DO WHILE (FAIL .AND. ICOUNT_FAIL .LE. MAXCOUNT_FAIL)
do i=nnt,nct
- if (itype(i).ne.10) then
-!d print *,'i=',i,' itype=',itype(i),' theta=',theta(i+1)
+ if (itype(i,1).ne.10) then
+!d print *,'i=',i,' itype=',itype(i,1),' theta=',theta(i+1)
fail=.true.
ii=0
do while (fail .and. ii .le. maxsi)
- call gen_side(itype(i),theta(i+1),alph(i),omeg(i),fail)
+ call gen_side(itype(i,1),theta(i+1),alph(i),omeg(i),fail)
ii = ii+1
enddo
endif
subroutine statout(itime)
use energy_data
- use control_data, only:refstr
+ use control_data
use MD_data
use MPI_data
use compare, only:rms_nac_nnc
character(len=4) :: format1,format2
character(len=30) :: format
!el local variables
- integer :: i,ii1,ii2
- real(kind=8) :: rms,frac,frac_nn,co
+ integer :: i,ii1,ii2,j
+ real(kind=8) :: rms,frac,frac_nn,co,distance
#ifdef AIX
if(itime.eq.0) then
open(istat,file=statname,access="append")
#endif
#endif
+ if (AFMlog.gt.0) then
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
+ write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,4f12.3,i5,$)')&
+ itime,totT,EK,potE,totE,&
+ rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
+ potEcomp(23),me
+ format1="a133"
+ else
+!C print *,'A CHUJ',potEcomp(23)
+ write (line1,'(i10,f15.2,7f12.3,i5,$)') &
+ itime,totT,EK,potE,totE,&
+ kinetic_T,t_bath,gyrate(),&
+ potEcomp(23),me
+ format1="a114"
+ endif
+ else if (selfguide.gt.0) then
+ distance=0.0
+ do j=1,3
+ distance=distance+(c(j,afmend)-c(j,afmbeg))**2
+ enddo
+ distance=dsqrt(distance)
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
+ write (line1,'(i10,f15.2,3f12.3,f7.2,2f6.3,f12.3,f10.1,2f8.2, &
+ f9.3,i5,$)') &
+ itime,totT,EK,potE,totE,&
+ rms,frac,frac_nn,kinetic_T,t_bath,gyrate(),&
+ distance,potEcomp(23),me
+ format1="a133"
+!C print *,"CHUJOWO"
+ else
+!C print *,'A CHUJ',potEcomp(23)
+ write (line1,'(i10,f15.2,8f12.3,i5,$)')&
+ itime,totT,EK,potE,totE, &
+ kinetic_T,t_bath,gyrate(),&
+ distance,potEcomp(23),me
+ format1="a114"
+ endif
+ else
if (refstr) then
call rms_nac_nnc(rms,frac,frac_nn,co,.false.)
write (line1,'(i10,f15.2,3f12.3,f7.2,4f6.3,3f12.3,i5,$)') &
amax,kinetic_T,t_bath,gyrate(),me
format1="a114"
endif
+ ENDIF
if(usampl.and.totT.gt.eq_time) then
write(line2,'(i5,2f9.4,300f7.4)') iset,uconst,uconst_back,&
(qfrag(ii1),ii1=1,nfrag),(qpair(ii2),ii2=1,npair),&
! include 'COMMON.BOUNDS'
! include 'COMMON.MD'
! include 'COMMON.SETUP'
- character(len=4),dimension(:),allocatable :: sequence !(maxres)
+ character(len=4),dimension(:,:),allocatable :: sequence !(maxres,maxmolecules)
! integer :: rescode
! double precision x(maxvar)
character(len=256) :: pdbfile
- character(len=320) :: weightcard
+ character(len=800) :: weightcard
character(len=80) :: weightcard_t!,ucase
! integer,dimension(:),allocatable :: itype_pdb !(maxres)
! common /pizda/ itype_pdb
integer,dimension(maxres) :: itype_alloc
integer :: iti,nsi,maxsi,itrial,itmp
- real(kind=8) :: wlong,scalscp,co
+ real(kind=8) :: wlong,scalscp,co,ssscale
allocate(weights(n_ene))
!-----------------------------
allocate(c(3,2*maxres+2)) !(3,maxres2+2) maxres2=2*maxres
allocate(dc(3,0:2*maxres)) !(3,0:maxres2)
- allocate(itype(maxres)) !(maxres)
+ allocate(itype(maxres,5)) !(maxres)
+ allocate(istype(maxres))
!
