source/maxlik/src_MD_T_maxlik-NEWCORR/molread_zs.F

   1       subroutine molread_zs(molnum)
   2 C
   3 C Read molecular data.
   4 C
   5       implicit real*8 (a-h,o-z)
   6       include 'DIMENSIONS'
   7       include 'DIMENSIONS.ZSCOPT'
   8       include 'COMMON.IOUNITS'
   9       include 'COMMON.GEO'
  10       include 'COMMON.VAR'
  11       include 'COMMON.INTERACT'
  12       include 'COMMON.LOCAL'
  13       include 'COMMON.NAMES'
  14       include 'COMMON.CHAIN'
  15       include 'COMMON.FFIELD'
  16       include 'COMMON.SBRIDGE'
  17       include 'COMMON.ALLPROT'
  18       include 'COMMON.TORCNSTR'
  19       character*4 sequence(maxres)
  20       integer rescode
  21       double precision x(maxvar)
  22       character*320 controlcard,ucase
  23       dimension itype_pdb(maxres)
  24       logical seq_comp
  25       call card_concat(controlcard,.true.)
  26       call reada(controlcard,'SCAL14',scal14,0.4d0)
  27       call reada(controlcard,'SCALSCP',scalscp,1.0d0)
  28       call reada(controlcard,'CUTOFF',cutoff_corr,7.0d0)
  29       call reada(controlcard,'DELT_CORR',delt_corr,0.5d0)
  30       r0_corr=cutoff_corr-delt_corr
  31       call readi(controlcard,"NRES",nres,0)
  32       iscode=index(controlcard,"ONE_LETTER")
  33       if (nres.le.0) then
  34         write (iout,*) "Error: no residues in molecule",molnum
  35         stop
  36       endif
  37       write(iout,*) 'molnum:',molnum,' nres=',nres
  38 C Read sequence of the protein
  39       if (iscode.gt.0) then
  40         read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
  41       else
  42         read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
  43       endif
  44 C Convert sequence to numeric code
  45       do i=1,nres
  46         itype(i)=rescode(i,sequence(i),iscode)
  47       enddo
  48       write (iout,*) "Numeric code:"
  49       write (iout,'(20i4)') (itype(i),i=1,nres)
  50       do i=1,nres-1
  51 #ifdef PROCOR
  52         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
  53 #else
  54         if (itype(i).eq.ntyp1) then
  55 #endif
  56           itel(i)=0
  57 #ifdef PROCOR
  58         else if (itype(i+1).ne.20) then
  59 #else
  60         else if (itype(i).ne.20) then
  61 #endif
  62           itel(i)=1
  63         else
  64           itel(i)=2
  65         endif
  66       enddo
  67       call read_bridge
  68       nnt=1
  69       nct=nres
  70       write(iout,*) 'NNT=',NNT,' NCT=',NCT
  71       if (itype(1).eq.ntyp1) nnt=2
  72       if (itype(nres).eq.ntyp1) nct=nct-1
  73       call setup_var
  74       call init_int_table
  75       call store_molinfo(molnum)
  76       if (ns_zs(molnum).gt.0) then
  77         write (iout,'(/a,i3,a)') 'The chain contains',ns_zs(molnum),
  78      &  ' disulfide-bridging cysteines.'
  79         write (iout,'(20i4)') (iss_zs(i,molnum),i=1,ns_zs(molnum))
  80         write (iout,'(/a/)') 'Pre-formed links are:'
  81         do i=1,nss_zs(1,molnum)
  82           i1=ihpb_zs(i,1,molnum)-nres_zs(molnum)
  83           i2=jhpb_zs(i,1,molnum)-nres_zs(molnum)
  84           it1=itype_zs(i1,molnum)
  85           it2=itype_zs(i2,molnum)
  86          write (iout,'(2a,i3,3a,i3,a,3f10.3)')
  87      &    restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',
  88      &    dhpb_zs(i,molnum),ebr,forcon_zs(i,molnum)
  89         enddo
  90       endif
  91       write (iout,*) "Protein:",molnum," leaving MOLREAD_ZS"
  92       call flush(iout)
  93       return
  94       end
  95 c-----------------------------------------------------------------------------
  96       logical function seq_comp(itypea,itypeb,length)
  97       implicit none
  98       integer length,itypea(length),itypeb(length)
  99       integer i
 100       do i=1,length
 101         if (itypea(i).ne.itypeb(i)) then
 102           seq_comp=.false.
