.0d0
 724             endif
 725             do j=1,3
 726               c(j,i)=c(j,i+1)-1.9d0*e2(j)
 727             enddo
 728           else !unres_pdb
 729            do j=1,3
 730             dcj=(c(j,i+3)-c(j,i+2))/2.0
 731             if (dcj.eq.0) dcj=1.23591524223
 732             c(j,i)=c(j,i+1)-dcj
 733             c(j,nres+i)=c(j,i)
 734            enddo
 735           endif !unres_pdb
 736          endif !itype(i+1).eq.ntyp1
 737         endif  !itype.eq.ntyp1
 738       enddo
 739 C Calculate the CM of the last side chain.
 740       if (unres_pdb) then
 741         do j=1,3
 742           dc(j,ires)=sccor(j,iii)
 743         enddo
 744       else
 745         call sccenter(ires,iii,sccor)
 746       endif
 747       nsup=nres
 748       nstart_sup=1
 749       if (itype(nres).ne.10) then
 750         nres=nres+1
 751         itype(nres)=ntyp1
 752         if (unres_pdb) then
 753 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
 754           call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
 755           if (fail) then
 756             e2(1)=0.0d0
 757             e2(2)=1.0d0
 758             e2(3)=0.0d0
 759           endif
 760           do j=1,3
 761             c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
 762           enddo
 763         else
 764         do j=1,3
 765           dcj=(c(j,nres-2)-c(j,nres-3))/2.0
 766             if (dcj.eq.0) dcj=1.23591524223
 767           c(j,nres)=c(j,nres-1)+dcj
 768           c(j,2*nres)=c(j,nres)
 769         enddo
 770       endif
 771       endif
 772       do i=2,nres-1
 773         do j=1,3
 774           c(j,i+nres)=dc(j,i)
 775         enddo
 776       enddo
 777       do j=1,3
 778         c(j,nres+1)=c(j,1)
 779         c(j,2*nres)=c(j,nres)
 780       enddo
 781       if (itype(1).eq.ntyp1) then
 782         nsup=nsup-1
 783         nstart_sup=2
 784         if (unres_pdb) then
 785 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
 786           call refsys(2,3,4,e1,e2,e3,fail)
 787           if (fail) then
 788             e2(1)=0.0d0
 789             e2(2)=1.0d0
 790             e2(3)=0.0d0
 791           endif
 792           do j=1,3
 793             c(j,1)=c(j,2)-1.9d0*e2(j)
 794           enddo
 795         else
 796         do j=1,3
 797           dcj=(c(j,4)-c(j,3))/2.0
 798           c(j,1)=c(j,2)-dcj
 799           c(j,nres+1)=c(j,1)
 800         enddo
 801         endif
 802       endif
 803 C Calculate internal coordinates.
 804       if (lprn) then
 805       write (iout,'(/a)')
 806      &  "Cartesian coordinates of the reference structure"
 807       write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
 808      & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
 809       do ires=1,nres
 810         write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
 811      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
 812      &    (c(j,ires+nres),j=1,3)
 813       enddo
 814       endif
 815 C Calculate internal coordinates.
 816        write (iout,'(a)')
 817      &   "Backbone and SC coordinates as read from the PDB"
 818        do ires=1,nres
 819         write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
 820      &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
 821      &    (c(j,nres+ires),j=1,3)
 822        enddo
 823       call int_from_cart(.true.,.false.)
 824       call sc_loc_geom(.false.)
 825       do i=1,nres
 826         thetaref(i)=theta(i)
 827         phiref(i)=phi(i)
 828       enddo
 829       do i=1,nres-1
 830         do j=1,3
 831           dc(j,i)=c(j,i+1)-c(j,i)
 832           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
 833         enddo
 834       enddo
 835       do i=2,nres-1
 836         do j=1,3
 837           dc(j,i+nres)=c(j,i+nres)-c(j,i)
 838           dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
 839         enddo
 840 c        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
 841 c     &   vbld_inv(i+nres)
 842       enddo
 843       do i=1,nres
 844         do j=1,3
 845           cref(j,i)=c(j,i)
 846           cref(j,i+nres)=c(j,i+nres)
 847         enddo
 848       enddo
 849       do i=1,2*nres
 850         do j=1,3
 851           chomo(j,i,k)=c(j,i)
 852         enddo
 853       enddo
 854
 855       return
 856       end
 857
 858