!
allocate(dsc(ntyp1)) !(ntyp1)
allocate(dsc_inv(ntyp1)) !(ntyp1)
+ allocate(nbondterm_nucl(ntyp_molec(2))) !(ntyp)
+ allocate(vbldsc0_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp)
+ allocate(aksc_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp)
allocate(nbondterm(ntyp)) !(ntyp)
allocate(vbldsc0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
allocate(aksc(maxbondterm,ntyp)) !(maxbondterm,ntyp)
- allocate(msc(ntyp+1)) !(ntyp+1)
- allocate(isc(ntyp+1)) !(ntyp+1)
- allocate(restok(ntyp+1)) !(ntyp+1)
+ allocate(msc(ntyp+1,5)) !(ntyp+1)
+ allocate(isc(ntyp+1,5)) !(ntyp+1)
+ allocate(restok(ntyp+1,5)) !(ntyp+1)
allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
allocate(long_r_sidechain(ntyp))
allocate(short_r_sidechain(ntyp))
endif
enddo
#else
- read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp,ip,pstok
- do i=1,ntyp
+ read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp(1),ip(1),pstok(1)
+ do i=1,ntyp_molec(1)
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),&
- j=1,nbondterm(i)),msc(i),isc(i),restok(i)
+ j=1,nbondterm(i)),msc(i,1),isc(i,1),restok(i,1)
dsc(i) = vbldsc0(1,i)
if (i.eq.10) then
dsc_inv(i)=0.0D0
endif
enddo
#endif
+ read (ibond_nucl,*) vbldp0_nucl,akp_nucl,mp(2),ip(2),pstok(2)
+ do i=1,ntyp_molec(2)
+ nbondterm_nucl(i)=1
+ read (ibond_nucl,*) vbldsc0_nucl(1,i),aksc_nucl(1,i),msc(i,2),isc(i,2),restok(i,2)
+! dsc(i) = vbldsc0_nucl(1,i)
+! if (i.eq.10) then
+! dsc_inv(i)=0.0D0
+! else
+! dsc_inv(i)=1.0D0/dsc(i)
+! endif
+ enddo
+! read (ibond_nucl,*) junk,vbldp0_nucl,akp_nucl,rjunk,mp(2),ip(2),pstok(2)
+! do i=1,ntyp_molec(2)
+! read (ibond_nucl,*) nbondterm_nucl(i),(vbldsc0_nucl(j,i),&
+! aksc_nucl(j,i),abond0_nucl(j,i),&
+! j=1,nbondterm_nucl(i)),msc(i,2),isc(i,2),restok(i,2)
+! dsc(i) = vbldsc0(1,i)
+! if (i.eq.10) then
+! dsc_inv(i)=0.0D0
+! else
+! dsc_inv(i)=1.0D0/dsc(i)
+! endif
+! enddo
+
if (lprint) then
write(iout,'(/a/)')"Dynamic constants of the interaction sites:"
write (iout,'(a10,a3,6a10)') 'Type','N','VBL','K','A0','mass',&
'inertia','Pstok'
- write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp,ip,pstok
+ write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp(1),ip(1),pstok(1)
do i=1,ntyp
write (iout,'(a10,i3,6f10.5)') restyp(i,1),nbondterm(i),&
- vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i),isc(i),restok(i)
+ vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i,1),isc(i,1),restok(i,1)
do j=2,nbondterm(i)
write (iout,'(13x,3f10.5)') &
vbldsc0(j,i),aksc(j,i),abond0(j,i)
close (ithep_pdb)
#endif
close(ithep)
+!--------------- Reading theta parameters for nucleic acid-------
+ read (ithep_nucl,*,err=111,end=111) nthetyp_nucl,ntheterm_nucl,&
+ ntheterm2_nucl,ntheterm3_nucl,nsingle_nucl,ndouble_nucl
+ nntheterm_nucl=max0(ntheterm_nucl,ntheterm2_nucl,ntheterm3_nucl)
+ allocate(ithetyp_nucl(ntyp1_molec(2))) !(-ntyp1:ntyp1)
+ allocate(aa0thet_nucl(nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ allocate(aathet_nucl(ntheterm_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+!(maxtheterm,-maxthetyp1:maxthetyp1,&
+! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ allocate(bbthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(ccthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(ddthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(eethet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,&
+! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ allocate(ffthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(ggthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1))
+
+!(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,&
+! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+
+ read (ithep_nucl,*,err=111,end=111) (ithetyp_nucl(i),i=1,ntyp1_molec(2))
+
+ aa0thet_nucl(:,:,:)=0.0d0
+ aathet_nucl(:,:,:,:)=0.0d0