 103           return
 104         endif
 105       enddo
 106       seq_comp=.true.
 107       return
 108       end
 109 c-----------------------------------------------------------------------------
 110       subroutine read_bridge
 111 C Read information about disulfide bridges.
 112       implicit real*8 (a-h,o-z)
 113       include 'DIMENSIONS'
 114       include 'DIMENSIONS.ZSCOPT'
 115       include 'COMMON.IOUNITS'
 116       include 'COMMON.GEO'
 117       include 'COMMON.VAR'
 118       include 'COMMON.INTERACT'
 119       include 'COMMON.NAMES'
 120       include 'COMMON.CHAIN'
 121       include 'COMMON.FFIELD'
 122       include 'COMMON.SBRIDGE'
 123       include 'COMMON.ALLPROT'
 124 C Read bridging residues.
 125       read (inp,*) ns,(iss(i),i=1,ns)
 126 c      print *,'ns=',ns
 127       write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
 128 C Check whether the specified bridging residues are cystines.
 129       do i=1,ns
 130         if (itype(iss(i)).ne.1) then
 131           write (iout,'(2a,i3,a)')
 132      &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
 133      &   ' can form a disulfide bridge?!!!'
 134           write (*,'(2a,i3,a)')
 135      &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
 136      &   ' can form a disulfide bridge?!!!'
 137          stop
 138         endif
 139       enddo
 140 C Read preformed bridges.
 141       if (ns.gt.0) then
 142       read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
 143       write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
 144       if (nss.gt.0) then
 145         nhpb=nss
 146 C Check if the residues involved in bridges are in the specified list of
 147 C bridging residues.
 148         do i=1,nss
 149           do j=1,i-1
 150             if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
 151      &      .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
 152               write (iout,'(a,i3,a)') 'Disulfide pair',i,
 153      &      ' contains residues present in other pairs.'
 154               write (*,'(a,i3,a)') 'Disulfide pair',i,
 155      &      ' contains residues present in other pairs.'
 156               stop
 157             endif
 158           enddo
 159           do j=1,ns
 160             if (ihpb(i).eq.iss(j)) goto 10
 161           enddo
 162           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
 163    10     continue
 164           do j=1,ns
 165             if (jhpb(i).eq.iss(j)) goto 20
 166           enddo
 167           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
 168    20     continue
 169           dhpb(i)=dbr
 170           forcon(i)=fbr
 171         enddo
 172         do i=1,nss
 173           ihpb(i)=ihpb(i)+nres
 174           jhpb(i)=jhpb(i)+nres
 175         enddo
 176       endif
 177       endif
 178       return
 179       end
 180 c------------------------------------------------------------------------------
 181       subroutine store_molinfo(molnum)
 182       implicit real*8 (a-h,o-z)
 183       include "DIMENSIONS"
 184       include 'DIMENSIONS.ZSCOPT'
 185       include "COMMON.ALLPROT"
 186       include 'COMMON.CHAIN'
 187       include 'COMMON.SBRIDGE'
 188       include "COMMON.VAR"
 189       include "COMMON.INTERACT"
 190       include "COMMON.LOCAL"
 191       include "COMMON.IOUNITS"
