X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fio_config.f90;h=3f4303ac0a17a5e96f77b87baf4ce8af642b1d10;hb=705644e0cbb7678faefd6fe1bc436159d38ad85d;hp=378086bd724037e38a53d88e4341bb95984e8afe;hpb=d5e2a0d87b8ff9f3e83fdfc98d0f920ef7f96aa3;p=unres4.git

diff --git a/source/unres/io_config.f90 b/source/unres/io_config.f90
index 378086b..3f4303a 100644
--- a/source/unres/io_config.f90
+++ b/source/unres/io_config.f90
@@ -782,9 +782,6 @@
       allocate(nbondterm(ntyp)) !(ntyp)
       allocate(vbldsc0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
       allocate(aksc(maxbondterm,ntyp)) !(maxbondterm,ntyp)
-      allocate(msc(ntyp+1,5)) !(ntyp+1)
-      allocate(isc(ntyp+1,5)) !(ntyp+1)
-      allocate(restok(ntyp+1,5)) !(ntyp+1)
       allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
       allocate(long_r_sidechain(ntyp))
       allocate(short_r_sidechain(ntyp))
@@ -792,6 +789,10 @@
       dsc_inv(:)=0.0d0
 
 #ifdef CRYST_BOND
+      allocate(msc(ntyp+1)) !(ntyp+1)
+      allocate(isc(ntyp+1)) !(ntyp+1)
+      allocate(restok(ntyp+1)) !(ntyp+1)
+
       read (ibond,*) vbldp0,akp,mp,ip,pstok
       do i=1,ntyp
         nbondterm(i)=1
@@ -804,6 +805,10 @@
         endif
       enddo
 #else
+      allocate(msc(ntyp+1,5)) !(ntyp+1)
+      allocate(isc(ntyp+1,5)) !(ntyp+1)
+      allocate(restok(ntyp+1,5)) !(ntyp+1)
+
       read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp(1),ip(1),pstok(1)
       do i=1,ntyp_molec(1)
         read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),&
@@ -2517,6 +2522,8 @@
       allocate(dhead_scphoi(ntyp_molec(1)))
       allocate(rborn_scphoi(ntyp_molec(1)))
       allocate(rborn_scphoj(ntyp_molec(1)))
+      allocate(alphi_scpho(ntyp_molec(1)))
+
 
 !      j=1
        do j=1,ntyp_molec(1) ! without U then we will take T for U
@@ -2531,7 +2538,8 @@
         read(isidep_scpho,*) &
        (wqdip_scpho(k,j),k=1,2),wqq_scpho(j),dhead_scphoi(j)
         read(isidep_scpho,*) &
-         epsintab_scpho(j),alphapol_scpho(j),rborn_scphoi(j),rborn_scphoj(j)
+         epsintab_scpho(j),alphapol_scpho(j),rborn_scphoi(j),rborn_scphoj(j), &
+         alphi_scpho(j)
        
        END DO
       allocate(aa_scpho(ntyp_molec(1)))
@@ -2777,15 +2785,27 @@
 !      write (2,*) "UNRES_PDB",unres_pdb
       ires=0
       ires_old=0
+#ifdef WHAM_RUN
+      do i=1,nres
+       do j=1,5
+        itype(i,j)=0
+       enddo
+      enddo
+#endif
       nres=0
       iii=0
       lsecondary=.false.
       nhfrag=0
       nbfrag=0
+      do j=1,5
+       nres_molec(j)=0
+      enddo
+      
+       
 !-----------------------------
       allocate(hfrag(2,maxres/3)) !(2,maxres/3)
       allocate(bfrag(4,maxres/3)) !(4,maxres/3)
-
+      if(.not. allocated(istype)) allocate(istype(maxres))
       do i=1,100000
         read (ipdbin,'(a80)',end=10) card
 !       write (iout,'(a)') card
@@ -2898,7 +2918,7 @@
 !              nres_molec(molecule)=nres_molec(molecule)+1
             else
              molecule=2
-              itype(ires,molecule)=rescode(ires,res(2:4),0,molecule)
+              itype(ires,molecule)=rescode(ires,res(2:3),0,molecule)
 !              nres_molec(molecule)=nres_molec(molecule)+1
              read (card(19:19),'(a1)') sugar
              isugar=sugarcode(sugar,ires)
@@ -2968,11 +2988,19 @@
 !              print *,ires,istype(ires)
             endif
             if (unres_pdb) then
+              molecule=2
+!              print *,"nres_molec(molecule)",nres_molec(molecule),ires
               read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+              nres_molec(molecule)=nres_molec(molecule)+1
+              print *,"nres_molec(molecule)",nres_molec(molecule),ires
+
             else
               iii=iii+1
               read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
             endif
+          else if ((atom.eq."C1'").and.unres_pdb) then
+              iii=iii+1
+              read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
 !            write (*,*) card(23:27),ires,itype(ires,1)
           else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. &
                    atom.ne.'N' .and. atom.ne.'C' .and. &
@@ -3013,7 +3041,8 @@
            molecule=5
            nres_molec(molecule)=nres_molec(molecule)+1
            print *,"HERE",nres_molec(molecule)
-           itype(ires,molecule)=rescode(ires,res(2:4),0,molecule)
+           res=res(2:3)//' '
+           itype(ires,molecule)=rescode(ires,res,0,molecule)
            read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
           endif
         endif !atom
@@ -3023,9 +3052,10 @@
 ! Calculate dummy residue coordinates inside the "chain" of a multichain
 ! system
       nres=ires
-      if ((ires_old.ne.ires).and.(molecule.ne.5)) &
+      if (((ires_old.ne.ires).and.(molecule.ne.5)) &
+        .and.(.not.unres_pdb)) &
          nres_molec(molecule)=nres_molec(molecule)-2
-!      print *,'I have', nres_molec(:)
+      print *,'I have',nres, nres_molec(:)
       
       do k=1,4 ! ions are without dummy 
        if (nres_molec(k).eq.0) cycle
@@ -3263,7 +3293,9 @@
 ! NOW LETS ROCK! SORTING
       allocate(c_temporary(3,2*nres))
       allocate(itype_temporary(nres,5))
-      allocate(molnum(nres+1))
+      if (.not.allocated(molnum)) allocate(molnum(nres+1))
+      if (.not.allocated(istype)) write(iout,*) &
+          "SOMETHING WRONG WITH ISTYTPE"
       allocate(istype_temp(nres))
        itype_temporary(:,:)=0
       seqalingbegin=1