Dzialajacy cluster dla D aminokwasow

diff --git a/bin/cluster/unres_clustMD-mult_MPICH-GAB.exe b/bin/cluster/unres_clustMD-mult_MPICH-GAB.exe
index fb4dea9..da95526 100755 (executable)
Binary files a/bin/cluster/unres_clustMD-mult_MPICH-GAB.exe and b/bin/cluster/unres_clustMD-mult_MPICH-GAB.exe differ

diff --git a/source/cluster/wham/src-M/COMMON.LOCAL b/source/cluster/wham/src-M/COMMON.LOCAL
index 1d0f3aa..7d8690a 100644 (file)
--- a/source/cluster/wham/src-M/COMMON.LOCAL
+++ b/source/cluster/wham/src-M/COMMON.LOCAL
@@ -4,9 +4,10 @@
       integer nlob,loc_start,loc_end,ithet_start,ithet_end,
      & iphi_start,iphi_end
 C Parameters of the virtual-bond-angle probability distribution
-      common /thetas/ a0thet(ntyp),athet(2,ntyp),bthet(2,ntyp),
-     &  polthet(0:3,ntyp),gthet(3,ntyp),theta0(ntyp),sig0(ntyp),
-     &  sigc0(ntyp)
+      common /thetas/ a0thet(-ntyp:ntyp),athet(2,-ntyp:ntyp,-1:1,-1:1)
+     &  ,bthet(2,-ntyp:ntyp,-1:1,-1:1),
+     &  polthet(0:3,-ntyp:ntyp),gthet(3,-ntyp:ntyp),theta0(-ntyp:ntyp),
+     &sig0(-ntyp:ntyp),  sigc0(-ntyp:ntyp)
 C Parameters of ab initio-derived potential of virtual-bond-angle bending
       integer nthetyp,ntheterm,ntheterm2,ntheterm3,nsingle,ndouble,
      & ithetyp(ntyp1),nntheterm
@@ -26,7 +27,8 @@ C Parameters of ab initio-derived potential of virtual-bond-angle bending
      &  ndouble,nntheterm
 C Parameters of the side-chain probability distribution
       common /sclocal/ dsc(ntyp1),dsc_inv(ntyp1),bsc(maxlob,ntyp),
-     &  censc(3,maxlob,ntyp),gaussc(3,3,maxlob,ntyp),dsc0(ntyp1),
+     &  censc(3,maxlob,-ntyp:ntyp),gaussc(3,3,maxlob,-ntyp:ntyp),
+     &    dsc0(ntyp1),
      &    nlob(ntyp1)
 C Virtual-bond lenghts
       common /peptbond/ vbl,vblinv,vblinv2,vbl_cis,vbl0

diff --git a/source/cluster/wham/src-M/COMMON.NAMES b/source/cluster/wham/src-M/COMMON.NAMES
index d42c725..7c5b6ee 100644 (file)
--- a/source/cluster/wham/src-M/COMMON.NAMES
+++ b/source/cluster/wham/src-M/COMMON.NAMES
@@ -1,4 +1,4 @@
-      common /names/ restyp(ntyp+1),onelet(ntyp+1)
+      common /names/ restyp(-ntyp1:ntyp1),onelet(-ntyp1:ntyp1)
       character*3 restyp
       character*1 onelet
       character*10 ename,wname

diff --git a/source/cluster/wham/src-M/COMMON.TORSION b/source/cluster/wham/src-M/COMMON.TORSION
index 8a12451..4da8585 100644 (file)
--- a/source/cluster/wham/src-M/COMMON.TORSION
+++ b/source/cluster/wham/src-M/COMMON.TORSION
@@ -1,25 +1,35 @@
 C Torsional constants of the rotation about virtual-bond dihedral angles
       double precision v1,v2,vlor1,vlor2,vlor3,v0
       integer itortyp,ntortyp,nterm,nlor,nterm_old
-      common/torsion/v0(maxtor,maxtor),v1(maxterm,maxtor,maxtor),
-     &    v2(maxterm,maxtor,maxtor),vlor1(maxlor,maxtor,maxtor),
+      common/torsion/v0(-maxtor:maxtor,-maxtor:maxtor,2),
+     &    v1(maxterm,-maxtor:maxtor,-maxtor:maxtor,2),
+     &    v2(maxterm,-maxtor:maxtor,-maxtor:maxtor,2),
+     &    vlor1(maxlor,maxtor,maxtor),
      &    vlor2(maxlor,maxtor,maxtor),vlor3(maxlor,maxtor,maxtor),
-     &    itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),nlor(maxtor,maxtor) 
+     &    itortyp(-ntyp:ntyp),ntortyp,
+     &    nterm(-maxtor:maxtor,-maxtor:maxtor,2),
+     &    nlor(-maxtor:maxtor,-maxtor:maxtor,2) 
      &    ,nterm_old
 C 6/23/01 - constants for double torsionals
       double precision v1c,v1s,v2c,v2s
       integer ntermd_1,ntermd_2
-      common /torsiond/ v1c(2,maxtermd_1,maxtor,maxtor,maxtor),
-     &    v1s(2,maxtermd_1,maxtor,maxtor,maxtor),
-     &    v2c(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor),
-     &    v2s(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor),
-     &    ntermd_1(maxtor,maxtor,maxtor),ntermd_2(maxtor,maxtor,maxtor)
+      common /torsiond/
+     &v1c(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2),
+     &v1s(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2),
+     &v2c(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,
+     & -maxtor:maxtor,2),
+     &v2s(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,
+     &   -maxtor:maxtor,2),
+     &    ntermd_1(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2),
+     &    ntermd_2(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
 C 9/18/99 - added Fourier coeffficients of the expansion of local energy 
 C           surface
       double precision b1,b2,cc,dd,ee,ctilde,dtilde,b1tilde
       integer nloctyp
-      common/fourier/ b1(2,maxtor),b2(2,maxtor),cc(2,2,maxtor),
-     &    dd(2,2,maxtor),ee(2,2,maxtor),ctilde(2,2,maxtor),
-     &    dtilde(2,2,maxtor),b1tilde(2,maxtor),nloctyp
+      common/fourier/ b1(2,-maxtor:maxtor),b2(2,-maxtor:maxtor),
+     &    cc(2,2,-maxtor:maxtor),
+     &    dd(2,2,-maxtor:maxtor),ee(2,2,-maxtor:maxtor),
+     &    ctilde(2,2,-maxtor:maxtor),
+     &    dtilde(2,2,-maxtor:maxtor),b1tilde(2,-maxtor:maxtor),nloctyp
       double precision b
-      common /fourier1/ b(13,maxtor)
+      common /fourier1/ b(13,0:maxtor)

