X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Freadrtns.F;h=6c69644d7b99dd41dbd7d4ac0c9bfa77bb877a5f;hb=e82267f59083eb992e3eaf3fba248e90d21d8643;hp=ded6c92f037b4cea42d00735355c7733353cd093;hpb=26f4da2c2e54e6b1bad2f055c4e4e76b5b877d05;p=unres.git

diff --git a/source/wham/src-M/readrtns.F b/source/wham/src-M/readrtns.F
index ded6c92..6c69644 100644
--- a/source/wham/src-M/readrtns.F
+++ b/source/wham/src-M/readrtns.F
@@ -17,6 +17,9 @@
       include "COMMON.FREE"
       include "COMMON.CONTROL"
       include "COMMON.ENERGIES"
+      include "COMMON.SPLITELE"
+      include "COMMON.SBRIDGE"
+      include "COMMON.SHIELD"
       character*800 controlcard
       integer i,j,k,ii,n_ene_found
       integer ind,itype1,itype2,itypf,itypsc,itypp
@@ -25,7 +28,7 @@
       character*16 ucase
       character*16 key
       external ucase
-
+      double precision pi
       call card_concat(controlcard,.true.)
       call readi(controlcard,"N_ENE",n_ene,max_ene)
       if (n_ene.gt.max_ene) then
@@ -74,12 +77,50 @@
       call readi(controlcard,"RESCALE",rescale_mode,1)
       check_conf=index(controlcard,"NO_CHECK_CONF").eq.0
       call reada(controlcard,'DISTCHAINMAX',distchainmax,50.0d0)
+       call reada(controlcard,'BOXX',boxxsize,100.0d0)
+       call reada(controlcard,'BOXY',boxysize,100.0d0)
+       call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+      call readi(controlcard,'TUBEMOD',tubelog,0)
+      write (iout,*) TUBElog,"TUBEMODE"
+      call readi(controlcard,'GENCONSTR',genconstr,0)
+
+c Cutoff range for interactions
+      call reada(controlcard,"R_CUT",r_cut,15.0d0)
+      call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+      call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
+      call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
+      if (lipthick.gt.0.0d0) then
+       bordliptop=(boxzsize+lipthick)/2.0
+       bordlipbot=bordliptop-lipthick
+C      endif
+      if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0))
+     & write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
+      buflipbot=bordlipbot+lipbufthick
+      bufliptop=bordliptop-lipbufthick
+      if ((lipbufthick*2.0d0).gt.lipthick)
+     &write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
+      endif
+      write(iout,*) "bordliptop=",bordliptop
+      write(iout,*) "bordlipbot=",bordlipbot
+      write(iout,*) "bufliptop=",bufliptop
+      write(iout,*) "buflipbot=",buflipbot
       call readi(controlcard,'SYM',symetr,1)
       write (iout,*) "DISTCHAINMAX",distchainmax
       write (iout,*) "delta",delta
       write (iout,*) "einicheck",einicheck
       write (iout,*) "rescale_mode",rescale_mode
       call flush(iout)
+      if (TUBElog.gt.0) then
+       call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
+       call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
+       call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
+       call reada(controlcard,"RTUBE",tubeR0,0.0d0)
+       call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
+       call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
+       call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
+       buftubebot=bordtubebot+tubebufthick
+       buftubetop=bordtubetop-tubebufthick
+      endif
       bxfile=index(controlcard,"BXFILE").gt.0
       cxfile=index(controlcard,"CXFILE").gt.0
       if (nslice .eq. 1 .and. .not.bxfile .and. .not.cxfile)
@@ -90,7 +131,35 @@
       zscfile=index(controlcard,"ZSCFILE").gt.0
       with_dihed_constr = index(controlcard,"WITH_DIHED_CONSTR").gt.0
       write (iout,*) "with_dihed_constr ",with_dihed_constr
+      with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
+      write (iout,*) "with_theta_constr ",with_theta_constr
+      call readi(controlcard,'SHIELD',shield_mode,0)
+C      if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+        write(iout,*) "shield_mode",shield_mode
+C      endif
+      call readi(controlcard,'TORMODE',tor_mode,0)
+C      if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+        write(iout,*) "torsional and valence angle mode",tor_mode
+      if (shield_mode.gt.0) then
+      pi=3.141592d0
+C VSolvSphere the volume of solving sphere
+C      print *,pi,"pi"
+C rpp(1,1) is the energy r0 for peptide group contact and will be used for it 
+C there will be no distinction between proline peptide group and normal peptide
+C group in case of shielding parameters
+      VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+      VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+      write (iout,*) VSolvSphere,VSolvSphere_div
+C long axis of side chain 
+C      do i=1,ntyp
+C      long_r_sidechain(i)=vbldsc0(1,i)
+C      short_r_sidechain(i)=sigma0(i)
+C      enddo
+      buff_shield=1.0d0
+      endif
+
       call readi(controlcard,'CONSTR_DIST',constr_dist,0)
+      dyn_ss=index(controlcard,"DYN_SS").gt.0
       return
       end
 c------------------------------------------------------------------------------
@@ -778,3 +847,87 @@ c-------------------------------------------------------------------------------
       iroof = ii
       return
       end
+C--------------------------------------------------------------------------
+      subroutine gen_dist_constr
+C Generate CA distance constraints.
