write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,&
' v3ss:',v3ss
endif
+ if (shield_mode.gt.0) then
+ pi=4.0D0*datan(1.0D0)
+!C VSolvSphere the volume of solving sphere
+ print *,pi,"pi"
+!C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
+!C there will be no distinction between proline peptide group and normal peptide
+!C group in case of shielding parameters
+ VSolvSphere=4.0/3.0*pi*(4.50d0)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
+ write (iout,*) VSolvSphere,VSolvSphere_div
+!C long axis of side chain
+ do i=1,ntyp
+ long_r_sidechain(i)=vbldsc0(1,i)
+! if (scelemode.eq.0) then
+ short_r_sidechain(i)=sigma(i,i)/sqrt(2.0)
+ if (short_r_sidechain(i).eq.0.0) short_r_sidechain(i)=0.2
+! else
+! short_r_sidechain(i)=sigma(i,i)
+! endif
+ write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
+ sigma0(i)
+ enddo
+ buff_shield=1.0d0
+ endif
+
return
111 write (iout,*) "Error reading bending energy parameters."
goto 999
use control_data
use compare_data
use MPI_data
- use control, only: rescode,sugarcode
+ ! use control, only: rescode,sugarcode
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.LOCAL'
if(.not. allocated(istype)) allocate(istype(maxres))
do i=1,100000
read (ipdbin,'(a80)',end=10) card
- ! write (iout,'(a)') card
+ write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
if (lprn) then
write (iout,'(/a)') &
"Cartesian coordinates of the reference structure"
- write (iout,'(a,3(3x,a5),5x,3(3x,a5))') &
+ write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
"Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
do ires=1,nres
- write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') &
+ write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
(restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
(c(j,ires+nres),j=1,3)
enddo
write (iout,'(a)') &
"Backbone and SC coordinates as read from the PDB"
do ires=1,nres
- write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') &
+ write (iout,'(i5,i3,2x,a,3f8.3,5x,3f8.3)') &
ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),&
(c(j,nres+ires),j=1,3)
enddo
if (lprn) then
write (iout,'(/a)') &
"Cartesian coordinates of the reference structure after sorting"
- write (iout,'(a,3(3x,a5),5x,3(3x,a5))') &
+ write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
"Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
do ires=1,nres
- write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') &
+ write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
(restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
(c(j,ires+nres),j=1,3)
enddo
write (iout,*) "symetr", symetr
do i=1,nres
lll=lll+1
- !c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
+ ! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
chain_length=lll-1
! write (iout,*) "spraw lancuchy",chain_length,symetr
! do i=1,4
! do kkk=1,chain_length
- ! write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
+ ! write (iout,*) itype(kkk,1),(chain_rep(j,kkk,i), j=1,3)
! enddo
! enddo
! enddiagnostic
cou=0
do kkk=1,symetr
icha=tabperm(i,kkk)
- ! write (iout,*) i,icha
+ write (iout,*) i,icha
do lll=1,chain_length
cou=cou+1
if (cou.le.nres) then
kupa=mod(lll,chain_length)
iprzes=(kkk-1)*chain_length+lll
if (kupa.eq.0) kupa=chain_length
- ! write (iout,*) "kupa", kupa
+ write (iout,*) "kupa", kupa
cref(j,iprzes,i)=chain_rep(j,kupa,icha)
cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
enddo
cref(3,i,kkk),cref(1,nres+i,kkk),&
cref(2,nres+i,kkk),cref(3,nres+i,kkk)
enddo
- 100 format (//' alpha-carbon coordinates ',&
+ 100 format (//' alpha-carbon coordinates ',&
' centroid coordinates'/ &
' ', 6X,'X',11X,'Y',11X,'Z', &
10X,'X',11X,'Y',11X,'Z')
- 110 format (a,'(',i3,')',6f12.5)
+ 110 format (a,'(',i5,')',6f12.5)
enddo
!c enddiag
write (iout,'(2a)') diagmeth(kdiag),&
' routine used to diagonalize matrices.'
if (shield_mode.gt.0) then
- pi=3.141592d0
+ pi=4.0D0*datan(1.0D0)
!C VSolvSphere the volume of solving sphere
-!C print *,pi,"pi"
+ print *,pi,"pi"
!C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
!C there will be no distinction between proline peptide group and normal peptide
!C group in case of shielding parameters
- VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
- VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+ VSolvSphere=4.0/3.0*pi*(4.50d0)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
write (iout,*) VSolvSphere,VSolvSphere_div
!C long axis of side chain
- do i=1,ntyp
- long_r_sidechain(i)=vbldsc0(1,i)
- short_r_sidechain(i)=sigma0(i)
- write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
- sigma0(i)
- enddo
+! do i=1,ntyp
+! long_r_sidechain(i)=vbldsc0(1,i)
+! short_r_sidechain(i)=sigma0(i)
+! write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
+! sigma0(i)
+! enddo
buff_shield=1.0d0
endif
return
large = index(controlcard,"LARGE").gt.0
print_compon = index(controlcard,"PRINT_COMPON").gt.0
rattle = index(controlcard,"RATTLE").gt.0
+ preminim=(index(controlcard,'PREMINIM').gt.0)
+ write (iout,*) "PREMINIM ",preminim
+ dccart=(index(controlcard,'CART').gt.0)
+ if (preminim) call read_minim
! if performing umbrella sampling, fragments constrained are read from the fragment file
nset=0
if(usampl) then
projects / unres4.git / commitdiff