compiling cluster before tests

diff --git a/source/cluster/wham/src-M/COMMON.CHAIN b/source/cluster/wham/src-M/COMMON.CHAIN
index d3f4c54..03b65c5 100644 (file)
--- a/source/cluster/wham/src-M/COMMON.CHAIN
+++ b/source/cluster/wham/src-M/COMMON.CHAIN
@@ -10,3 +10,7 @@
      &  chain_rep(3,maxres2+2,maxsym), nsup,nstart_sup,
      &  nstart_seq,
      &  nend_sup, chain_length,tabperm(maxperm,maxsym)
+      double precision boxxsize,boxysize,boxzsize,enecut,sscut,sss,
+     &sssgrad
+      common /box/  boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad
+

diff --git a/source/cluster/wham/src-M/include_unres/COMMON.INTERACT b/source/cluster/wham/src-M/include_unres/COMMON.INTERACT
index 650af0d..0db8895 100644 (file)
--- a/source/cluster/wham/src-M/include_unres/COMMON.INTERACT
+++ b/source/cluster/wham/src-M/include_unres/COMMON.INTERACT
@@ -20,7 +20,9 @@ C 12/1/95 Array EPS included in the COMMON block.
      & eps_scp(ntyp,2),rscp(ntyp,2),eps_orig(ntyp,ntyp)
 c 12/5/03 modified 09/18/03 Bond stretching parameters.
       double precision vbldp0,vbldsc0,akp,aksc,abond0,distchainmax
+     &,vbldpDUM
       integer nbondterm
       common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
      & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),
      & distchainmax,nbondterm(ntyp)
+     &,vbldpDUM

diff --git a/source/cluster/wham/src-M/include_unres/COMMON.SPLITELE b/source/cluster/wham/src-M/include_unres/COMMON.SPLITELE
new file mode 100644 (file)
index 0000000..a2f0447
--- /dev/null
+++ b/source/cluster/wham/src-M/include_unres/COMMON.SPLITELE
@@ -0,0 +1,2 @@
+      double precision r_cut,rlamb
+      common /splitele/ r_cut,rlamb

diff --git a/source/cluster/wham/src-M/parmread.F b/source/cluster/wham/src-M/parmread.F
index f02e1a2..7adfb30 100644 (file)
--- a/source/cluster/wham/src-M/parmread.F
+++ b/source/cluster/wham/src-M/parmread.F
@@ -34,8 +34,8 @@ C Assign virtual-bond length
       vblinv=1.0D0/vbl
       vblinv2=vblinv*vblinv
 #ifdef CRYST_BOND
-      read (ibond,*) vbldp0,akp
-      do i=1,ntyp
+      read (ibond,*) vbldp0,vbldpdum,akp
+       do i=1,ntyp
         nbondterm(i)=1
         read (ibond,*) vbldsc0(1,i),aksc(1,i)
         dsc(i) = vbldsc0(1,i)
@@ -46,7 +46,7 @@ C Assign virtual-bond length
         endif
       enddo
 #else
-      read (ibond,*) ijunk,vbldp0,akp,rjunk
+       read (ibond,*) ijunk,vbldp0,vbldpdum,akp,rjunk
       do i=1,ntyp
         read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),
      &   j=1,nbondterm(i))

diff --git a/source/cluster/wham/src-M/readpdb.f b/source/cluster/wham/src-M/readpdb.f
index 725065a..d6742c6 100644 (file)
--- a/source/cluster/wham/src-M/readpdb.f
+++ b/source/cluster/wham/src-M/readpdb.f
@@ -22,7 +22,8 @@ C geometry.
           goto 10
         else if (card(:3).eq.'TER') then
 C End current chain
-          ires_old=ires+1 
+          ires_old=ires+2
+          itype(ires_old-1)=ntyp1
           itype(ires_old)=ntyp1
           ibeg=2
 c          write (iout,*) "Chain ended",ires,ishift,ires_old
@@ -82,13 +83,29 @@ C system
       do i=2,nres-1
 c        write (iout,*) i,itype(i)
         if (itype(i).eq.ntyp1) then
+         if (itype(i+1).eq.ntyp1) then
+
 c          write (iout,*) "dummy",i,itype(i)
-          do j=1,3
-            c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
+C          do j=1,3
+C            c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
 c            c(j,i)=(c(j,i-1)+c(j,i+1))/2
-            dc(j,i)=c(j,i)
-          enddo
-        endif
+C            dc(j,i)=c(j,i)
+C          enddo
+           do j=1,3
+             dcj=(c(j,i-2)-c(j,i-3))/2.0
+             c(j,i)=c(j,i-1)+dcj
+             c(j,nres+i)=c(j,i)
+           enddo
+C          endif   !unres_pdb
+         else     !itype(i+1).eq.ntyp1
+           do j=1,3
+            dcj=(c(j,i+3)-c(j,i+2))/2.0
+            c(j,i)=c(j,i+1)-dcj
+            c(j,nres+i)=c(j,i)
+           enddo
+C          endif !unres_pdb
+         endif !itype(i+1).eq.ntyp1
+        endif  !itype.eq.ntyp1
       enddo
 C Calculate the CM of the last side chain.
       call sccenter(ires,iii,sccor)
@@ -98,7 +115,7 @@ C Calculate the CM of the last side chain.
         nres=nres+1
         itype(nres)=ntyp1
         do j=1,3
-          dcj=c(j,nres-2)-c(j,nres-3)
+          dcj=(c(j,nres-2)-c(j,nres-3))/2.0
           c(j,nres)=c(j,nres-1)+dcj
           c(j,2*nres)=c(j,nres)
         enddo
@@ -116,7 +133,7 @@ C Calculate the CM of the last side chain.
         nsup=nsup-1
         nstart_sup=2
         do j=1,3
-          dcj=c(j,4)-c(j,3)
+          dcj=(c(j,4)-c(j,3))/2.0
           c(j,1)=c(j,2)-dcj
           c(j,nres+1)=c(j,1)
         enddo

diff --git a/source/cluster/wham/src-M/readrtns.F b/source/cluster/wham/src-M/readrtns.F
index f29d6f7..936cb42 100644 (file)
--- a/source/cluster/wham/src-M/readrtns.F
+++ b/source/cluster/wham/src-M/readrtns.F
@@ -15,6 +15,7 @@ C
       include 'COMMON.FFIELD'
       include 'COMMON.FREE'
       include 'COMMON.INTERACT'
+      include "COMMON.SPLITELE"
       character*320 controlcard,ucase
 #ifdef MPL
       include 'COMMON.INFO'