 192       nres_zs(molnum)=nres
 193       nnt_zs(molnum)=nnt
 194       nct_zs(molnum)=nct
 195       iatsc_s_zs(molnum)=iatsc_s
 196       iatsc_e_zs(molnum)=iatsc_e
 197       iatel_s_zs(molnum)=iatel_s
 198       iatel_e_zs(molnum)=iatel_e
 199       iturn3_start_zs(molnum)=iturn3_start
 200       iturn3_end_zs(molnum)=iturn3_end
 201       iturn4_start_zs(molnum)=iturn4_start
 202       iturn4_end_zs(molnum)=iturn4_end
 203       iatscp_s_zs(molnum)=iatscp_s
 204       iatscp_e_zs(molnum)=iatscp_e
 205       loc_start_zs(molnum)=loc_start
 206       loc_end_zs(molnum)=loc_end
 207       ithet_start_zs(molnum)=ithet_start
 208       ithet_end_zs(molnum)=ithet_end
 209       iphi_start_zs(molnum)=iphi_start
 210       iphi_end_zs(molnum)=iphi_end
 211       itau_start_zs(molnum)=itau_start
 212       itau_end_zs(molnum)=itau_end
 213       nvar_zs(molnum)=nvar
 214       nphi_zs(molnum)=nphi
 215       ntheta_zs(molnum)=ntheta
 216       nside_zs(molnum)=nside
 217       do i=1,nres
 218         ialph_zs(i,1,molnum)=ialph(i,1)
 219         ialph_zs(i,2,molnum)=ialph(i,2)
 220       enddo
 221       do i=1,nres
 222         nint_gr_zs(i,molnum)=nint_gr(i)
 223         nscp_gr_zs(i,molnum)=nscp_gr(i)
 224         do j=1,nint_gr(i)
 225           istart_zs(i,j,molnum)=istart(i,j)
 226           iend_zs(i,j,molnum)=iend(i,j)
 227         enddo
 228         itype_zs(i,molnum)=itype(i)
 229         itel_zs(i,molnum)=itel(i)
 230         ielstart_zs(i,molnum)=ielstart(i)
 231         ielend_zs(i,molnum)=ielend(i)
 232 c        write (iout,*) "i",i," nscp_gr",nscp_gr(i),
 233 c     &   " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
 234         do j=1,nscp_gr(i)
 235           iscpstart_zs(i,j,molnum)=iscpstart(i,j)
 236           iscpend_zs(i,j,molnum)=iscpend(i,j)
 237         enddo
 238       enddo
 239       ns_zs(molnum)=ns
 240 c      nss_zs(molnum)=nss
 241 c      nfree_zs(molnum)=nfree
 242 c      do i=1,ns
 243 c        iss_zs(i,molnum)=iss(i)
 244 c      enddo
 245 c      do i=1,nss
 246 c        ihpb_zs(i,molnum)=ihpb(i)
 247 c        jhpb_zs(i,molnum)=jhpb(i)
 248 c        dhpb_zs(i,molnum)=dhpb(i)
 249 c        forcon_zs(i,molnum)=forcon(i)
 250 c      enddo
 251       link_start_zs(molnum)=link_start
 252       link_end_zs(molnum)=link_end
 253       return
 254       end
 255 c------------------------------------------------------------------------------
 256       subroutine restore_molinfo(molnum)
 257       implicit real*8 (a-h,o-z)
 258       include "DIMENSIONS"
 259       include 'DIMENSIONS.ZSCOPT'
 260       include "COMMON.ALLPROT"
 261       include "COMMON.SBRIDGE"
 262       include "COMMON.CHAIN"
 263       include "COMMON.VAR"
 264       include "COMMON.INTERACT"
 265       include "COMMON.TORCNSTR"
 266       include "COMMON.LOCAL"
 267       ndih_constr=0
 268       nres=nres_zs(molnum)
 269       nnt=nnt_zs(molnum)
 270       nct=nct_zs(molnum)
 271       iatsc_s=iatsc_s_zs(molnum)
 272       iatsc_e=iatsc_e_zs(molnum)
 273       iatel_s=iatel_s_zs(molnum)
 274       iatel_e=iatel_e_zs(molnum)
 275       iturn3_start=iturn3_start_zs(molnum)
 276       iturn3_end=iturn3_end_zs(molnum)
 277       iturn4_start=iturn4_start_zs(molnum)
 278       iturn4_end=iturn4_end_zs(molnum)
 279       iatscp_s=iatscp_s_zs(molnum)
 280       iatscp_e=iatscp_e_zs(molnum)
 281       ithet_start=ithet_start_zs(molnum)