+      implicit real*8 (a-h,o-z)
+      include "DIMENSIONS"
+      include "DIMENSIONS.ZSCOPT"
+      include "DIMENSIONS.FREE"
+      include "COMMON.TORSION"
+      include "COMMON.INTERACT"
+      include "COMMON.IOUNITS"
+      include "COMMON.TIME1"
+      include "COMMON.PROT"
+      include "COMMON.PROTFILES"
+      include "COMMON.CHAIN"
+      include "COMMON.NAMES"
+      include "COMMON.FFIELD"
+      include "COMMON.ENEPS"
+      include "COMMON.WEIGHTS"
+      include "COMMON.FREE"
+      include "COMMON.CONTROL"
+      include "COMMON.ENERGIES"
+      include "COMMON.SPLITELE"
+      include "COMMON.SBRIDGE"
+      include "COMMON.SHIELD"
+      dimension itype_pdb(maxres)
+      common /pizda/ itype_pdb
+      character*2 iden
+cd      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
+cd      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
+cd     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
+cd     & ' nsup',nsup
+      if (constr_dist.eq.11) then
+             do i=nstart_sup,nstart_sup+nsup-1
+              do j=i+2,nstart_sup+nsup-1
+                 distance=dist(i,j)
+                 if (distance.le.15.0) then
+                 nhpb=nhpb+1
+                 ihpb(nhpb)=i+nstart_seq-nstart_sup
+                 jhpb(nhpb)=j+nstart_seq-nstart_sup
+                 forcon(nhpb)=sqrt(0.04*distance)
+                 fordepth(nhpb)=sqrt(40.0/distance)
+                 dhpb(nhpb)=distance-0.1d0
+                 dhpb1(nhpb)=distance+0.1d0
+
+C#ifdef MPI
+C          if (.not.out1file .or. me.eq.king)
+C     &    write (iout,'(a,3i5,f8.2,f10.2)') "+dist.constr ",
+C     &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+C#else
+          write (iout,'(a,3i5,f8.2,f10.2)') "+dist.constr ",
+     &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+C#endif
+            endif
+             enddo
+           enddo
+      else
+      do i=nstart_sup,nstart_sup+nsup-1
+cd      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
+cd     &    ' seq_pdb', restyp(itype_pdb(i))
+        do j=i+2,nstart_sup+nsup-1
+          nhpb=nhpb+1
+          ihpb(nhpb)=i+nstart_seq-nstart_sup
+          jhpb(nhpb)=j+nstart_seq-nstart_sup
+          forcon(nhpb)=weidis
+          dhpb(nhpb)=dist(i,j)
+        enddo
+      enddo
+      endif
+cd      write (iout,'(a)') 'Distance constraints:' 
+cd      do i=nss+1,nhpb
+cd        ii=ihpb(i)
+cd        jj=jhpb(i)
+cd        iden='CA'
+cd        if (ii.gt.nres) then
+cd          iden='SC'
+cd          ii=ii-nres
+cd          jj=jj-nres
+cd        endif
+cd        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)') 
+cd     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
+cd     &  dhpb(i),forcon(i)
+cd      enddo
+      return
+      end