working peptide-phosphate

[unres4.git] / source / unres / io.f90

diff --git a/source/unres/io.f90 b/source/unres/io.f90
index 8505d11..0458733 100644 (file)
--- a/source/unres/io.f90
+++ b/source/unres/io.f90
@@ -720,7 +720,7 @@
 !      integer :: rescode
 !      double precision x(maxvar)
       character(len=256) :: pdbfile
-      character(len=320) :: weightcard
+      character(len=800) :: weightcard
       character(len=80) :: weightcard_t!,ucase
 !      integer,dimension(:),allocatable :: itype_pdb   !(maxres)
 !      common /pizda/ itype_pdb
@@ -742,6 +742,7 @@
       allocate(c(3,2*maxres+2)) !(3,maxres2+2) maxres2=2*maxres
       allocate(dc(3,0:2*maxres)) !(3,0:maxres2)
       allocate(itype(maxres,5)) !(maxres)
+      allocate(istype(maxres))
 !
 ! Zero out tables.
 !
@@ -768,6 +769,19 @@
       call reada(weightcard,'WTURN6',wturn6,1.0D0)
       call reada(weightcard,'WSCCOR',wsccor,1.0D0)
       call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
+      call reada(weightcard,'WVDWPP_NUCL',wvdwpp_nucl,1.0D0)
+      call reada(weightcard,'WELPP',welpp,1.0d0)
+      call reada(weightcard,'WVDWPSB',wvdwpsb,1.0d0)
+      call reada(weightcard,'WELPSB',welpsb,1.0D0)
+      call reada(weightcard,'WVDWSB',wvdwsb,1.0d0)
+      call reada(weightcard,'WELSB',welsb,1.0D0)
+      call reada(weightcard,'WBOND_NUCL',wbond_nucl,1.0D0)
+      call reada(weightcard,'WANG_NUCL',wang_nucl,1.0D0)
+      call reada(weightcard,'WSBLOC',wsbloc,1.0D0)
+      call reada(weightcard,'WTOR_NUCL',wtor_nucl,1.0D0)
+      call reada(weightcard,'WTORD_NUCL',wtor_d_nucl,1.0D0)
+      call reada(weightcard,'WCORR_NUCL',wcorr_nucl,1.0D0)
+      call reada(weightcard,'WCORR3_NUCL',wcorr3_nucl,1.0D0)
       call reada(weightcard,'WBOND',wbond,1.0D0)
       call reada(weightcard,'WTOR',wtor,1.0D0)
       call reada(weightcard,'WTORD',wtor_d,1.0D0)
@@ -782,7 +796,15 @@
       call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
       call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
       call reada(weightcard,'TEMP0',temp0,300.0d0)
+      call reada(weightcard,'WSCBASE',wscbase,1.0D0)
       if (index(weightcard,'SOFT').gt.0) ipot=6
+      call reada(weightcard,'WBOND_NUCL',wbond_nucl,1.0D0)
+      call reada(weightcard,'WCATCAT',wcatcat,0.0d0)
+      call reada(weightcard,'WCATPROT',wcatprot,0.0d0)
+      call reada(weightcard,'WPEPBASE',wpepbase,1.0d0)
+      call reada(weightcard,'WSCPHO',wscpho,1.0d0)
+      call reada(weightcard,'WPEPPHO',wpeppho,1.0d0)
+
 ! 12/1/95 Added weight for the multi-body term WCORR
       call reada(weightcard,'WCORRH',wcorr,1.0D0)
       if (wcorr4.gt.0.0d0) wcorr=wcorr4
@@ -967,8 +989,8 @@
       if (indpdb.eq.0) then
       nres_molec(:)=0
         allocate(sequence(maxres,5))
-
-     if (protein) then
+!      itype(:,:)=0
+      if (protein) then
 ! Read sequence if not taken from the pdb file.
         molec=1
         read (inp,*) nres_molec(molec)
@@ -978,12 +1000,17 @@
         else
           read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec))
         endif
+!        read(inp,*) weightcard_t
+!        print *,"po seq" weightcard_t
 ! Convert sequence to numeric code
         
         do i=1,nres_molec(molec)
           itype(i,1)=rescode(i,sequence(i,molec),iscode,molec)
         enddo
        endif
+!        read(inp,*) weightcard_t
+!        print *,"po seq", weightcard_t
+
        if (nucleic) then
 ! Read sequence if not taken from the pdb file.
         molec=2
@@ -996,7 +1023,7 @@
 
         do i=1,nres_molec(molec)
           istype(i)=sugarcode(sequence(i,molec)(1:1),i)
-          itype(i,1)=rescode(i,sequence(i,molec)(2:4),iscode,molec)
+          itype(i,1)=rescode(i,sequence(i,molec)(2:2),iscode,molec)
         enddo
        endif
 
@@ -1020,6 +1047,17 @@
        
 ! Assign initial virtual bond lengths
 !elwrite(iout,*) "test_alloc"
+        if(.not.allocated(molnum)) then
+         allocate(molnum(nres))
+         itmp=0
+        do i=1,5
+               do j=1,nres_molec(i)
+               itmp=itmp+1
+              molnum(itmp)=i
+               enddo
+         enddo
+!        print *,nres_molec(i)
+        endif
         if(.not.allocated(vbld)) allocate(vbld(2*nres))
 !elwrite(iout,*) "test_alloc"
         if(.not.allocated(vbld_inv)) allocate(vbld_inv(2*nres))
@@ -1089,6 +1127,7 @@
       enddo
       if(me.eq.king.or..not.out1file)then
        write (iout,*) "ITEL"
+       print *,nres,"nres"
        do i=1,nres-1
          write (iout,*) i,itype(i,1),itel(i)
        enddo
@@ -1096,6 +1135,7 @@
       endif
       call read_bridge
 !--------------------------------
+       print *,"tu dochodze"
 ! znamy nres oraz nss można zaalokowac potrzebne tablice
       call alloc_geo_arrays
       call alloc_ener_arrays
@@ -1185,9 +1225,9 @@
       endif
 #endif
       nct=nres
-!d      print *,'NNT=',NNT,' NCT=',NCT
-      if (itype(1,1).eq.ntyp1) nnt=2
-      if (itype(nres,1).eq.ntyp1) nct=nct-1
+      print *,'NNT=',NNT,' NCT=',NCT
+      if (itype(1,molnum(1)).eq.ntyp1_molec(molnum(1))) nnt=2
+      if (itype(nres,molnum(nres)).eq.ntyp1_molec(molnum(nres))) nct=nct-1
       if (pdbref) then
         if(me.eq.king.or..not.out1file) &
          write (iout,'(a,i3)') 'nsup=',nsup