+ bbthet_nucl(:,:,:,:,:)=0.0d0
+ ccthet_nucl(:,:,:,:,:)=0.0d0
+ ddthet_nucl(:,:,:,:,:)=0.0d0
+ eethet_nucl(:,:,:,:,:)=0.0d0
+ ffthet_nucl(:,:,:,:,:,:)=0.0d0
+ ggthet_nucl(:,:,:,:,:,:)=0.0d0
+
+ do i=1,nthetyp_nucl
+ do j=1,nthetyp_nucl
+ do k=1,nthetyp_nucl
+ read (ithep_nucl,'(3a)',end=111,err=111) t1,t2,t3
+ read (ithep_nucl,*,end=111,err=111) aa0thet_nucl(i,j,k)
+ read (ithep_nucl,*,end=111,err=111)(aathet_nucl(l,i,j,k),l=1,ntheterm_nucl)
+ read (ithep_nucl,*,end=111,err=111) &
+ (((bbthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
+ (ccthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
+ (ddthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
+ (eethet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl)),ll=1,ntheterm2_nucl)
+ read (ithep_nucl,*,end=111,err=111) &
+ (((ffthet_nucl(llll,lll,ll,i,j,k),ffthet_nucl(lll,llll,ll,i,j,k), &
+ ggthet_nucl(llll,lll,ll,i,j,k),ggthet_nucl(lll,llll,ll,i,j,k), &
+ llll=1,lll-1),lll=2,ndouble_nucl),ll=1,ntheterm3_nucl)
+ enddo
+ enddo
+ enddo
!-------------------------------------------
allocate(nlob(ntyp1)) !(ntyp1)
character(len=80) :: card
real(kind=8),dimension(3,20) :: sccor
integer :: kkk,lll,icha,kupa,molecule,counter,seqalingbegin !rescode,
- integer :: isugar
+ integer :: isugar,molecprev
character*1 :: sugar
real(kind=8) :: cou
real(kind=8),dimension(3) :: ccc
! nres_molec(molecule)=nres_molec(molecule)+1
else
molecule=2
- itype(ires,molecule)=rescode(ires,res(3:4),0,molecule)
+ itype(ires,molecule)=rescode(ires,res(2:4),0,molecule)
! nres_molec(molecule)=nres_molec(molecule)+1
endif
endif
atom.ne.'OXT' .and. atom(:2).ne.'3H' &
.and. atom.ne.'P '.and. &
atom(1:1).ne.'H' .and. &
- atom.ne.'OP1' .and. atom.ne.'OP2 ') then
+ atom.ne.'OP1' .and. atom.ne.'OP2 '.and. atom.ne.'OP3'&
+ ) then
! write (iout,*) "sidechain ",atom
! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3)
if ((molecule.ne.2).or.(atom(3:3).ne."'")) then
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
endif
endif
- endif
+ else if ((ions).and.(card(1:6).eq.'HETATM')) then
+
+ read (card(12:16),*) atom
+ print *,"HETATOM", atom
+ read (card(18:20),'(a3)') res
+ if ((atom(1:2).eq.'NA').or.(atom(1:2).eq.'CL').or.&
+ (atom(1:2).eq.'CA').or.(atom(1:2).eq.'MG') &
+ .or.(atom(1:2).eq.'K ')) &
+ then
+ ires=ires+1
+ if (molecule.ne.5) molecprev=molecule
+ molecule=5
+ nres_molec(molecule)=nres_molec(molecule)+1
+ itype(ires,molecule)=rescode(ires,res(2:4),0,molecule)
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+ endif
+ endif !atom
enddo
10 write (iout,'(a,i5)') ' Number of residues found: ',ires
if (ires.eq.0) return
if (ires_old.ne.ires) nres_molec(molecule)=nres_molec(molecule)-2
! print *,'I have', nres_molec(:)
- do k=1,5
+ do k=1,4 ! ions are without dummy
if (nres_molec(k).eq.0) cycle
do i=2,nres-1
! write (iout,*) i,itype(i,1)
nsup=nres
nstart_sup=1
! print *,"molecule",molecule
- if (itype(nres,1).ne.10) then
+ if ((itype(nres,1).ne.10)) then
nres=nres+1
+ if (molecule.eq.5) molecule=molecprev
itype(nres,molecule)=ntyp1_molec(molecule)
nres_molec(molecule)=nres_molec(molecule)+1
if (unres_pdb) then
! NOW LETS ROCK! SORTING
allocate(c_temporary(3,2*nres))
allocate(itype_temporary(nres,5))
+ allocate(molnum(nres))
itype_temporary(:,:)=0
seqalingbegin=1
do k=1,5
enddo
itype_temporary(seqalingbegin,k)=itype(i,k)
+ molnum(seqalingbegin)=k
seqalingbegin=seqalingbegin+1
endif
enddo
if(me.eq.king.or..not.out1file) &
write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:",&
eta
- gamp=scal_fric*(pstok+rwat)*eta
+ gamp=scal_fric*(pstok(i)+rwat)*eta
stdfp=dsqrt(2*Rb*t_bath/d_time)
allocate(gamsc(ntyp1),stdfsc(ntyp1)) !(ntyp1)
do i=1,ntyp
- gamsc(i)=scal_fric*(restok(i)+rwat)*eta
+ gamsc(i)=scal_fric*(restok(i,1)+rwat)*eta
stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
enddo