diff --git a/source/cluster/wham/src-M/cartprint.o b/source/cluster/wham/src-M/cartprint.o
index 5094de3..3e54ec3 100644 (file)
Binary files a/source/cluster/wham/src-M/cartprint.o and b/source/cluster/wham/src-M/cartprint.o differ

diff --git a/source/cluster/wham/src-M/chainbuild.f b/source/cluster/wham/src-M/chainbuild.f
index 5774ba6..1e72ff8 100644 (file)
--- a/source/cluster/wham/src-M/chainbuild.f
+++ b/source/cluster/wham/src-M/chainbuild.f
@@ -208,8 +208,8 @@ C
       include 'COMMON.INTERACT'
       dimension xx(3)
 
-      dsci=dsc(itype(i))
-      dsci_inv=dsc_inv(itype(i))
+      dsci=dsc(iabs(itype(i)))
+      dsci_inv=dsc_inv(iabs(itype(i)))
       alphi=alph(i)
       omegi=omeg(i)
       cosalphi=dcos(alphi)

diff --git a/source/cluster/wham/src-M/chainbuild.o b/source/cluster/wham/src-M/chainbuild.o
index 91e249f..384c7c5 100644 (file)
Binary files a/source/cluster/wham/src-M/chainbuild.o and b/source/cluster/wham/src-M/chainbuild.o differ

diff --git a/source/cluster/wham/src-M/contact.f b/source/cluster/wham/src-M/contact.f
index b17f153..6f01564 100644 (file)
--- a/source/cluster/wham/src-M/contact.f
+++ b/source/cluster/wham/src-M/contact.f
@@ -12,9 +12,9 @@
       kkk=3
 c     print *,'nnt=',nnt,' nct=',nct
       do i=nnt+kkk,nct
-        iti=itype(i)
+        iti=iabs(itype(i))
         do j=nnt,i-kkk
-          itj=itype(j)
+          itj=iabs(itype(j))
           if (ipot.ne.4) then
 c           rcomp=sigmaii(iti,itj)+1.0D0
             rcomp=facont*sigmaii(iti,itj)

diff --git a/source/cluster/wham/src-M/contact.o b/source/cluster/wham/src-M/contact.o
index 07d23b9..8ebb51e 100644 (file)
Binary files a/source/cluster/wham/src-M/contact.o and b/source/cluster/wham/src-M/contact.o differ

diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F
index c02d085..030de74 100644 (file)
--- a/source/cluster/wham/src-M/energy_p_new.F
+++ b/source/cluster/wham/src-M/energy_p_new.F
@@ -363,9 +363,9 @@ cd    print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       evdw_t=0.0d0
       do i=iatsc_s,iatsc_e
-        itypi=itype(i)
+        itypi=iabs(itype(i))
         if (itypi.eq.21) cycle
-        itypi1=itype(i+1)
+        itypi1=iabs(itype(i+1))
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -378,7 +378,7 @@ C
 cd        write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
 cd   &                  'iend=',iend(i,iint)
           do j=istart(i,iint),iend(i,iint)
-            itypj=itype(j)
+            itypj=iabs(itype(j))
             if (itypj.eq.21) cycle
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
@@ -528,9 +528,9 @@ c     print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
       evdw=0.0D0
       evdw_t=0.0d0
       do i=iatsc_s,iatsc_e
-        itypi=itype(i)
+        itypi=iabs(itype(i))
         if (itypi.eq.21) cycle
-        itypi1=itype(i+1)
+        itypi1=iabs(itype(i+1))
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -539,7 +539,7 @@ C Calculate SC interaction energy.
 C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
-            itypj=itype(j)
+            itypj=iabs(itype(j))
             if (itypj.eq.21) cycle
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
@@ -632,9 +632,9 @@ c     else
 c     endif
       ind=0
       do i=iatsc_s,iatsc_e
-        itypi=itype(i)
+        itypi=iabs(itype(i))
         if (itypi.eq.21) cycle
-        itypi1=itype(i+1)
+        itypi1=iabs(itype(i+1))
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -648,7 +648,7 @@ C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
             ind=ind+1
-            itypj=itype(j)
+            itypj=iabs(itype(j))
             if (itypj.eq.21) cycle
             dscj_inv=vbld_inv(j+nres)
             chi1=chi(itypi,itypj)
@@ -761,9 +761,9 @@ c     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
 c      if (icall.gt.0) lprn=.true.
       ind=0
       do i=iatsc_s,iatsc_e
-        itypi=itype(i)
+        itypi=iabs(itype(i))
         if (itypi.eq.21) cycle
-        itypi1=itype(i+1)
+        itypi1=iabs(itype(i+1))
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -777,7 +777,7 @@ C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
             ind=ind+1
-            itypj=itype(j)
+            itypj=iabs(itype(j))
             if (itypj.eq.21) cycle
             dscj_inv=vbld_inv(j+nres)
             sig0ij=sigma(itypi,itypj)
@@ -900,9 +900,9 @@ c     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
 c      if (icall.gt.0) lprn=.true.
       ind=0
       do i=iatsc_s,iatsc_e
-        itypi=itype(i)
+        itypi=iabs(itype(i))
         if (itypi.eq.21) cycle
-        itypi1=itype(i+1)
+        itypi1=iabs(itype(i+1))
         xi=c(1,nres+i)
         yi=c(2,nres+i)
         zi=c(3,nres+i)
@@ -916,7 +916,7 @@ C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
             ind=ind+1
-            itypj=itype(j)
+            itypj=iabs(itype(j))
             if (itypj.eq.21) cycle
             dscj_inv=vbld_inv(j+nres)
             sig0ij=sigma(itypi,itypj)
@@ -2769,7 +2769,7 @@ c     &   " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
         do iint=1,nscp_gr(i)
 
