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 continue
 171 #ifdef DEBUG
 172       write (iout,'(a,i5)') ' Number of residues found: ',ires
 173 #endif
 174       if (ires.eq.0) return
 175 C Calculate the CM of the last side chain.
 176       if (iii.gt.0)  then
 177       if (unres_pdb) then
 178         do j=1,3
 179           dc(j,ires)=sccor(j,iii)
 180         enddo
 181       else
 182         call sccenter(ires,iii,sccor)
 183       endif
 184       endif
 185       nres=ires
 186       nsup=nres
 187       nstart_sup=1
 188       if (itype(nres).ne.10) then
 189         nres=nres+1
 190         itype(nres)=ntyp1
 191         if (unres_pdb) then
 192 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
 193           call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
 194           if (fail) then
 195             e2(1)=0.0d0
 196             e2(2)=1.0d0
 197             e2(3)=0.0d0
 198           endif
 199           do j=1,3
 200             c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
 201           enddo
 202         else
 203         do j=1,3
 204           dcj=c(j,nres-2)-c(j,nres-3)
 205           c(j,nres)=c(j,nres-1)+dcj
 206           c(j,2*nres)=c(j,nres)
 207         enddo
 208         endif
 209       endif
 210       do i=2,nres-1
 211         do j=1,3
 212           c(j,i+nres)=dc(j,i)
 213         enddo
 214       enddo
 215       do j=1,3
 216         c(j,nres+1)=c(j,1)
 217         c(j,2*nres)=c(j,nres)
 218       enddo
 219       if (itype(1).eq.ntyp1) then
 220         nsup=nsup-1
 221         nstart_sup=2
 222         if (unres_pdb) then
 223 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
 224           call refsys(2,3,4,e1,e2,e3,fail)
 225           if (fail) then
 226             e2(1)=0.0d0
 227             e2(2)=1.0d0
 228             e2(3)=0.0d0
 229           endif
 230           do j=1,3
 231             c(j,1)=c(j,2)-3.8d0*e2(j)
 232           enddo
 233         else
 234         do j=1,3
 235           dcj=c(j,4)-c(j,3)
 236           c(j,1)=c(j,2)-dcj
 237           c(j,nres+1)=c(j,1)
 238         enddo
 239         endif
 240       endif
 241 C Copy the coordinates to reference coordinates
 242 c      do i=1,2*nres
 243 c        do j=1,3
 244 c          cref(j,i)=c(j,i)
 245 c        enddo
 246 c      enddo
 247 C Calculate internal coordinates.
 248       if (lprn) then
 249       write (iout,'(/a)')
 250      &  "Cartesian coordinates of the reference structure"
 251       write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
 252      & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
 253       do ires=1,nres
 254         write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
 255      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
 256      &    (c(j,ires+nres),j=1,3)
 257       enddo
 258       endif
 259 C Calculate internal coordinates.
 260        write (iout,'(a)')
 261      &   "Backbone and SC coordinates as read from the PDB"
 262        do ires=1,nres
 263         write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
 264      &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
 265      &    (c(j,nres+ires),j=1,3)
 266        enddo
 267       call int_from_cart(.true.,.false.)
 268       call sc_loc_geom(.false.)