if(me.eq.king.or..not.out1file)then
" stochastic forces of fully exposed sites"
write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
do i=1,ntyp
- write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i),&
+ write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i,1),&
gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
enddo
endif
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old',readonly,shared)
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old',readonly,shared)
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',readonly,shared)
call getenv_loc('ROTPAR',rotname)
open (ielep,file=elename,status='old',readonly,shared)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly,shared)
+
+ call getenv_loc('THETPAR_NUCL',thetname_nucl)
+ open (ithep_nucl,file=thetname_nucl,status='old',readonly,shared)
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old',readonly,shared)
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old',readonly,shared)
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old',readonly,shared)
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old',readonly,shared)
+
+
#elif (defined CRAY) || (defined AIX)
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
action='read')
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old',action='read')
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old',action='read')
+
! print *,"Processor",myrank," opened file IBOND"
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',action='read')
! print *,"Processor",myrank," opened file IELEP"
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',action='read')
+
+ call getenv_loc('THETPAR_NUCL',thetname_nucl)
+ open (ithep_nucl,file=thetname_nucl,status='old',action='read')
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old',action='read')
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old',action='read')
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old',action='read')
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old',action='read')
+
call getenv_loc('LIPTRANPAR',liptranname)
open (iliptranpar,file=liptranname,status='old',action='read')
call getenv_loc('TUBEPAR',tubename)
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old')
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old')
+
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old')
call getenv_loc('ROTPAR',rotname)
open (ielep,file=elename,status='old')
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old')
+
+ open (ithep_nucl,file=thetname_nucl,status='old')
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old')
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old')
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old')
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old')
+
call getenv_loc('LIPTRANPAR',liptranname)
open (iliptranpar,file=liptranname,status='old')
call getenv_loc('TUBEPAR',tubename)
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old',action='read')
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old',action='read')
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',action='read')
call getenv_loc('ROTPAR',rotname)
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+
+ call getenv_loc('THETPAR_NUCL',thetname_nucl)
+ open (ithep_nucl,file=thetname_nucl,status='old',action='read')
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old',action='read')
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old',action='read')
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old',action='read')
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old',action='read')
+
call getenv_loc('LIPTRANPAR',liptranname)
open (iliptranpar,file=liptranname,status='old',action='read')
call getenv_loc('TUBEPAR',tubename)
projects / unres4.git / blobdiff