         do j=iscpstart(i,iint),iscpend(i,iint)
-          itypj=itype(j)
+          itypj=iabs(itype(j))
           if (itypj.eq.21) cycle
 C Uncomment following three lines for SC-p interactions
 c         xj=c(1,nres+j)-xi
@@ -2880,7 +2880,8 @@ C iii and jjj point to the residues for which the distance is assigned.
         endif
 C 24/11/03 AL: SS bridges handled separately because of introducing a specific
 C    distance and angle dependent SS bond potential.
-        if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+        if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+     &  iabs(itype(jjj)).eq.1) then
           call ssbond_ene(iii,jjj,eij)
           ehpb=ehpb+2*eij
         else
@@ -2940,7 +2941,7 @@ C
       include 'COMMON.VAR'
       include 'COMMON.IOUNITS'
       double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
-      itypi=itype(i)
+      itypi=iabs(itype(i))
       xi=c(1,nres+i)
       yi=c(2,nres+i)
       zi=c(3,nres+i)
@@ -2948,7 +2949,7 @@ C
       dyi=dc_norm(2,nres+i)
       dzi=dc_norm(3,nres+i)
       dsci_inv=dsc_inv(itypi)
-      itypj=itype(j)
+      itypj=iabs(itype(j))
       dscj_inv=dsc_inv(itypj)
       xj=c(1,nres+j)-xi
       yj=c(2,nres+j)-yi
@@ -3026,6 +3027,7 @@ c
       logical energy_dec /.false./
       double precision u(3),ud(3)
       estr=0.0d0
+      estr1=0.0d0
       do i=nnt+1,nct
         if (itype(i-1).eq.21 .or. itype(i).eq.21) then
           estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
@@ -3045,12 +3047,12 @@ c          write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
         endif
 
       enddo
-      estr=0.5d0*AKP*estr
+      estr=0.5d0*AKP*estr+estr1
 c
 c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
 c
       do i=nnt,nct
-        iti=itype(i)
+        iti=iabs(itype(i))
         if (iti.ne.10 .and. iti.ne.21) then
           nbi=nbondterm(iti)
           if (nbi.eq.1) then
@@ -3131,6 +3133,18 @@ c      write (iout,*) ithet_start,ithet_end
 C Zero the energy function and its derivative at 0 or pi.
         call splinthet(theta(i),0.5d0*delta,ss,ssd)
         it=itype(i-1)
+        ichir1=isign(1,itype(i-2))
+        ichir2=isign(1,itype(i))
+         if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+         if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+         if (itype(i-1).eq.10) then
+          itype1=isign(10,itype(i-2))
+          ichir11=isign(1,itype(i-2))
+          ichir12=isign(1,itype(i-2))
+          itype2=isign(10,itype(i))
+          ichir21=isign(1,itype(i))
+          ichir22=isign(1,itype(i))
+         endif
         if (i.gt.3 .and. itype(i-2).ne.21) then
 #ifdef OSF
           phii=phi(i)
@@ -3168,8 +3182,12 @@ C dependent on the adjacent virtual-bond-valence angles (gamma1 & gamma2).
 C In following comments this theta will be referred to as t_c.
         thet_pred_mean=0.0d0
         do k=1,2
-          athetk=athet(k,it)
-          bthetk=bthet(k,it)
+            athetk=athet(k,it,ichir1,ichir2)
+            bthetk=bthet(k,it,ichir1,ichir2)
+          if (it.eq.10) then
+             athetk=athet(k,itype1,ichir11,ichir12)
+             bthetk=bthet(k,itype2,ichir21,ichir22)
+          endif
           thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
         enddo
 c        write (iout,*) "thet_pred_mean",thet_pred_mean
@@ -3177,8 +3195,16 @@ c        write (iout,*) "thet_pred_mean",thet_pred_mean
         thet_pred_mean=thet_pred_mean*ss+a0thet(it)
 c        write (iout,*) "thet_pred_mean",thet_pred_mean
 C Derivatives of the "mean" values in gamma1 and gamma2.
-        dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
-        dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+        dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+     &+athet(2,it,ichir1,ichir2)*y(1))*ss
+         dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+     &          +bthet(2,it,ichir1,ichir2)*z(1))*ss
+         if (it.eq.10) then
+      dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+     &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+        dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+     &         +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+         endif
         if (theta(i).gt.pi-delta) then
           call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
      &         E_tc0)
@@ -3354,7 +3380,8 @@ c      write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
         dephii=0.0d0
         dephii1=0.0d0
         theti2=0.5d0*theta(i)
-        ityp2=ithetyp(itype(i-1))
+CC Ta zmina jest niewlasciwa
+        ityp2=ithetyp(iabs(itype(i-1)))
         do k=1,nntheterm
           coskt(k)=dcos(k*theti2)
           sinkt(k)=dsin(k*theti2)
@@ -3366,7 +3393,7 @@ c      write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
 #else
           phii=phi(i)
 #endif
-          ityp1=ithetyp(itype(i-2))
+          ityp1=ithetyp(iabs(itype(i-2)))
           do k=1,nsingle
             cosph1(k)=dcos(k*phii)
             sinph1(k)=dsin(k*phii)
@@ -3387,7 +3414,7 @@ c      write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
 #else
           phii1=phi(i+1)
 #endif
-          ityp3=ithetyp(itype(i))
+          ityp3=ithetyp(iabs(itype(i)))
           do k=1,nsingle
             cosph2(k)=dcos(k*phii1)
             sinph2(k)=dsin(k*phii1)
@@ -3542,7 +3569,7 @@ c     write (iout,'(a)') 'ESC'
         it=itype(i)
         if (it.eq.21) cycle
         if (it.eq.10) goto 1
-        nlobit=nlob(it)
+        nlobit=nlob(iabs(it))
 c       print *,'i=',i,' it=',it,' nlobit=',nlobit
 c       write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
         theti=theta(i+1)-pipol
@@ -3697,7 +3724,7 @@ C Compute the contribution to SC energy and derivatives
         do iii=-1,1
 
           do j=1,nlobit
-            expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+            expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
 cd          print *,'j=',j,' expfac=',expfac
             escloc_i=escloc_i+expfac
             do k=1,3
@@ -3778,7 +3805,7 @@ C Compute the contribution to SC energy and derivatives
 