 269       do i=1,nres
 270         thetaref(i)=theta(i)
 271         phiref(i)=phi(i)
 272       enddo
 273       do i=1,nres-1
 274         do j=1,3
 275           dc(j,i)=c(j,i+1)-c(j,i)
 276           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
 277         enddo
 278       enddo
 279       do i=2,nres-1
 280         do j=1,3
 281           dc(j,i+nres)=c(j,i+nres)-c(j,i)
 282           dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
 283         enddo
 284 c        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
 285 c     &   vbld_inv(i+nres)
 286       enddo
 287 c      call chainbuild
 288 C Copy the coordinates to reference coordinates
 289       do i=1,2*nres
 290         do j=1,3
 291           cref(j,i)=c(j,i)
 292         enddo
 293       enddo
 294
 295
 296       do j=1,nbfrag
 297         do i=1,4
 298          bfrag(i,j)=bfrag(i,j)-ishift
 299         enddo
 300       enddo
 301
 302       do j=1,nhfrag
 303         do i=1,2
 304          hfrag(i,j)=hfrag(i,j)-ishift
 305         enddo
 306       enddo
 307       ishift_pdb=ishift
 308       return
 309       end
 310 c---------------------------------------------------------------------------
 311       subroutine int_from_cart(lside,lprn)
 312       implicit real*8 (a-h,o-z)
 313       include 'DIMENSIONS'
 314       include 'COMMON.LOCAL'
 315       include 'COMMON.VAR'
 316       include 'COMMON.CHAIN'
 317       include 'COMMON.INTERACT'
 318       include 'COMMON.IOUNITS'
 319       include 'COMMON.GEO'
 320       include 'COMMON.NAMES'
 321       character*3 seq,res
 322 c      character*5 atom
 323       character*80 card
 324       dimension sccor(3,20)
 325       integer rescode
 326       logical lside,lprn
 327        if (lprn) then
 328         write (iout,'(/a)')
 329      &  'Internal coordinates calculated from crystal structure.'
 330         if (lside) then
 331           write (iout,'(8a)') '  Res  ','       dvb','     Theta',
 332      & '     Gamma','    Dsc_id','       Dsc','     Alpha',
 333      & '     Beta '
 334         else
 335           write (iout,'(4a)') '  Res  ','       dvb','     Theta',
 336      & '     Gamma'
 337         endif
 338        endif
 339       do i=1,nres-1
 340         iti=itype(i)
 341         if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
 342           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
 343 ctest          stop
 344         endif
 345         vbld(i+1)=dist(i,i+1)
 346         vbld_inv(i+1)=1.0d0/vbld(i+1)
 347         if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
 348         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
 349       enddo
 350 c      if (unres_pdb) then
 351 c        if (itype(1).eq.ntyp1) then
 352 c          theta(3)=90.0d0*deg2rad
 353 c          phi(4)=180.0d0*deg2rad
 354 c          vbld(2)=3.8d0
 355 c          vbld_inv(2)=1.0d0/vbld(2)
 356 c        endif
 357 c        if (itype(nres).eq.ntyp1) then
 358 c          theta(nres)=90.0d0*deg2rad
 359 c          phi(nres)=180.0d0*deg2rad
 360 c          vbld(nres)=3.8d0
 361 c          vbld_inv(nres)=1.0d0/vbld(2)
 362 c        endif
 363 c      endif
 364       if (lside) then
 365         do i=2,nres-1
 366           do j=1,3
 367             c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
 368      &     +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
 369           enddo
 370           iti=itype(i)
 371           di=dist(i,nres+i)
 372 C 10/03/12 Adam: Correction for zero SC-SC bond length
 373           if (itype(i).ne.10 .and. itype(i).ne.ntyp1. and. di.eq.0.0d0)
 374      &     di=dsc(itype(i))
 375           vbld(i+nres)=di
 376           if (itype(i).ne.10) then
 377             vbld_inv(i+nres)=1.0d0/di
 378           else
 379             vbld_inv(i+nres)=0.0d0
 380           endif
 381           if (iti.ne.10) then
 382             alph(i)=alpha(nres+i,i,maxres2)
 383             omeg(i)=beta(nres+i,i,maxres2,i+1)
 384           endif
 385            if (lprn)
 386      &     write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
 387      &     rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
 388      &     rad2deg*alph(i),rad2deg*omeg(i)
 389         enddo
 390       else if (lprn) then
 391         do i=2,nres
 392           iti=itype(i)
 393           write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
 394      &     rad2deg*theta(i),rad2deg*phi(i)
 395         enddo
 396       endif
 397       return
 398       end
 399 c-------------------------------------------------------------------------------