! Zero out tables.
!
c(:,:)=0.0D0
dc(:,:)=0.0D0
- itype(:)=0
+ itype(:,:)=0
!-----------------------------
!
! Body
call reada(weightcard,'WTURN6',wturn6,1.0D0)
call reada(weightcard,'WSCCOR',wsccor,1.0D0)
call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
+ call reada(weightcard,'WVDWPP_NUCL',wvdwpp_nucl,0.0D0)
+ call reada(weightcard,'WELPP',welpp,0.0d0)
+ call reada(weightcard,'WVDWPSB',wvdwpsb,0.0d0)
+ call reada(weightcard,'WELPSB',welpsb,0.0D0)
+ call reada(weightcard,'WVDWSB',wvdwsb,0.0d0)
+ call reada(weightcard,'WELSB',welsb,0.0D0)
+ call reada(weightcard,'WBOND_NUCL',wbond_nucl,0.0D0)
+ call reada(weightcard,'WANG_NUCL',wang_nucl,0.0D0)
+ call reada(weightcard,'WSBLOC',wsbloc,0.0D0)
+ call reada(weightcard,'WTOR_NUCL',wtor_nucl,0.0D0)
+ call reada(weightcard,'WTORD_NUCL',wtor_d_nucl,0.0D0)
+ call reada(weightcard,'WCORR_NUCL',wcorr_nucl,0.0D0)
+ call reada(weightcard,'WCORR3_NUCL',wcorr3_nucl,0.0D0)
call reada(weightcard,'WBOND',wbond,1.0D0)
call reada(weightcard,'WTOR',wtor,1.0D0)
call reada(weightcard,'WTORD',wtor_d,1.0D0)
call reada(weightcard,'WSHIELD',wshield,0.05D0)
call reada(weightcard,'LIPSCALE',lipscale,1.0D0)
call reada(weightcard,'WLT',wliptran,1.0D0)
+ call reada(weightcard,'WTUBE',wtube,1.0d0)
call reada(weightcard,'WANG',wang,1.0D0)
call reada(weightcard,'WSCLOC',wscloc,1.0D0)
call reada(weightcard,'SCAL14',scal14,0.4D0)
call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
call reada(weightcard,'TEMP0',temp0,300.0d0)
+ call reada(weightcard,'WSCBASE',wscbase,0.0D0)
if (index(weightcard,'SOFT').gt.0) ipot=6
+ call reada(weightcard,'WBOND_NUCL',wbond_nucl,0.0D0)
+ call reada(weightcard,'WCATCAT',wcatcat,0.0d0)
+ call reada(weightcard,'WCATPROT',wcatprot,0.0d0)
+ call reada(weightcard,'WPEPBASE',wpepbase,1.0d0)
+ call reada(weightcard,'WSCPHO',wscpho,0.0d0)
+ call reada(weightcard,'WPEPPHO',wpeppho,0.0d0)
+
! 12/1/95 Added weight for the multi-body term WCORR
call reada(weightcard,'WCORRH',wcorr,1.0D0)
if (wcorr4.gt.0.0d0) wcorr=wcorr4
call reada(weightcard,"V2SS",v2ss,7.61d0)
call reada(weightcard,"V3SS",v3ss,13.7d0)
call reada(weightcard,"EBR",ebr,-5.50D0)
+ call reada(weightcard,"ATRISS",atriss,0.301D0)
+ call reada(weightcard,"BTRISS",btriss,0.021D0)
+ call reada(weightcard,"CTRISS",ctriss,1.001D0)
+ call reada(weightcard,"DTRISS",dtriss,1.001D0)
+ call reada(weightcard,"SSSCALE",ssscale,1.0D0)
dyn_ss=(index(weightcard,'DYN_SS').gt.0)
call reada(weightcard,"HT",Ht,0.0D0)
if (dyn_ss) then
- ss_depth=ebr/wsc-0.25*eps(1,1)
- Ht=Ht/wsc-0.25*eps(1,1)
- akcm=akcm*wstrain/wsc