       dersc12=0.0d0
       do j=1,nlobit
-        expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+        expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
         escloc_i=escloc_i+expfac
         do k=1,2
           dersc(k)=dersc(k)+Ax(k,j)*expfac
@@ -3842,7 +3869,7 @@ C
         cosfac=dsqrt(cosfac2)
         sinfac2=0.5d0/(1.0d0-costtab(i+1))
         sinfac=dsqrt(sinfac2)
-        it=itype(i)
+        it=iabs(itype(i))
         if (it.eq.10) goto 1
 c
 C  Compute the axes of tghe local cartesian coordinates system; store in
@@ -3882,7 +3909,7 @@ c
         do j = 1,3
           xx = xx + x_prime(j)*dc_norm(j,i+nres)
           yy = yy + y_prime(j)*dc_norm(j,i+nres)
-          zz = zz + z_prime(j)*dc_norm(j,i+nres)
+          zz = zz + dsign(1.0,itype(i))*z_prime(j)*dc_norm(j,i+nres)
         enddo
 
         xxtab(i)=xx
@@ -3892,7 +3919,7 @@ C
 C Compute the energy of the ith side cbain
 C
 c        write (2,*) "xx",xx," yy",yy," zz",zz
-        it=itype(i)
+        it=iabs(itype(i))
         do j = 1,65
           x(j) = sc_parmin(j,it) 
         enddo
@@ -4312,14 +4339,19 @@ c      lprn=.true.
         if (itype(i-2).eq.21 .or. itype(i-1).eq.21
      &       .or. itype(i).eq.21) cycle
         if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+         if (iabs(itype(i)).eq.20) then
+         iblock=2
+         else
+         iblock=1
+         endif
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
         phii=phi(i)
         gloci=0.0D0
 C Regular cosine and sine terms
-        do j=1,nterm(itori,itori1)
-          v1ij=v1(j,itori,itori1)
-          v2ij=v2(j,itori,itori1)
+        do j=1,nterm(itori,itori1,iblock)
+          v1ij=v1(j,itori,itori1,iblock)
+          v2ij=v2(j,itori,itori1,iblock)
           cosphi=dcos(j*phii)
           sinphi=dsin(j*phii)
           etors=etors+v1ij*cosphi+v2ij*sinphi
@@ -4332,7 +4364,7 @@ C          [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1
 C
         cosphi=dcos(0.5d0*phii)
         sinphi=dsin(0.5d0*phii)
-        do j=1,nlor(itori,itori1)
+        do j=1,nlor(itori,itori1,iblock)
           vl1ij=vlor1(j,itori,itori1)
           vl2ij=vlor2(j,itori,itori1)
           vl3ij=vlor3(j,itori,itori1)
@@ -4343,11 +4375,11 @@ C
           gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
         enddo
 C Subtract the constant term
-        etors=etors-v0(itori,itori1)
+        etors=etors-v0(itori,itori1,iblock)
         if (lprn)
      &  write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
      &  restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
-     &  (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+     &  (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6)
         gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
 c       write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
  1215   continue
@@ -4414,12 +4446,14 @@ c     lprn=.true.
         phii1=phi(i+1)
         gloci1=0.0D0
         gloci2=0.0D0
+        iblock=1
+        if (iabs(itype(i+1)).eq.20) iblock=2
 C Regular cosine and sine terms
-        do j=1,ntermd_1(itori,itori1,itori2)
-          v1cij=v1c(1,j,itori,itori1,itori2)
-          v1sij=v1s(1,j,itori,itori1,itori2)
-          v2cij=v1c(2,j,itori,itori1,itori2)
-          v2sij=v1s(2,j,itori,itori1,itori2)
+       do j=1,ntermd_1(itori,itori1,itori2,iblock)
+          v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+          v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+          v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+          v2sij=v1s(2,j,itori,itori1,itori2,iblock)
           cosphi1=dcos(j*phii)
           sinphi1=dsin(j*phii)
           cosphi2=dcos(j*phii1)
@@ -4429,12 +4463,12 @@ C Regular cosine and sine terms
           gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
           gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
         enddo
-        do k=2,ntermd_2(itori,itori1,itori2)
+        do k=2,ntermd_2(itori,itori1,itori2,iblock)
           do l=1,k-1
-            v1cdij = v2c(k,l,itori,itori1,itori2)
-            v2cdij = v2c(l,k,itori,itori1,itori2)
-            v1sdij = v2s(k,l,itori,itori1,itori2)
-            v2sdij = v2s(l,k,itori,itori1,itori2)
+            v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+            v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+            v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+            v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
             cosphi1p2=dcos(l*phii+(k-l)*phii1)
             cosphi1m2=dcos(l*phii-(k-l)*phii1)
             sinphi1p2=dsin(l*phii+(k-l)*phii1)

diff --git a/source/cluster/wham/src-M/energy_p_new.o b/source/cluster/wham/src-M/energy_p_new.o
index 6b5c262..08503d2 100644 (file)
Binary files a/source/cluster/wham/src-M/energy_p_new.o and b/source/cluster/wham/src-M/energy_p_new.o differ

diff --git a/source/cluster/wham/src-M/geomout.o b/source/cluster/wham/src-M/geomout.o
index bfb6f26..ca04f1b 100644 (file)
Binary files a/source/cluster/wham/src-M/geomout.o and b/source/cluster/wham/src-M/geomout.o differ

diff --git a/source/cluster/wham/src-M/hc.o b/source/cluster/wham/src-M/hc.o
index ae35516..6532401 100644 (file)
Binary files a/source/cluster/wham/src-M/hc.o and b/source/cluster/wham/src-M/hc.o differ

