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[unres.git]
/
source
/
unres
/
src_MD-M-SAXS-homology
/
readpdb.F
diff --git
a/source/unres/src_MD-M-SAXS-homology/readpdb.F
b/source/unres/src_MD-M-SAXS-homology/readpdb.F
index
d4fc28f
..
68db17c
100644
(file)
--- a/
source/unres/src_MD-M-SAXS-homology/readpdb.F
+++ b/
source/unres/src_MD-M-SAXS-homology/readpdb.F
@@
-107,9
+107,9
@@
c write (2,*) "ires",ires," ishift",ishift
endif
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
read(card(61:66),*) bfac(ires)
endif
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
read(card(61:66),*) bfac(ires)
- if(me.eq.king.or..not.out1file)
- & write (iout,'(2i3,2x,a,3f8.3)')
- & ires,itype(ires),res,(c(j,ires),j=1,3)
+c if(me.eq.king.or..not.out1file)
+c & write (iout,'(2i3,2x,a,3f8.3)')
+c & ires,itype(ires),res,(c(j,ires),j=1,3)
iii=1
do j=1,3
sccor(j,iii)=c(j,ires)
iii=1
do j=1,3
sccor(j,iii)=c(j,ires)
@@
-251,8
+251,8
@@
C Calculate internal coordinates.
enddo
endif
call flush(iout)
enddo
endif
call flush(iout)
- write(iout,*)"before int_from_cart nres",nres
- call int_from_cart(.true.,.true.)
+c write(iout,*)"before int_from_cart nres",nres
+ call int_from_cart(.true.,.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
@@
-262,19
+262,19
@@
C Calculate internal coordinates.
dc(j,i)=c(j,i+1)-c(j,i)
dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
enddo
dc(j,i)=c(j,i+1)-c(j,i)
dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
enddo
- write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3),
- & vbld_inv(i+1)
+c write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3),
+c & vbld_inv(i+1)
enddo
do i=2,nres-1
do j=1,3
dc(j,i+nres)=c(j,i+nres)-c(j,i)
dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
enddo
enddo
do i=2,nres-1
do j=1,3
dc(j,i+nres)=c(j,i+nres)-c(j,i)
dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
enddo
- write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
- & vbld_inv(i+nres)
+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
enddo
- call sc_loc_geom(.true.)
- call int_from_cart1(.true.)
+ call sc_loc_geom(.false.)
+ call int_from_cart1(.false.)
c call chainbuild
C Copy the coordinates to reference coordinates
do i=1,nres
c call chainbuild
C Copy the coordinates to reference coordinates
do i=1,nres
@@
-350,6
+350,8
@@
ctest stop
endif
vbld(i+1)=dist(i,i+1)
vbld_inv(i+1)=1.0d0/vbld(i+1)
endif
vbld(i+1)=dist(i,i+1)
vbld_inv(i+1)=1.0d0/vbld(i+1)
+c write (iout,*) "i",i+1," vbld",vbld(i+1)," vbld_inv",
+c & vbld_inv(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 (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
@@
-432,12
+434,16
@@
c-------------------------------------------------------------------------------
do j=1,3
dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
enddo
do j=1,3
dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
enddo
+c write (iout,*) "i",i," dc",(dc_norm(j,i),j=1,3),
+c & " vbld",vbld_inv(i+1)
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
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
+c write (iout,*) "i",i," dc",(dc_norm(j,i+nres),j=1,3),
+c & " vbld",vbld_inv(i+nres)
else
do j=1,3
dc_norm(j,i+nres)=0.0d0
else
do j=1,3
dc_norm(j,i+nres)=0.0d0
@@
-499,17
+505,17
@@
c
endif
enddo
if (lprn) then
endif
enddo
if (lprn) then
- do i=2,nres
- iti=itype(i)
#ifdef MPI
#ifdef MPI
- if(me.eq.king.or..not.out1file)
- & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
- & yyref(i),zzref(i)
-#else
- write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
- & zzref(i)
+ if (me.eq.king.or..not.out1file) then
#endif
#endif
+ write (iout,*) "xxref,yyref,zzref"
+ do i=2,nres
+ write (iout,'(a3,i4,3f10.5)')
+ & restyp(itype(i)),i,xxref(i),yyref(i),zzref(i)
enddo
enddo
+#ifdef MPI
+ endif
+#endif
endif
return
end
endif
return
end
@@
-539,11
+545,24
@@
c---------------------------------------------------------------------------
include 'COMMON.CHAIN'
do i=1,nres-1
vbld(i+1)=vbl
include 'COMMON.CHAIN'
do i=1,nres-1
vbld(i+1)=vbl
- vbld_inv(i+1)=1.0d0/vbld(i+1)
+ vbld_inv(i+1)=vblinv
vbld(i+1+nres)=dsc(iabs(itype(i+1)))
vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
c print *,vbld(i+1),vbld(i+1+nres)
enddo
vbld(i+1+nres)=dsc(iabs(itype(i+1)))
vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
c print *,vbld(i+1),vbld(i+1+nres)
enddo
+c Adam 2/26/20 Alter virtual bonds for non-blocking end groups of each chain
+ do i=1,nchain
+ i1=chain_border(1,i)
+ i2=chain_border(2,i)
+ if (i1.gt.1) then
+ vbld(i1)=vbld(i1)/2
+ vbld_inv(i1)=vbld_inv(i1)*2
+ endif
+ if (i2.lt.nres) then
+ vbld(i2+1)=vbld(i2+1)/2
+ vbld_inv(i2+1)=vbld_inv(i2+1)*2
+ endif
+ enddo
return
end
c---------------------------------------------------------------------------
return
end
c---------------------------------------------------------------------------
@@
-835,7
+854,7
@@
C Calculate internal coordinates.
enddo
endif
C Calculate internal coordinates.
enddo
endif
C Calculate internal coordinates.
- call int_from_cart(.true.,.false.)
+ call int_from_cart(.true.,.true.)
call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)