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cluster_wham Adam's changes
[unres.git]
/
source
/
cluster
/
wham
/
src-HCD-5D
/
readpdb.F
diff --git
a/source/cluster/wham/src-HCD-5D/readpdb.F
b/source/cluster/wham/src-HCD-5D/readpdb.F
index
a7bb52b
..
f7cfb86
100644
(file)
--- a/
source/cluster/wham/src-HCD-5D/readpdb.F
+++ b/
source/cluster/wham/src-HCD-5D/readpdb.F
@@
-77,7
+77,7
@@
c write (2,*) "UNRES_PDB",unres_pdb
sccalc=.true.
endif
! Read free energy
sccalc=.true.
endif
! Read free energy
- if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
+c if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
! Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
sccalc=.false.
! Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
sccalc=.false.
@@
-98,7
+98,7
@@
c write (2,'(a)') card
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires_old)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
enddo
else
call sccenter(ires_old,iii,sccor)
@@
-347,17
+347,20
@@
c character*5 atom
& ' Gamma'
endif
endif
& ' Gamma'
endif
endif
- do i=1,nres-1
+ do i=2,nres
iti=itype(i)
iti=itype(i)
- if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
+c 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.ntyp1 .and. itype(i).ne.ntyp1 .and.
+ & (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
-ctest stop
+c stop
endif
endif
- 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)
+ vbld(i)=dist(i-1,i)
+ vbld_inv(i)=1.0d0/vbld(i)
+ 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.2) phi(i+1)=beta(i-2,i-1,i,i+1)
enddo
+
c if (unres_pdb) then
c if (itype(1).eq.ntyp1) then
c theta(3)=90.0d0*deg2rad
c if (unres_pdb) then
c if (itype(1).eq.ntyp1) then
c theta(3)=90.0d0*deg2rad
@@
-806,7
+809,7
@@
C 2/15/2013 by Adam: corrected insertion of the first dummy residue
endif
endif
C Calculate internal coordinates.
endif
endif
C Calculate internal coordinates.
- if (lprn) then
+ if (out_template_coord) then
write (iout,'(/a)')
& "Cartesian coordinates of the reference structure"
write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
write (iout,'(/a)')
& "Cartesian coordinates of the reference structure"
write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
@@
-818,6
+821,7
@@
C Calculate internal coordinates.
enddo
endif
C Calculate internal coordinates.
enddo
endif
C Calculate internal coordinates.
+#ifdef DEBUG
write (iout,'(a)')
& "Backbone and SC coordinates as read from the PDB"
do ires=1,nres
write (iout,'(a)')
& "Backbone and SC coordinates as read from the PDB"
do ires=1,nres
@@
-825,7
+829,8
@@
C Calculate internal coordinates.
& ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
& (c(j,nres+ires),j=1,3)
enddo
& ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
& (c(j,nres+ires),j=1,3)
enddo
- call int_from_cart(.true.,.false.)
+#endif
+ call int_from_cart(.true.,out_template_coord)
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)