diff --git a/source/cluster/wham/src-M/initialize_p.F b/source/cluster/wham/src-M/initialize_p.F
index e1905f8..501c4da 100644 (file)
--- a/source/cluster/wham/src-M/initialize_p.F
+++ b/source/cluster/wham/src-M/initialize_p.F
@@ -101,8 +101,12 @@ C
        rr0(i)=0.0D0
        a0thet(i)=0.0D0
        do j=1,2
-         athet(j,i)=0.0D0
-         bthet(j,i)=0.0D0
+         do ichir1=-1,1
+          do ichir2=-1,1
+          athet(j,i,ichir1,ichir2)=0.0D0
+          bthet(j,i,ichir1,ichir2)=0.0D0
+          enddo
+         enddo
         enddo
        do j=0,3
          polthet(j,i)=0.0D0
@@ -128,15 +132,37 @@ C
       enddo
       nlob(ntyp1)=0
       dsc(ntyp1)=0.0D0
-      do i=1,maxtor
+      do i=-maxtor,maxtor
        itortyp(i)=0
-       do j=1,maxtor
-         do k=1,maxterm
-           v1(k,j,i)=0.0D0
-           v2(k,j,i)=0.0D0
-          enddo
-        enddo
+       do iblock=1,2
+        do j=-maxtor,maxtor
+          do k=1,maxterm
+            v1(k,j,i,iblock)=0.0D0
+            v2(k,j,i,iblock)=0.0D0
+           enddo
+         enddo      
+       enddo
       enddo
+      do iblock=1,2
+       do i=-maxtor,maxtor
+        do j=-maxtor,maxtor
+         do k=-maxtor,maxtor
+          do l=1,maxtermd_1
+            v1c(1,l,i,j,k,iblock)=0.0D0
+            v1s(1,l,i,j,k,iblock)=0.0D0
+            v1c(2,l,i,j,k,iblock)=0.0D0
+            v1s(2,l,i,j,k,iblock)=0.0D0
+          enddo !l
+          do l=1,maxtermd_2
+           do m=1,maxtermd_2
+            v2c(m,l,i,j,k,iblock)=0.0D0
+            v2s(m,l,i,j,k,iblock)=0.0D0
+           enddo !m
+          enddo !l
+        enddo !k
+       enddo !j
+      enddo !i
+      enddo !iblock
       do i=1,maxres
        itype(i)=0
        itel(i)=0
@@ -214,9 +240,13 @@ c-------------------------------------------------------------------------
       include 'COMMON.NAMES'
       include 'COMMON.FFIELD'
       data restyp /
+     &'DD','DPR','DLY','DAR','DHI','DAS','DGL','DSG','DGN','DSN','DTH',
+     &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER',
      &'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
      &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/
       data onelet /
+     &'z','p','k','r','h','d','e','n','q','s','t','g',
+     &'a','y','w','v','l','i','f','m','c','x',
      &'C','M','F','I','L','V','W','Y','A','G','T',
      &'S','Q','N','E','D','H','R','K','P','X'/
       data potname /'LJ','LJK','BP','GB','GBV'/

diff --git a/source/cluster/wham/src-M/initialize_p.o b/source/cluster/wham/src-M/initialize_p.o
index 9115499..33cc385 100644 (file)
Binary files a/source/cluster/wham/src-M/initialize_p.o and b/source/cluster/wham/src-M/initialize_p.o differ

diff --git a/source/cluster/wham/src-M/int_from_cart1.o b/source/cluster/wham/src-M/int_from_cart1.o
index 111cbfe..cc8482b 100644 (file)
Binary files a/source/cluster/wham/src-M/int_from_cart1.o and b/source/cluster/wham/src-M/int_from_cart1.o differ

diff --git a/source/cluster/wham/src-M/main_clust.o b/source/cluster/wham/src-M/main_clust.o
index 78c2d48..468a8be 100644 (file)
Binary files a/source/cluster/wham/src-M/main_clust.o and b/source/cluster/wham/src-M/main_clust.o differ

