Wham po zmianach i dzialajac dla D aminokwasow i BEZ roznic energi ESTR.

[unres.git] / source / wham / src-M / energy_p_new.F

diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F
index fcc52c0..b389917 100644 (file)
--- a/source/wham/src-M/energy_p_new.F
+++ b/source/wham/src-M/energy_p_new.F
@@ -368,9 +368,9 @@ 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)
@@ -383,7 +383,7 @@ 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
@@ -541,9 +541,9 @@ 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)
@@ -552,7 +552,7 @@ 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
@@ -654,9 +654,9 @@ 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)
@@ -670,7 +670,7 @@ 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)
@@ -792,9 +792,9 @@ 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)
@@ -808,7 +808,7 @@ 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)
@@ -942,9 +942,9 @@ 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)
@@ -958,7 +958,7 @@ 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)
@@ -2816,7 +2816,7 @@ 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
@@ -2927,7 +2927,8 @@ 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
@@ -2987,7 +2988,7 @@ 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)
@@ -2995,7 +2996,7 @@ 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
@@ -3073,6 +3074,7 @@ c
       logical energy_dec /.false./
       double precision u(3),ud(3)
       estr=0.0d0
+      estr1=0.0d0
       write (iout,*) "distchainmax",distchainmax
       do i=nnt+1,nct
         if (itype(i-1).eq.21 .or. itype(i).eq.21) then
@@ -3094,12 +3096,12 @@ 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
@@ -3180,6 +3182,19 @@ 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)
@@ -3217,8 +3232,12 @@ 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
@@ -3226,8 +3245,16 @@ 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)
@@ -3403,7 +3430,7 @@ 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))
+        ityp2=ithetyp(iabs(itype(i-1)))
         do k=1,nntheterm
           coskt(k)=dcos(k*theti2)
           sinkt(k)=dsin(k*theti2)
@@ -3415,7 +3442,7 @@ 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)
@@ -3436,7 +3463,7 @@ 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)
@@ -3591,7 +3618,7 @@ 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
@@ -3746,7 +3773,7 @@ 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
@@ -3827,7 +3854,7 @@ 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
@@ -4361,14 +4388,19 @@ 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
@@ -4381,22 +4413,24 @@ 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)
           pom=vl2ij*cosphi+vl3ij*sinphi
           pom1=1.0d0/(pom*pom+1.0d0)
           etors=etors+vl1ij*pom1
+c          if (energy_dec) etors_ii=etors_ii+
+c     &                vl1ij*pom1
           pom=-pom*pom1*pom1
           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
@@ -4463,12 +4497,14 @@ 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)
@@ -4478,12 +4514,12 @@ 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)
@@ -4493,7 +4529,7 @@ C Regular cosine and sine terms
             gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2
      &        -v1cdij*sinphi1p2-v2cdij*sinphi1m2)
             gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2
-     &        -v1cdij*sinphi1p2+v2cdij*sinphi1m2) 
+     &        -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
           enddo
         enddo
         gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*fact2*gloci1
@@ -4535,8 +4571,8 @@ c      write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
       do i=iphi_start,iphi_end
         if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle
         esccor_ii=0.0D0
-        itori=itype(i-2)
-        itori1=itype(i-1)
+        itori=iabs(itype(i-2))
+        itori1=iabs(itype(i-1))
         phii=phi(i)
         gloci=0.0D0
         do j=1,nterm_sccor