 282       ithet_end=ithet_end_zs(molnum)
 283       iphi_start=iphi_start_zs(molnum)
 284       iphi_end=iphi_end_zs(molnum)
 285       itau_start=itau_start_zs(molnum)
 286       itau_end=itau_end_zs(molnum)
 287       loc_start=loc_start_zs(molnum)
 288       loc_end=loc_end_zs(molnum)
 289       nvar=nvar_zs(molnum)
 290       nphi=nphi_zs(molnum)
 291       ntheta=ntheta_zs(molnum)
 292       nside=nside_zs(molnum)
 293       do i=1,nres
 294         ialph(i,1)=ialph_zs(i,1,molnum)
 295         ialph(i,2)=ialph_zs(i,2,molnum)
 296       enddo
 297       do i=1,nres
 298         nint_gr(i)=nint_gr_zs(i,molnum)
 299         nscp_gr(i)=nscp_gr_zs(i,molnum)
 300         do j=1,nint_gr(i)
 301           istart(i,j)=istart_zs(i,j,molnum)
 302           iend(i,j)=iend_zs(i,j,molnum)
 303         enddo
 304         itype(i)=itype_zs(i,molnum)
 305         itel(i)=itel_zs(i,molnum)
 306         ielstart(i)=ielstart_zs(i,molnum)
 307         ielend(i)=ielend_zs(i,molnum)
 308         do j=1,nscp_gr(i)
 309           iscpstart(i,j)=iscpstart_zs(i,j,molnum)
 310           iscpend(i,j)=iscpend_zs(i,j,molnum)
 311         enddo
 312       enddo
 313       ns=ns_zs(molnum)
 314 c      nss=nss_zs(molnum)
 315 c      nfree=nfree_zs(molnum)
 316 c      do i=1,ns
 317 c        iss(i)=iss_zs(i,molnum)
 318 c      enddo
 319 c      do i=1,nss
 320 c        ihpb(i)=ihpb_zs(i,molnum)
 321 c        jhpb(i)=jhpb_zs(i,molnum)
 322 c        dhpb(i)=dhpb_zs(i,molnum)
 323 c        forcon(i)=forcon_zs(i,molnum)
 324 c      enddo
 325       link_start=link_start_zs(molnum)
 326       link_end=link_end_zs(molnum)
 327       return
 328       end
 329 c------------------------------------------------------------------------------
 330       subroutine read_angles(kanal,iscor,energ,iprot,*)
 331       implicit real*8 (a-h,o-z)
 332       include 'DIMENSIONS'
 333       include 'DIMENSIONS.ZSCOPT'
 334       include 'COMMON.INTERACT'
 335       include 'COMMON.SBRIDGE'
 336       include 'COMMON.GEO'
 337       include 'COMMON.VAR'
 338       include 'COMMON.CHAIN'
 339       include 'COMMON.IOUNITS'
 340       character*80 lineh
 341       read(kanal,'(a80)',end=10,err=10) lineh
 342       read(lineh(:5),*,err=8) ic
 343       read(lineh(6:),*,err=8) energ
 344       goto 9
 345     8 ic=1
 346       print *,'error, assuming e=1d10',lineh
 347       energ=1d10
 348       nss=0
 349     9 continue
 350       read(lineh(18:),*,end=10,err=10) nss
 351       IF (NSS.LT.9) THEN
 352         read (lineh(20:),*,end=10,err=10)
 353      &  (IHPB(I),JHPB(I),I=1,NSS),iscor
 354       ELSE
 355         read (lineh(20:),*,end=10,err=10) (IHPB(I),JHPB(I),I=1,8)
 356         read (kanal,*,end=10,err=10) (IHPB(I),JHPB(I),
 357      &    I=9,NSS),iscor
 358       ENDIF
 359 c      print *,"energy",energ," iscor",iscor
 360       read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
 361       read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
 362       read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
 363       read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
 364       do i=1,nres
 365         theta(i)=deg2rad*theta(i)
 366         phi(i)=deg2rad*phi(i)
 367         alph(i)=deg2rad*alph(i)
 368         omeg(i)=deg2rad*omeg(i)
 369       enddo
 370       return
 371    10 return1
 372       end