diff --git a/source/cluster/wham/src-M/parmread.F b/source/cluster/wham/src-M/parmread.F
index d29bb1f..069feec 100644 (file)
--- a/source/cluster/wham/src-M/parmread.F
+++ b/source/cluster/wham/src-M/parmread.F
@@ -18,7 +18,7 @@ C
       include 'COMMON.SCCOR'
       include 'COMMON.SCROT'
       character*1 t1,t2,t3
-      character*1 onelett(4) /"G","A","P","D"/
+      character*1 onelett(-2:2) /"p","a","G","A","P"/
       logical lprint
       dimension blower(3,3,maxlob)
       double precision ip,mp
@@ -78,12 +78,47 @@ C Read the parameters of the probability distribution/energy expression
 C of the virtual-bond valence angles theta
 C
       do i=1,ntyp
-        read (ithep,*) a0thet(i),(athet(j,i),j=1,2),(bthet(j,i),j=1,2)
+        read (ithep,*) a0thet(i),(athet(j,i,1,1),j=1,2),
+     &    (bthet(j,i,1,1),j=1,2)
         read (ithep,*) (polthet(j,i),j=0,3)
        read (ithep,*) (gthet(j,i),j=1,3)
        read (ithep,*) theta0(i),sig0(i),sigc0(i)
        sigc0(i)=sigc0(i)**2
       enddo
+      do i=1,ntyp
+      athet(1,i,1,-1)=athet(1,i,1,1)
+      athet(2,i,1,-1)=athet(2,i,1,1)
+      bthet(1,i,1,-1)=-bthet(1,i,1,1)
+      bthet(2,i,1,-1)=-bthet(2,i,1,1)
+      athet(1,i,-1,1)=-athet(1,i,1,1)
+      athet(2,i,-1,1)=-athet(2,i,1,1)
+      bthet(1,i,-1,1)=bthet(1,i,1,1)
+      bthet(2,i,-1,1)=bthet(2,i,1,1)
+      enddo
+      do i=-ntyp,-1
+      a0thet(i)=a0thet(-i)
+      athet(1,i,-1,-1)=athet(1,-i,1,1)
+      athet(2,i,-1,-1)=-athet(2,-i,1,1)
+      bthet(1,i,-1,-1)=bthet(1,-i,1,1)
+      bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
+      athet(1,i,-1,1)=athet(1,-i,1,1)
+      athet(2,i,-1,1)=-athet(2,-i,1,1)
+      bthet(1,i,-1,1)=-bthet(1,-i,1,1)
+      bthet(2,i,-1,1)=bthet(2,-i,1,1)
+      athet(1,i,1,-1)=-athet(1,-i,1,1)
+      athet(2,i,1,-1)=athet(2,-i,1,1)
+      bthet(1,i,1,-1)=bthet(1,-i,1,1)
+      bthet(2,i,1,-1)=-bthet(2,-i,1,1)
+      theta0(i)=theta0(-i)
+      sig0(i)=sig0(-i)
+      sigc0(i)=sigc0(-i)
+       do j=0,3
+        polthet(j,i)=polthet(j,-i)
+       enddo
+       do j=1,3
+         gthet(j,i)=gthet(j,-i)
+       enddo
+      enddo
       close (ithep)
       if (lprint) then
 c       write (iout,'(a)') 
@@ -119,7 +154,8 @@ c       enddo
      & '   b1*10^1    ','    b2*10^1   '        
         do i=1,ntyp
           write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),
-     &        a0thet(i),(100*athet(j,i),j=1,2),(10*bthet(j,i),j=1,2)
+     &        a0thet(i),(100*athet(j,i,1,1),j=1,2),
+     &        (10*bthet(j,i,1,1),j=1,2)
         enddo
        write (iout,'(/a/9x,5a/79(1h-))') 
      & 'Parameters of the expression for sigma(theta_c):',
@@ -272,10 +308,17 @@ C
         enddo  
        bsc(1,i)=0.0D0
         read(irotam,*)(censc(k,1,i),k=1,3),((blower(k,l,1),l=1,k),k=1,3)
+        censc(1,1,-i)=censc(1,1,i)
+        censc(2,1,-i)=censc(2,1,i)
+        censc(3,1,-i)=-censc(3,1,i)
        do j=2,nlob(i)
          read (irotam,*) bsc(j,i)
          read (irotam,*) (censc(k,j,i),k=1,3),
      &                                 ((blower(k,l,j),l=1,k),k=1,3)
+        censc(1,j,-i)=censc(1,j,i)
+        censc(2,j,-i)=censc(2,j,i)
+        censc(3,j,-i)=-censc(3,j,i)
+C BSC is amplitude of Gaussian
         enddo
        do j=1,nlob(i)
          do k=1,3
@@ -286,6 +329,14 @@ C
               enddo
              gaussc(k,l,j,i)=akl
              gaussc(l,k,j,i)=akl
+             if (((k.eq.3).and.(l.ne.3))
+     &        .or.((l.eq.3).and.(k.ne.3))) then
+                gaussc(k,l,j,-i)=-akl
+                gaussc(l,k,j,-i)=-akl
+              else
+                gaussc(k,l,j,-i)=akl
+                gaussc(l,k,j,-i)=akl
+              endif
             enddo
           enddo 
        enddo
@@ -373,23 +424,37 @@ C
       read (itorp,*) ntortyp
       read (itorp,*) (itortyp(i),i=1,ntyp)
       write (iout,*) 'ntortyp',ntortyp
-      do i=1,ntortyp
-       do j=1,ntortyp
-         read (itorp,*) nterm(i,j),nlor(i,j)
+      do iblock=1,2
+      do i=-ntyp,-1
+       itortyp(i)=-itortyp(-i)
+      enddo
+c      write (iout,*) 'ntortyp',ntortyp
+      do i=0,ntortyp-1
+        do j=-ntortyp+1,ntortyp-1
+          read (itorp,*) nterm(i,j,iblock),
+     &          nlor(i,j,iblock)
+          nterm(-i,-j,iblock)=nterm(i,j,iblock)
+          nlor(-i,-j,iblock)=nlor(i,j,iblock)
           v0ij=0.0d0
           si=-1.0d0
-         do k=1,nterm(i,j)
-           read (itorp,*) kk,v1(k,i,j),v2(k,i,j) 
-            v0ij=v0ij+si*v1(k,i,j)
+          do k=1,nterm(i,j,iblock)
+            read (itorp,*) kk,v1(k,i,j,iblock),
+     &      v2(k,i,j,iblock)
+            v1(k,-i,-j,iblock)=v1(k,i,j,iblock)
+            v2(k,-i,-j,iblock)=-v2(k,i,j,iblock)
+            v0ij=v0ij+si*v1(k,i,j,iblock)
             si=-si
           enddo
-         do k=1,nlor(i,j)
-           read (itorp,*) kk,vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j) 
+          do k=1,nlor(i,j,iblock)
+            read (itorp,*) kk,vlor1(k,i,j),
+     &        vlor2(k,i,j),vlor3(k,i,j)
             v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2)
           enddo
-          v0(i,j)=v0ij
+          v0(i,j,iblock)=v0ij
+          v0(-i,-j,iblock)=v0ij
         enddo
       enddo
+      enddo
       close (itorp)
       if (lprint) then
        write (iout,'(/a/)') 'Torsional constants:'
@@ -397,11 +462,12 @@ C
          do j=1,ntortyp
             write (iout,*) 'ityp',i,' jtyp',j
             write (iout,*) 'Fourier constants'
-            do k=1,nterm(i,j)
-             write (iout,'(2(1pe15.5))') v1(k,i,j),v2(k,i,j)
+            do k=1,nterm(i,j,iblock)
+             write (iout,'(2(1pe15.5))') v1(k,i,j,iblock),
+     &        v2(k,i,j,iblock)            
             enddo
             write (iout,*) 'Lorenz constants'
-            do k=1,nlor(i,j)
+            do k=1,nlor(i,j,iblock)
              write (iout,'(3(1pe15.5))') 
      &         vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
             enddo
@@ -411,9 +477,10 @@ C
 C
 C 6/23/01 Read parameters for double torsionals
 C
-      do i=1,ntortyp
-        do j=1,ntortyp
-          do k=1,ntortyp
+      do iblock=1,2
+      do i=0,ntortyp-1
+        do j=-ntortyp+1,ntortyp-1
+          do k=-ntortyp+1,ntortyp-1
             read (itordp,'(3a1)') t1,t2,t3
             if (t1.ne.onelett(i) .or. t2.ne.onelett(j) 
      &        .or. t3.ne.onelett(k)) then
@@ -421,48 +488,81 @@ C
      &         i,j,k,t1,t2,t3
                stop "Error in double torsional parameter file"
             endif
-            read (itordp,*) ntermd_1(i,j,k),ntermd_2(i,j,k)
