D i L aminokwasy tuz przed testami

diff --git a/source/unres/src_MD/COMMON.TORSION b/source/unres/src_MD/COMMON.TORSION
index 2ceb636..3c9ae39 100644 (file)
--- a/source/unres/src_MD/COMMON.TORSION
+++ b/source/unres/src_MD/COMMON.TORSION
@@ -13,11 +13,15 @@ C Torsional constants of the rotation about virtual-bond dihedral angles
 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,b2tilde

diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f
index c5dc2ce..89171a1 100644 (file)
--- a/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@ -1,10 +1,10 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 2 5 336
+C 2 5 341
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 2.5 build 336'
-      write(iout,*)'compiled Thu Jul  5 08:53:57 2012'
+      write(iout,*)'Version 2.5 build 341'
+      write(iout,*)'compiled Mon Jul  9 03:40:18 2012'
       write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '

diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F
index 87555f9..31584d0 100644 (file)
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@ -5873,15 +5873,17 @@ c     lprn=.true.
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
         itori2=itortyp(itype(i))
+        iblock=1
+        if (iabs(itype(i+1).eq.20)) iblock=2
         phii=phi(i)
         phii1=phi(i+1)
         gloci1=0.0D0
         gloci2=0.0D0
-        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)
@@ -5891,12 +5893,12 @@ c     lprn=.true.
           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/unres/src_MD/initialize_p.F b/source/unres/src_MD/initialize_p.F
index 8880628..62706fb 100644 (file)
--- a/source/unres/src_MD/initialize_p.F
+++ b/source/unres/src_MD/initialize_p.F
@@ -191,10 +191,10 @@ c      call memmon_print_usage()
       enddo
       nlob(ntyp1)=0
       dsc(ntyp1)=0.0D0
-      do i=1,maxtor
+      do i=-maxtor,maxtor
        itortyp(i)=0
        do iblock=1,2
-       do j=1,maxtor
+       do j=-maxtor,maxtor
          do k=1,maxterm
            v1(k,j,i,iblock)=0.0D0
            v2(k,j,i,iblock)=0.0D0
@@ -202,6 +202,26 @@ c      call memmon_print_usage()
         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

diff --git a/source/unres/src_MD/parmread.F b/source/unres/src_MD/parmread.F
index 2e953a2..942a463 100644 (file)
--- a/source/unres/src_MD/parmread.F
+++ b/source/unres/src_MD/parmread.F
@@ -28,6 +28,7 @@ C
       include 'COMMON.SETUP'
       character*1 t1,t2,t3
       character*1 onelett(4) /"G","A","P","D"/
+      character*1 toronelet(-2:2) /"p","a","G","A","P"/
       logical lprint,LaTeX
       dimension blower(3,3,maxlob)
       dimension b(13)
@@ -470,7 +471,7 @@ C
       do i=-ntyp,-1
        itortyp(i)=-itortyp(-i)
       enddo
-      write (iout,*) 'ntortyp',ntortyp
+c      write (iout,*) 'ntortyp',ntortyp
       do i=0,ntortyp-1
        do j=-ntortyp+1,ntortyp-1
          read (itorp,*,end=113,err=113) nterm(i,j,iblock),
@@ -486,7 +487,7 @@ C
             v2(k,-i,-j,iblock)=-v2(k,i,j,iblock)
             v0ij=v0ij+si*v1(k,i,j,iblock)
             si=-si
-         write(iout,*) i,j,k,iblock,nterm(i,j,iblock),v1(k,-i,-j,iblock)
+c         write(iout,*) i,j,k,iblock,nterm(i,j,iblock),v1(k,-i,-j,iblock)
           enddo
          do k=1,nlor(i,j,iblock)
             read (itorp,*,end=113,err=113) kk,vlor1(k,i,j),
@@ -520,12 +521,16 @@ 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)',end=114,err=114) t1,t2,t3
-            if (t1.ne.onelett(i) .or. t2.ne.onelett(j) 
-     &        .or. t3.ne.onelett(k)) then
+              write (iout,*) "OK onelett",
+     &         i,j,k,t1,t2,t3
+
+            if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j) 
+     &        .or. t3.ne.toronelet(k)) then
               write (iout,*) "Error in double torsional parameter file",
      &         i,j,k,t1,t2,t3
 #ifdef MPI
@@ -533,55 +538,76 @@ C
 #endif
                stop "Error in double torsional parameter file"
             endif
-            read (itordp,*,end=114,err=114) ntermd_1(i,j,k),
-     &         ntermd_2(i,j,k)
-            read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k),l=1,
-     &         ntermd_1(i,j,k))
-            read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k),l=1,
-     &         ntermd_1(i,j,k))
-            read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k),l=1,
-     &         ntermd_1(i,j,k))
-            read (itordp,*,end=114,err=114) (v1s(2,l,i,j,k),l=1,
-     &         ntermd_1(i,j,k))
-            read (itordp,*,end=114,err=114) ((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
-      if (lprint) then
+            read (itordp,*,end=114,err=114) ntermd_1(i,j,k,iblock),
+     &         ntermd_2(i,j,k,iblock)
+            read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k,iblock),l=1,
+     &         ntermd_1(i,j,k,iblock))
+            read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k,iblock),l=1,
+     &         ntermd_1(i,j,k,iblock))
+            read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k,iblock),l=1,
+     &         ntermd_1(i,j,k,iblock))
+            read (itordp,*,end=114,err=114) (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)
+            enddo
+            read (itordp,*,end=114,err=114) ((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
+cc     if (lprint) then
       write (iout,*) 
       write (iout,*) 'Constants for double torsionals'
       do i=1,ntortyp
-        do j=1,ntortyp 
-          do k=1,ntortyp
+        do j=-ntortyp,ntortyp 
+          do k=-ntortyp,ntortyp
             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,'(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),m=1,ntermd_2(i,j,k))
+     &         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,'(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),m=1,ntermd_2(i,j,k))
+     &         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
-      endif
+cc      endif
 #endif
 C Read of Side-chain backbone correlation parameters
 C Modified 11 May 2012 by Adasko

diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F
index 27f9010..4b2dc0c 100644 (file)
--- a/source/wham/src/energy_p_new.F
+++ b/source/wham/src/energy_p_new.F
@@ -4463,16 +4463,24 @@ c     lprn=.true.
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
         itori2=itortyp(itype(i))
+c        iblock=1
+c        if (iabs(itype(i+1)).eq.20) iblock=2
         phii=phi(i)
         phii1=phi(i+1)
         gloci1=0.0D0
         gloci2=0.0D0
 C Regular cosine and sine terms
-        do j=1,ntermd_1(itori,itori1,itori2)
+c c       do j=1,ntermd_1(itori,itori1,itori2,iblock)
+c          v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+c          v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+c          v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+c          v2sij=v1s(2,j,itori,itori1,itori2,iblock)
+       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)
+
           cosphi1=dcos(j*phii)
           sinphi1=dsin(j*phii)
           cosphi2=dcos(j*phii1)
@@ -4483,7 +4491,12 @@ C Regular cosine and sine terms
           gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
         enddo
         do k=2,ntermd_2(itori,itori1,itori2)
+c        do k=2,ntermd_2(itori,itori1,itori2,iblock)
           do l=1,k-1
+c            v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+c            v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+c            v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+c            v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
             v1cdij = v2c(k,l,itori,itori1,itori2)
             v2cdij = v2c(l,k,itori,itori1,itori2)
             v1sdij = v2s(k,l,itori,itori1,itori2)

diff --git a/source/wham/src/parmread.F b/source/wham/src/parmread.F
index 9b5e224..d8d7817 100644 (file)
--- a/source/wham/src/parmread.F
+++ b/source/wham/src/parmread.F
@@ -23,6 +23,7 @@ C
       include 'COMMON.FREE'
       character*1 t1,t2,t3
       character*1 onelett(4) /"G","A","P","D"/
+      character*1 toronelet(-2:2)/"p","a","G","A","P"/
       logical lprint
       dimension blower(3,3,maxlob)
       character*800 controlcard
@@ -528,12 +529,12 @@ C
 C
 C 6/23/01 Read parameters for double torsionals
 C
-      do i=1,ntortyp
-        do j=1,ntortyp
+      do i=0,ntortyp-1
+        do j=-ntortyp,ntortyp
           do k=1,ntortyp
             read (itordp,'(3a1)') t1,t2,t3
-            if (t1.ne.onelett(i) .or. t2.ne.onelett(j) 
-     &        .or. t3.ne.onelett(k)) then
+            if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j) 
+     &        .or. t3.ne.toronelet(k)) then
               write (iout,*) "Error in double torsional parameter file",
      &         i,j,k,t1,t2,t3
                stop "Error in double torsional parameter file"