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intoduction of quartic restrains in multichain, bugfix in single chain
[unres.git]
/
source
/
unres
/
src_MD-M
/
readpdb.F
diff --git
a/source/unres/src_MD-M/readpdb.F
b/source/unres/src_MD-M/readpdb.F
index
8b6f331
..
71daf6f
100644
(file)
--- a/
source/unres/src_MD-M/readpdb.F
+++ b/
source/unres/src_MD-M/readpdb.F
@@
-47,7
+47,7
@@
crc----------------------------------------
else if (card(:3).eq.'TER') then
C End current chain
ires_old=ires+1
else if (card(:3).eq.'TER') then
C End current chain
ires_old=ires+1
- itype(ires_old)=21
+ itype(ires_old)=ntyp1
ibeg=2
c write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
ibeg=2
c write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
@@
-80,7
+80,7
@@
c write (iout,'(a80)') card
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
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
endif
c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
ibeg=0
@@
-93,7
+93,7
@@
c write (iout,*) "New chain started",ires,ishift
ires=ires-ishift
c write (2,*) "ires",ires," ishift",ishift
if (res.eq.'ACE') then
ires=ires-ishift
c write (2,*) "ires",ires," ishift",ishift
if (res.eq.'ACE') then
- ity=10
+ itype(ires)=10
else
itype(ires)=rescode(ires,res,0)
endif
else
itype(ires)=rescode(ires,res,0)
endif
@@
-119,7
+119,7
@@
C system
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) 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 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
@@
-140,7
+140,7
@@
C Calculate the CM of the last side chain.
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
- itype(nres)=21
+ itype(nres)=ntyp1
if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the last dummy residue
call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
if (unres_pdb) then
C 2/15/2013 by Adam: corrected insertion of the last dummy residue
call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
@@
-169,7
+169,7
@@
C 2/15/2013 by Adam: corrected insertion of the last dummy residue
c(j,nres+1)=c(j,1)
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
if (unres_pdb) then
nsup=nsup-1
nstart_sup=2
if (unres_pdb) then
@@
-199,6
+199,7
@@
C Calculate internal coordinates.
& (c(j,nres+ires),j=1,3)
enddo
endif
& (c(j,nres+ires),j=1,3)
enddo
endif
+C print *,"before int_from_cart"
call int_from_cart(.true.,.false.)
call sc_loc_geom(.true.)
do i=1,nres
call int_from_cart(.true.,.false.)
call sc_loc_geom(.true.)
do i=1,nres
@@
-229,7
+230,7
@@
C Splits to single chain if occurs
lll=lll+1
cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
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)) then
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
@@
-245,6
+246,8
@@
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
endif
enddo
enddo
endif
enddo
enddo
+ write (iout,*) chain_length
+ if (chain_length.eq.0) chain_length=nres
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
@@
-364,7
+367,7
@@
c---------------------------------------------------------------------------
#endif
do i=1,nres-1
iti=itype(i)
#endif
do i=1,nres-1
iti=itype(i)
- if (iti.ne.21 .and. itype(i+1).ne.21 .and.
+ 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
ctest stop
& (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
ctest stop
@@
-388,6
+391,7
@@
c vbld(nres)=3.8d0
c vbld_inv(nres)=1.0d0/vbld(2)
c endif
c endif
c vbld_inv(nres)=1.0d0/vbld(2)
c endif
c endif
+ print *,"A TU2"
if (lside) then
do i=2,nres-1
do j=1,3
if (lside) then
do i=2,nres-1
do j=1,3
@@
-447,7
+451,7
@@
c-------------------------------------------------------------------------------
enddo
enddo
do i=2,nres-1
enddo
enddo
do i=2,nres-1
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ 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
do j=1,3
dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
enddo
@@
-467,7
+471,7
@@
c-------------------------------------------------------------------------------
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
it=itype(i)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
it=itype(i)
- if (it.ne.10 .and. itype(i).ne.21) then
+ 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
C Compute the axes of tghe local cartesian coordinates system; store in
c x_prime, y_prime and z_prime
@@
-546,8
+550,8
@@
c---------------------------------------------------------------------------
do i=1,nres-1
vbld(i+1)=vbl
vbld_inv(i+1)=1.0d0/vbld(i+1)
do i=1,nres-1
vbld(i+1)=vbl
vbld_inv(i+1)=1.0d0/vbld(i+1)
- vbld(i+1+nres)=dsc(itype(i+1))
- vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+ 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
return
c print *,vbld(i+1),vbld(i+1+nres)
enddo
return