-            read (itordp,*) (v1c(1,l,i,j,k),l=1,ntermd_1(i,j,k))
-            read (itordp,*) (v1s(1,l,i,j,k),l=1,ntermd_1(i,j,k))
-            read (itordp,*) (v1c(2,l,i,j,k),l=1,ntermd_1(i,j,k))
-            read (itordp,*) (v1s(2,l,i,j,k),l=1,ntermd_1(i,j,k))
-            read (itordp,*) ((v2c(l,m,i,j,k),v2c(m,l,i,j,k),
-     &       v2s(l,m,i,j,k),v2s(m,l,i,j,k),m=1,l-1),l=1,ntermd_2(i,j,k))
-          enddo
-        enddo
-      enddo
+          read (itordp,*) ntermd_1(i,j,k,iblock),
+     &         ntermd_2(i,j,k,iblock)
+            ntermd_1(-i,-j,-k,iblock)=ntermd_1(i,j,k,iblock)
+            ntermd_2(-i,-j,-k,iblock)=ntermd_2(i,j,k,iblock)
+            read (itordp,*) (v1c(1,l,i,j,k,iblock),l=1,
+     &         ntermd_1(i,j,k,iblock))
+            read (itordp,*) (v1s(1,l,i,j,k,iblock),l=1,
+     &         ntermd_1(i,j,k,iblock))
+            read (itordp,*) (v1c(2,l,i,j,k,iblock),l=1,
+     &         ntermd_1(i,j,k,iblock))
+            read (itordp,*) (v1s(2,l,i,j,k,iblock),l=1,
+     &         ntermd_1(i,j,k,iblock))
+C Martix of D parameters for one dimesional foureir series
+            do l=1,ntermd_1(i,j,k,iblock)
+             v1c(1,l,-i,-j,-k,iblock)=v1c(1,l,i,j,k,iblock)
+             v1s(1,l,-i,-j,-k,iblock)=-v1s(1,l,i,j,k,iblock)
+             v1c(2,l,-i,-j,-k,iblock)=v1c(2,l,i,j,k,iblock)
+             v1s(2,l,-i,-j,-k,iblock)=-v1s(2,l,i,j,k,iblock)
+c            write(iout,*) "whcodze" ,
+c     & v1s(2,l,-i,-j,-k,iblock),v1s(2,l,i,j,k,iblock)
+            enddo
+            read (itordp,*) ((v2c(l,m,i,j,k,iblock),
+     &         v2c(m,l,i,j,k,iblock),v2s(l,m,i,j,k,iblock),
+     &         v2s(m,l,i,j,k,iblock),
+     &         m=1,l-1),l=1,ntermd_2(i,j,k,iblock))
+C Martix of D parameters for two dimesional fourier series
+            do l=1,ntermd_2(i,j,k,iblock)
+             do m=1,l-1
+             v2c(l,m,-i,-j,-k,iblock)=v2c(l,m,i,j,k,iblock)
+             v2c(m,l,-i,-j,-k,iblock)=v2c(m,l,i,j,k,iblock)
+             v2s(l,m,-i,-j,-k,iblock)=-v2s(l,m,i,j,k,iblock)
+             v2s(m,l,-i,-j,-k,iblock)=-v2s(m,l,i,j,k,iblock)
+             enddo!m
+            enddo!l
+          enddo!k
+        enddo!j
+      enddo!i
+      enddo!iblock
       if (lprint) then
       write (iout,*) 
       write (iout,*) 'Constants for double torsionals'
-      do i=1,ntortyp
-        do j=1,ntortyp 
-          do k=1,ntortyp
+      do iblock=1,2
+      do i=0,ntortyp-1
+        do j=-ntortyp+1,ntortyp-1
+          do k=-ntortyp+1,ntortyp-1
             write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k,
-     &        ' nsingle',ntermd_1(i,j,k),' ndouble',ntermd_2(i,j,k)
+     &        ' nsingle',ntermd_1(i,j,k,iblock),
+     &        ' ndouble',ntermd_2(i,j,k,iblock)
             write (iout,*)
             write (iout,*) 'Single angles:'
-            do l=1,ntermd_1(i,j,k)
-              write (iout,'(i5,2f10.5,5x,2f10.5)') l,
-     &           v1c(1,l,i,j,k),v1s(1,l,i,j,k),
-     &           v1c(2,l,i,j,k),v1s(2,l,i,j,k)
+            do l=1,ntermd_1(i,j,k,iblock)
+              write (iout,'(i5,2f10.5,5x,2f10.5,5x,2f10.5)') l,
+     &           v1c(1,l,i,j,k,iblock),v1s(1,l,i,j,k,iblock),
+     &           v1c(2,l,i,j,k,iblock),v1s(2,l,i,j,k,iblock),
+     &           v1s(1,l,-i,-j,-k,iblock),v1s(2,l,-i,-j,-k,iblock)
             enddo
             write (iout,*)
             write (iout,*) 'Pairs of angles:'
-            write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
-            do l=1,ntermd_2(i,j,k)
-              write (iout,'(i5,20f10.5)') 
-     &         l,(v2c(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+            write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
+            do l=1,ntermd_2(i,j,k,iblock)
+              write (iout,'(i5,20f10.5)')
+     &         l,(v2c(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock))
             enddo
             write (iout,*)
-            write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
-            do l=1,ntermd_2(i,j,k)
-              write (iout,'(i5,20f10.5)') 
-     &         l,(v2s(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+           write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
+            do l=1,ntermd_2(i,j,k,iblock)
+              write (iout,'(i5,20f10.5)')
+     &         l,(v2s(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock)),
+     &         (v2s(l,m,-i,-j,-k,iblock),m=1,ntermd_2(i,j,k,iblock))
             enddo
             write (iout,*)
           enddo
         enddo
       enddo
+      enddo
       endif
 #endif
 C
@@ -496,7 +596,7 @@ C 9/18/99 (AL) Read coefficients of the Fourier expansion of the local
 C         interaction energy of the Gly, Ala, and Pro prototypes.
 C
       read (ifourier,*) nloctyp
-      do i=1,nloctyp
+      do i=0,nloctyp-1
         read (ifourier,*)
         read (ifourier,*) (b(ii,i),ii=1,13)
         if (lprint) then
@@ -505,30 +605,56 @@ C
         endif
         B1(1,i)  = b(3,i)
         B1(2,i)  = b(5,i)
+        B1(1,-i) = b(3,i)
+        B1(2,-i) = -b(5,i)
         B1tilde(1,i) = b(3,i)
         B1tilde(2,i) =-b(5,i) 
+        B1tilde(1,-i) =-b(3,i)
+        B1tilde(2,-i) =b(5,i)
         B2(1,i)  = b(2,i)
         B2(2,i)  = b(4,i)
+        B2(1,-i)  =b(2,i)
+        B2(2,-i)  =-b(4,i)
         CC(1,1,i)= b(7,i)
         CC(2,2,i)=-b(7,i)
         CC(2,1,i)= b(9,i)
         CC(1,2,i)= b(9,i)
+        CC(1,1,-i)= b(7,i)
+        CC(2,2,-i)=-b(7,i)
+        CC(2,1,-i)=-b(9,i)
+        CC(1,2,-i)=-b(9,i)
         Ctilde(1,1,i)=b(7,i)
         Ctilde(1,2,i)=b(9,i)
         Ctilde(2,1,i)=-b(9,i)
         Ctilde(2,2,i)=b(7,i)
+        Ctilde(1,1,-i)=b(7,i)
+        Ctilde(1,2,-i)=-b(9,i)
+        Ctilde(2,1,-i)=b(9,i)
+        Ctilde(2,2,-i)=b(7,i)
         DD(1,1,i)= b(6,i)
         DD(2,2,i)=-b(6,i)
         DD(2,1,i)= b(8,i)
         DD(1,2,i)= b(8,i)
+        DD(1,1,-i)= b(6,i)
+        DD(2,2,-i)=-b(6,i)
+        DD(2,1,-i)=-b(8,i)
+        DD(1,2,-i)=-b(8,i)
         Dtilde(1,1,i)=b(6,i)
         Dtilde(1,2,i)=b(8,i)
         Dtilde(2,1,i)=-b(8,i)
         Dtilde(2,2,i)=b(6,i)
+        Dtilde(1,1,-i)=b(6,i)
+        Dtilde(1,2,-i)=-b(8,i)
+        Dtilde(2,1,-i)=b(8,i)
+        Dtilde(2,2,-i)=b(6,i)
         EE(1,1,i)= b(10,i)+b(11,i)
         EE(2,2,i)=-b(10,i)+b(11,i)
         EE(2,1,i)= b(12,i)-b(13,i)
         EE(1,2,i)= b(12,i)+b(13,i)
+        EE(1,1,-i)= b(10,i)+b(11,i)
+        EE(2,2,-i)=-b(10,i)+b(11,i)
+        EE(2,1,-i)=-b(12,i)+b(13,i)
+        EE(1,2,-i)=-b(12,i)-b(13,i)
       enddo
       if (lprint) then
       do i=1,nloctyp

