C geometry.
implicit none
include 'DIMENSIONS'
+ include 'DIMENSIONS.FREE'
include 'DIMENSIONS.ZSCOPT'
include 'COMMON.CONTROL'
include 'COMMON.LOCAL'
goto 10
else if (card(:3).eq.'TER') then
C End current chain
- ires_old=ires+1
- itype(ires_old)=21
+c 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
call sccenter(ires,iii,sccor)
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
- itype(1)=21
+ itype(1)=ntyp1
endif
c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
ibeg=0
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
- if (itype(i).eq.21) 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 c(j,i)=(c(j,i-1)+c(j,i+1))/2
- dc(j,i)=c(j,i)
- enddo
- endif
+
+ if (itype(i).eq.ntyp1) then
+ if (itype(i+1).eq.ntyp1) then
+C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+C if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+C call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+C if (fail) then
+C e2(1)=0.0d0
+C e2(2)=1.0d0
+C e2(3)=0.0d0
+C endif !fail
+C do j=1,3
+C c(j,i)=c(j,i-1)-1.9d0*e2(j)
+C enddo
+C else !unres_pdb
+ 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
+C if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+C call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+C if (fail) then
+C e2(1)=0.0d0
+C e2(2)=1.0d0
+C e2(3)=0.0d0
+C endif
+C do j=1,3
+C c(j,i)=c(j,i+1)-1.9d0*e2(j)
+C enddo
+C else !unres_pdb
+ 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)
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
- itype(nres)=21
+ 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
c(j,nres+1)=c(j,1)
c(j,2*nres)=c(j,nres)
enddo
- if (itype(1).eq.21) then
+ if (itype(1).eq.ntyp1) then
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
& ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
& (c(j,nres+ires),j=1,3)
enddo
+ call int_from_cart1(.false.)
call int_from_cart(.true.,.false.)
+ call sc_loc_geom(.true.)
write (iout,*) "After int_from_cart"
call flush(iout)
do i=1,nres-1
c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
c & vbld_inv(i+nres)
enddo
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+c
+ phi_ref(i)=phi(i)
+ theta_ref(i)=theta(i)
+ alph_ref(i)=alph(i)
+ omeg_ref(i)=omeg(i)
+ enddo
+
c call chainbuild
C Copy the coordinates to reference coordinates
c do i=1,2*nres
lll=lll+1
cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
- if (itype(i-1).eq.21) then
+ if ((itype(i-1).eq.ntyp1).and.(i.gt.2).and.(i.ne.nres)) then
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
do j=1,3
cref(j,i,cou)=c(j,i)
cref(j,i+nres,cou)=c(j,i+nres)
- if ((i.le.nres).and.(symetr.gt.1)) then
+ if (i.le.nres) then
chain_rep(j,lll,kkk)=c(j,i)
chain_rep(j,lll+nres,kkk)=c(j,i+nres)
endif
enddo
enddo
- if (symetr.gt.1) then
+ if (chain_length.eq.0) chain_length=nres
+ write (iout,*) chain_length
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
&=chain_rep(j,chain_length+nres,1)
enddo
- endif
c diagnostic
c diagnostic
& ' Phi'
endif
endif
- do i=2,nres
+ do i=1,nres-1
iti=itype(i)
- write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
- if (itype(i-1).ne.21 .and. itype(i).ne.21 .and.
- & (dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0)) then
+ if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
+ & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
stop
endif
- theta(i+1)=alpha(i-1,i,i+1)
+ vbld(i+1)=dist(i,i+1)
+ vbld_inv(i+1)=1.0d0/vbld(i+1)
+ if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
enddo
- if (itype(1).eq.21) then
- do j=1,3
- c(j,1)=c(j,2)+(c(j,3)-c(j,4))
- enddo
- endif
- if (itype(nres).eq.21) then
- do j=1,3
- c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
- enddo
- endif
if (lside) then
do i=2,nres-1
do j=1,3
endif
return
end
+
+c-------------------------------------------------------------------------------
+ subroutine sc_loc_geom(lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.NAMES'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SETUP'
+ double precision x_prime(3),y_prime(3),z_prime(3)
+ logical lprn
+ do i=1,nres-1
+ do j=1,3
+ dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
+ enddo
+ enddo
+ do i=2,nres-1
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ do j=1,3
+ dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
+ enddo
+ else
+ do j=1,3
+ dc_norm(j,i+nres)=0.0d0
+ enddo
+ endif
+ enddo
+ do i=2,nres-1
+ costtab(i+1) =dcos(theta(i+1))
+ sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
+ cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
+ sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
+ cosfac2=0.5d0/(1.0d0+costtab(i+1))
+ cosfac=dsqrt(cosfac2)
+ sinfac2=0.5d0/(1.0d0-costtab(i+1))
+ sinfac=dsqrt(sinfac2)
+ it=itype(i)
+ if (it.ne.10 .and. itype(i).ne.ntyp1) then
+c
+C Compute the axes of tghe local cartesian coordinates system; store in
+c x_prime, y_prime and z_prime
+c
+ do j=1,3
+ x_prime(j) = 0.00
+ y_prime(j) = 0.00
+ z_prime(j) = 0.00
+ enddo
+ do j = 1,3
+ x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
+ y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
+ enddo
+ call vecpr(x_prime,y_prime,z_prime)
+c
+C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
+C to local coordinate system. Store in xx, yy, zz.
+c
+ xx=0.0d0
+ yy=0.0d0
+ zz=0.0d0
+ 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)
+ enddo
+
+ xxref(i)=xx
+ yyref(i)=yy
+ zzref(i)=zz
+ else
+ xxref(i)=0.0d0
+ yyref(i)=0.0d0
+ zzref(i)=0.0d0
+ endif
+ enddo
+ if (lprn) then
+ do i=2,nres
+ iti=itype(i)
+ if(me.eq.king.or..not.out1file)
+ & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
+ & yyref(i),zzref(i)
+ enddo
+ endif
+ return
+ end
c---------------------------------------------------------------------------
subroutine sccenter(ires,nscat,sccor)
implicit none
projects / unres.git / blobdiff