 400       subroutine sc_loc_geom(lprn)
 401       implicit real*8 (a-h,o-z)
 402       include 'DIMENSIONS'
 403       include 'COMMON.LOCAL'
 404       include 'COMMON.VAR'
 405       include 'COMMON.CHAIN'
 406       include 'COMMON.INTERACT'
 407       include 'COMMON.IOUNITS'
 408       include 'COMMON.GEO'
 409       include 'COMMON.NAMES'
 410       include 'COMMON.CONTROL'
 411       double precision x_prime(3),y_prime(3),z_prime(3)
 412       logical lprn
 413       do i=1,nres-1
 414         do j=1,3
 415           dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
 416         enddo
 417       enddo
 418       do i=2,nres-1
 419         if (itype(i).ne.10) then
 420           do j=1,3
 421             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
 422           enddo
 423         else
 424           do j=1,3
 425             dc_norm(j,i+nres)=0.0d0
 426           enddo
 427         endif
 428       enddo
 429       do i=2,nres-1
 430         costtab(i+1) =dcos(theta(i+1))
 431         sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
 432         cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
 433         sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
 434         cosfac2=0.5d0/(1.0d0+costtab(i+1))
 435         cosfac=dsqrt(cosfac2)
 436         sinfac2=0.5d0/(1.0d0-costtab(i+1))
 437         sinfac=dsqrt(sinfac2)
 438         it=itype(i)
 439         if (it.ne.10) then
 440 c
 441 C  Compute the axes of tghe local cartesian coordinates system; store in
 442 c   x_prime, y_prime and z_prime
 443 c
 444         do j=1,3
 445           x_prime(j) = 0.00
 446           y_prime(j) = 0.00
 447           z_prime(j) = 0.00
 448         enddo
 449         do j = 1,3
 450           x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
 451           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
 452         enddo
 453         call vecpr(x_prime,y_prime,z_prime)
 454 c
 455 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
 456 C to local coordinate system. Store in xx, yy, zz.
 457 c
 458         xx=0.0d0
 459         yy=0.0d0
 460         zz=0.0d0
 461         do j = 1,3
 462           xx = xx + x_prime(j)*dc_norm(j,i+nres)
 463           yy = yy + y_prime(j)*dc_norm(j,i+nres)
 464           zz = zz + z_prime(j)*dc_norm(j,i+nres)
 465         enddo
 466
 467         xxref(i)=xx
 468         yyref(i)=yy
 469         zzref(i)=zz
 470         else
 471         xxref(i)=0.0d0
 472         yyref(i)=0.0d0
 473         zzref(i)=0.0d0
 474         endif
 475       enddo
 476       if (lprn) then
 477         do i=2,nres
 478           iti=itype(i)
 479           write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
 480      &      yyref(i),zzref(i)
 481         enddo
 482       endif
 483       return
 484       end
 485 c---------------------------------------------------------------------------
 486       subroutine sccenter(ires,nscat,sccor)
 487       implicit real*8 (a-h,o-z)
 488       include 'DIMENSIONS'
 489       include 'COMMON.CHAIN'
 490       dimension sccor(3,20)
 491       do j=1,3
 492         sccmj=0.0D0
 493         do i=1,nscat
 494           sccmj=sccmj+sccor(j,i)
 495         enddo
 496         dc(j,ires)=sccmj/nscat
 497       enddo
 498       return
 499       end
 500 c---------------------------------------------------------------------------
 501       subroutine bond_regular
 502       implicit none
 503       include 'DIMENSIONS'
 504       include 'COMMON.VAR'
 505       include 'COMMON.LOCAL'
 506       include 'COMMON.INTERACT'
 507       include 'COMMON.CHAIN'
 508       integer i,i1,i2
 509       do i=1,nres-1
 510        vbld(i+1)=vbl
 511        vbld_inv(i+1)=vblinv
 512        vbld(i+1+nres)=dsc(iabs(itype(i+1)))
 513        vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
 514 c       print *,vbld(i+1),vbld(i+1+nres)
 515       enddo
 516 c Adam 2/26/20 Alter virtual bonds for non-blocking end groups of each chain
 517       do i=1,nchain
 518         i1=chain_border(1,i)
 519         i2=chain_border(2,i)
 520         if (i1.gt.1) then
 521           vbld(i1)=vbld(i1)/2
 522           vbld_inv(i1)=vbld_inv(i1)*2
 523         endif
 524         if (i2.lt.nres) then
 525           vbld(i2+1)=vbld(i2+1)/2
 526           vbld_inv(i2+1)=vbld_inv(i2+1)*2
 527         endif
 528       enddo
 529       return
 530       end
 531 c---------------------------------------------------------------------------
 532       subroutine readpdb_template(k)