- akth=akth*wstrain/wsc
- akct=akct*wstrain/wsc
- v1ss=v1ss*wstrain/wsc
- v2ss=v2ss*wstrain/wsc
- v3ss=v3ss*wstrain/wsc
+ ss_depth=(ebr/wsc-0.25*eps(1,1))*ssscale
+ Ht=(Ht/wsc-0.25*eps(1,1))*ssscale
+ akcm=akcm/wsc*ssscale
+ akth=akth/wsc*ssscale
+ akct=akct/wsc*ssscale
+ v1ss=v1ss/wsc*ssscale
+ v2ss=v2ss/wsc*ssscale
+ v3ss=v3ss/wsc*ssscale
else
ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
endif
!el if(.not.allocated(itype_pdb))
allocate(itype_pdb(nres))
do i=1,nres
- itype_pdb(i)=itype(i)
+ itype_pdb(i)=itype(i,1)
enddo
close (ipdbin)
nnt=nstart_sup
nct=nstart_sup+nsup-1
!el if(.not.allocated(icont_ref))
- allocate(icont_ref(2,12*nres)) ! maxcont=12*maxres
+ allocate(icont_ref(2,(nres/2)*nres)) ! maxcont=12*maxres
call contact(.false.,ncont_ref,icont_ref,co)
if (sideadd) then
write(iout,*)'Adding sidechains'
maxsi=1000
do i=2,nres-1
- iti=itype(i)
- if (iti.ne.10 .and. itype(i).ne.ntyp1) then
+ iti=itype(i,1)
+ if (iti.ne.10 .and. itype(i,1).ne.ntyp1) then
nsi=0
fail=.true.
do while (fail.and.nsi.le.maxsi)
enddo
endif
endif
-
+
if (indpdb.eq.0) then
+ nres_molec(:)=0
+ allocate(sequence(maxres,5))
+! itype(:,:)=0
+ itmp=0
+ if (protein) then
! Read sequence if not taken from the pdb file.
- read (inp,*) nres
-! print *,'nres=',nres
- allocate(sequence(nres))
+ molec=1
+ read (inp,*) nres_molec(molec)
+ print *,'nres=',nres
if (iscode.gt.0) then
- read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
+ read (inp,'(80a1)') (sequence(i,molec)(1:1),i=1,nres_molec(molec))
else
- read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
+ read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec))
endif
+! read(inp,*) weightcard_t
+! print *,"po seq" weightcard_t
! Convert sequence to numeric code
- do i=1,nres
- itype(i)=rescode(i,sequence(i),iscode)
+
+ do i=1,nres_molec(molec)
+ itmp=itmp+1
+ itype(i,1)=rescode(i,sequence(i,molec),iscode,molec)
+ print *,itype(i,1)
+
+ enddo
+ endif
+! read(inp,*) weightcard_t
+! print *,"po seq", weightcard_t
+
+ if (nucleic) then
+! Read sequence if not taken from the pdb file.
+ molec=2
+ read (inp,*) nres_molec(molec)
+! print *,'nres=',nres
+! allocate(sequence(maxres,5))
+! if (iscode.gt.0) then
+ read (inp,'(20a4)') (sequence(i,molec),i=1,nres_molec(molec))
+! Convert sequence to numeric code
+
+ do i=1,nres_molec(molec)
+ itmp=itmp+1
+ istype(itmp)=sugarcode(sequence(i,molec)(1:1),i)
+ itype(itmp,molec)=rescode(i,sequence(i,molec)(2:2),iscode,molec)
+ enddo
+ endif
+
+ if (ions) then
+! Read sequence if not taken from the pdb file.