diff --git a/source/cluster/wham/src-M/parmread.o b/source/cluster/wham/src-M/parmread.o
index 0733796..f73068d 100644 (file)
Binary files a/source/cluster/wham/src-M/parmread.o and b/source/cluster/wham/src-M/parmread.o differ

diff --git a/source/cluster/wham/src-M/permut.o b/source/cluster/wham/src-M/permut.o
index 3a49989..7ec6dbe 100644 (file)
Binary files a/source/cluster/wham/src-M/permut.o and b/source/cluster/wham/src-M/permut.o differ

diff --git a/source/cluster/wham/src-M/proc_proc.o b/source/cluster/wham/src-M/proc_proc.o
index a38ab2d..73d93c8 100644 (file)
Binary files a/source/cluster/wham/src-M/proc_proc.o and b/source/cluster/wham/src-M/proc_proc.o differ

diff --git a/source/cluster/wham/src-M/read_coords.F b/source/cluster/wham/src-M/read_coords.F
index c34aca4..37951bd 100644 (file)
--- a/source/cluster/wham/src-M/read_coords.F
+++ b/source/cluster/wham/src-M/read_coords.F
@@ -404,7 +404,8 @@ c------------------------------------------------------------------------------
       enddo
       do j=nnt,nct
         itj=itype(j)
-        if (itype(j).ne.10 .and. (vbld(nres+j)-dsc(itj)).gt.2.0d0) then
+        if (itype(j).ne.10 .and. (vbld(nres+j)-dsc(iabs(itj))).gt.2.0d0)
+     &  then
           write (iout,*) "Conformation",jjj,jj+1
           write (iout,*) "Bad CA-SC bond length",j," ",vbld(nres+j)
           write (iout,*) "The Cartesian geometry is:"

diff --git a/source/cluster/wham/src-M/read_coords.o b/source/cluster/wham/src-M/read_coords.o
index 7b8eb30..603a561 100644 (file)
Binary files a/source/cluster/wham/src-M/read_coords.o and b/source/cluster/wham/src-M/read_coords.o differ

diff --git a/source/cluster/wham/src-M/read_ref_str.o b/source/cluster/wham/src-M/read_ref_str.o
index 91d152b..ee00297 100644 (file)
Binary files a/source/cluster/wham/src-M/read_ref_str.o and b/source/cluster/wham/src-M/read_ref_str.o differ

diff --git a/source/cluster/wham/src-M/readpdb.o b/source/cluster/wham/src-M/readpdb.o
index 3ad016d..85a004b 100644 (file)
Binary files a/source/cluster/wham/src-M/readpdb.o and b/source/cluster/wham/src-M/readpdb.o differ

diff --git a/source/cluster/wham/src-M/readrtns.F b/source/cluster/wham/src-M/readrtns.F
index a723920..0140df4 100644 (file)
--- a/source/cluster/wham/src-M/readrtns.F
+++ b/source/cluster/wham/src-M/readrtns.F
@@ -213,9 +213,9 @@ C Convert sequence to numeric code
 #endif
           itel(i)=0
 #ifdef PROCOR
-        else if (itype(i+1).ne.20) then
+        else if (iabs(itype(i+1)).ne.20) then
 #else
-        else if (itype(i).ne.20) then
+        else if (iabs(itype(i)).ne.20) then
 #endif
           itel(i)=1
         else

diff --git a/source/cluster/wham/src-M/readrtns.o b/source/cluster/wham/src-M/readrtns.o
index eb4181e..6f47578 100644 (file)
Binary files a/source/cluster/wham/src-M/readrtns.o and b/source/cluster/wham/src-M/readrtns.o differ

diff --git a/source/cluster/wham/src-M/rescode.f b/source/cluster/wham/src-M/rescode.f
index ca0305c..fb68350 100644 (file)
--- a/source/cluster/wham/src-M/rescode.f
+++ b/source/cluster/wham/src-M/rescode.f
@@ -6,7 +6,7 @@
 
       if (itype.eq.0) then
 
-      do i=1,ntyp1
+      do i=-ntyp1,ntyp1
         if (ucase(nam).eq.restyp(i)) then
           rescode=i
           return
@@ -15,7 +15,7 @@
 
       else
 
-      do i=1,ntyp1
+      do i=-ntyp1,ntyp1
         if (nam(1:1).eq.onelet(i)) then
           rescode=i
           return  

diff --git a/source/cluster/wham/src-M/rescode.o b/source/cluster/wham/src-M/rescode.o
index cc3968c..3b97f0a 100644 (file)
Binary files a/source/cluster/wham/src-M/rescode.o and b/source/cluster/wham/src-M/rescode.o differ

diff --git a/source/cluster/wham/src-M/xdrf/libxdrf.a b/source/cluster/wham/src-M/xdrf/libxdrf.a
index 755f9e6..9716545 100644 (file)
Binary files a/source/cluster/wham/src-M/xdrf/libxdrf.a and b/source/cluster/wham/src-M/xdrf/libxdrf.a differ