 533 C Read the PDB file with gaps for read_constr_homology with read2sigma
 534 C and convert the peptide geometry into virtual-chain geometry.
 535       implicit real*8 (a-h,o-z)
 536       include 'DIMENSIONS'
 537       include 'COMMON.LOCAL'
 538       include 'COMMON.VAR'
 539       include 'COMMON.CHAIN'
 540       include 'COMMON.INTERACT'
 541       include 'COMMON.IOUNITS'
 542       include 'COMMON.GEO'
 543       include 'COMMON.NAMES'
 544       include 'COMMON.CONTROL'
 545       integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
 546       logical lprn /.false./,fail
 547       double precision e1(3),e2(3),e3(3)
 548       double precision dcj,efree_temp
 549       character*3 seq,res
 550       character*5 atom
 551       character*80 card
 552       double precision sccor(3,20)
 553       integer rescode
 554       efree_temp=0.0d0
 555       ibeg=1
 556       ishift1=0
 557       ishift=0
 558 c      write (2,*) "UNRES_PDB",unres_pdb
 559       ires=0
 560       ires_old=0
 561       iii=0
 562       lsecondary=.false.
 563       nhfrag=0
 564       nbfrag=0
 565       do
 566         read (ipdbin,'(a80)',end=10) card
 567 c        write (iout,'(a)') card
 568         if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
 569 C Fish out the ATOM cards.
 570         if (index(card(1:4),'ATOM').gt.0) then
 571           read (card(12:16),*) atom
 572 c          write (iout,*) "! ",atom," !",ires
 573 c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
 574           read (card(23:26),*) ires
 575           read (card(18:20),'(a3)') res
 576 c          write (iout,*) "ires",ires,ires-ishift+ishift1,
 577 c     &      " ires_old",ires_old
 578 c          write (iout,*) "ishift",ishift," ishift1",ishift1
 579 c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
 580           if (ires-ishift+ishift1.ne.ires_old) then
 581 C Calculate the CM of the preceding residue.
 582 c            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
 583             if (ibeg.eq.0) then
 584 c              write (iout,*) "Calculating sidechain center iii",iii
 585               if (unres_pdb) then
 586                 do j=1,3
 587                   dc(j,ires)=sccor(j,iii)
 588                 enddo
 589               else
 590                 call sccenter(ires_old,iii,sccor)
 591               endif
 592               iii=0
 593             endif
 594 C Start new residue.
 595             if (res.eq.'Cl-' .or. res.eq.'Na+') then
 596               ires=ires_old
 597               cycle
 598             else if (ibeg.eq.1) then
 599 c              write (iout,*) "BEG ires",ires
 600               ishift=ires-1
 601               if (res.ne.'GLY' .and. res.ne. 'ACE') then
 602                 ishift=ishift-1
 603                 itype(1)=ntyp1
 604               endif
 605               ires=ires-ishift+ishift1
 606               ires_old=ires
 607 c              write (iout,*) "ishift",ishift," ires",ires,
 608 c     &         " ires_old",ires_old
 609               ibeg=0
 610             else
 611               ishift=ishift-(ires-ishift+ishift1-ires_old-1)
 612               ires=ires-ishift+ishift1
 613               ires_old=ires
 614             endif
 615             if (res.eq.'ACE' .or. res.eq.'NHE') then
 616               itype(ires)=10
 617             else
 618               itype(ires)=rescode(ires,res,0)
 619             endif
 620           else
 621             ires=ires-ishift+ishift1
 622           endif
 623 c          write (iout,*) "ires_old",ires_old," ires",ires
 624           if (card(27:27).eq."A" .or. card(27:27).eq."B") then
 625 c            ishift1=ishift1+1
 626           endif
 627 c          write (2,*) "ires",ires," res ",res," ity",ity
 628           if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
 629      &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
 630             read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
 631 c            write (iout,*) "backbone ",atom
 632 #ifdef DEBUG
 633             write (iout,'(2i3,2x,a,3f8.3)')
 634      &      ires,itype(ires),res,(c(j,ires),j=1,3)
 635 #endif
 636             iii=iii+1
 637             do j=1,3
 638               sccor(j,iii)=c(j,ires)
 639             enddo
 640             if (ishift.ne.0) then
 641               ires_ca=ires+ishift-ishift1
 642             else
 643               ires_ca=ires
 644             endif
 645 c            write (*,*) card(23:27),ires,itype(ires)
 646           else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
 647      &             atom.ne.'N' .and. atom.ne.'C' .and.
 648      &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
 649      &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
 650 c            write (iout,*) "sidechain ",atom
 651             iii=iii+1
 652             read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
 653           endif
 654         endif
 655       enddo
 656    10 continue
 657 #ifdef DEBUG
 658       write (iout,'(a,i5)') ' Number of residues found: ',ires
 659 #endif
 660       if (ires.eq.0) return
 661 C Calculate the CM of the last side chain.
 662       if (iii.gt.0)  then
 663       if (unres_pdb) then
 664         do j=1,3
 665           dc(j,ires)=sccor(j,iii)
 666         enddo
 667       else
 668         call sccenter(ires,iii,sccor)
 669       endif
 670       endif
 671       nres=ires
 672       nsup=nres
 673       nstart_sup=1
 674       if (itype(nres).ne.10) then
 675         nres=nres+1
 676         itype(nres)=ntyp1
 677         do j=1,3
 678           dcj=c(j,nres-2)-c(j,nres-3)
 679           c(j,nres)=c(j,nres-1)+dcj
 680           c(j,2*nres)=c(j,nres)
 681         enddo
 682       endif
 683       do i=2,nres-1
 684         do j=1,3
 685           c(j,i+nres)=dc(j,i)
 686         enddo
 687       enddo
 688       do j=1,3
 689         c(j,nres+1)=c(j,1)
 690         c(j,2*nres)=c(j,nres)
 691       enddo
 692       if (itype(1).eq.ntyp1) then
 693         nsup=nsup-1
 694         nstart_sup=2
 695         if (unres_pdb) then
 696 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
 697           call refsys(2,3,4,e1,e2,e3,fail)
 698           if (fail) then
 699             e2(1)=0.0d0
 700             e2(2)=1.0d0
 701             e2(3)=0.0d0
 702           endif
 703           do j=1,3
 704             c(j,1)=c(j,2)-3.8d0*e2(j)
 705           enddo
 706         else
 707         do j=1,3
 708           dcj=c(j,4)-c(j,3)
 709           c(j,1)=c(j,2)-dcj
 710           c(j,nres+1)=c(j,1)
 711         enddo
 712         endif
 713       endif
 714 C Calculate internal coordinates.
 715       if (lprn) then
 716       write (iout,'(/a)')
 717      &  "Cartesian coordinates of the reference structure"
 718       write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
 719      & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
 720       do ires=1,nres
 721         write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
 722      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
 723      &    (c(j,ires+nres),j=1,3)
 724       enddo
 725       endif
 726 C Calculate internal coordinates.
 727        write (iout,'(a)')
 728      &   "Backbone and SC coordinates as read from the PDB"
 729        do ires=1,nres
 730         write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
 731      &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
 732      &    (c(j,nres+ires),j=1,3)
 733        enddo
 734       call int_from_cart(.true.,.false.)
 735       call sc_loc_geom(.false.)
 736       do i=1,nres
 737         thetaref(i)=theta(i)
 738         phiref(i)=phi(i)
 739       enddo
 740       do i=1,nres-1
 741         do j=1,3
 742           dc(j,i)=c(j,i+1)-c(j,i)
 743           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
 744         enddo
 745       enddo
 746       do i=2,nres-1
 747         do j=1,3
 748           dc(j,i+nres)=c(j,i+nres)-c(j,i)
 749           dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
 750         enddo
 751 c        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
 752 c     &   vbld_inv(i+nres)
 753       enddo
 754 c      call chainbuild
 755 C Copy the coordinates to reference coordinates
 756       do i=1,2*nres
 757         do j=1,3
 758           cref(j,i)=c(j,i)
 759           chomo(j,i,k)=c(j,i)
 760         enddo
 761       enddo
 762
 763
 764       ishift_pdb=ishift
 765       return
 766       end