+ molec=5
+ read (inp,*) nres_molec(molec)
+! print *,'nres=',nres
+ read (inp,'(20(1x,a3))') (sequence(i,molec),i=1,nres_molec(molec))
+! Convert sequence to numeric code
+ print *,nres_molec(molec)
+ do i=1,nres_molec(molec)
+ itmp=itmp+1
+ print *,itmp,"itmp"
+ itype(itmp,molec)=rescode(i,sequence(i,molec),iscode,molec)
enddo
+ endif
+ nres=0
+ do i=1,5
+ nres=nres+nres_molec(i)
+ print *,nres_molec(i)
+ enddo
+
! Assign initial virtual bond lengths
-!elwrite(iout,*) "test_alloc"
+ if(.not.allocated(molnum)) then
+ allocate(molnum(nres+1))
+ itmp=0
+ do i=1,5
+ do j=1,nres_molec(i)
+ itmp=itmp+1
+ molnum(itmp)=i
+ enddo
+ enddo
+! print *,nres_molec(i)
+ endif
if(.not.allocated(vbld)) allocate(vbld(2*nres))
-!elwrite(iout,*) "test_alloc"
if(.not.allocated(vbld_inv)) allocate(vbld_inv(2*nres))
-!elwrite(iout,*) "test_alloc"
do i=2,nres
vbld(i)=vbl
vbld_inv(i)=vblinv
enddo
do i=2,nres-1
- vbld(i+nres)=dsc(iabs(itype(i)))
- vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
-! write (iout,*) "i",i," itype",itype(i),
-! & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
+ print *, "molnum",molnum(i),itype(i,molnum(i))
+ vbld(i+nres)=dsc(iabs(itype(i,molnum(i))))
+ vbld_inv(i+nres)=dsc_inv(iabs(itype(i,molnum(i))))
+! write (iout,*) "i",i," itype",itype(i,1),
+! & " dsc",dsc(itype(i,1))," vbld",vbld(i),vbld(i+nres)
enddo
endif
! print *,nres
-! print '(20i4)',(itype(i),i=1,nres)
+! print '(20i4)',(itype(i,1),i=1,nres)
!----------------------------
!el reallocate tables
! do i=1,maxres2
! enddo
! enddo
! do i=1,maxres
-!elwrite(iout,*) "itype",i,itype(i)
-! itype_alloc(i)=itype(i)
+!elwrite(iout,*) "itype",i,itype(i,1)
+! itype_alloc(i)=itype(i,1)
! enddo
! deallocate(c)
! enddo
! enddo
! do i=1,nres+2
-! itype(i)=itype_alloc(i)
+! itype(i,1)=itype_alloc(i)
! itel(i)=0
! enddo
!--------------------------
do i=1,nres
#ifdef PROCOR
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) then
#else
- if (itype(i).eq.ntyp1) then
+ if (itype(i,1).eq.ntyp1) then
#endif
itel(i)=0
#ifdef PROCOR
- else if (iabs(itype(i+1)).ne.20) then
+ else if (iabs(itype(i+1,1)).ne.20) then
#else
- else if (iabs(itype(i)).ne.20) then
+ else if (iabs(itype(i,1)).ne.20) then
#endif
itel(i)=1
else
enddo
if(me.eq.king.or..not.out1file)then
write (iout,*) "ITEL"
+ print *,nres,"nres"
do i=1,nres-1
- write (iout,*) i,itype(i),itel(i)
+ write (iout,*) i,itype(i,1),itel(i)
enddo
print *,'Call Read_Bridge.'
endif
call read_bridge
!--------------------------------
+ print *,"tu dochodze"
! znamy nres oraz nss można zaalokowac potrzebne tablice
call alloc_geo_arrays
call alloc_ener_arrays
if (ndih_constr.gt.0) then
allocate(idih_constr(ndih_constr),idih_nconstr(ndih_constr)) !(maxdih_constr)
allocate(phi0(ndih_constr),drange(ndih_constr)) !(maxdih_constr)
+
read (inp,*) ftors
read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
if(me.eq.king.or..not.out1file)then
phibound(2,ii) = phi0(i)+drange(i)
enddo
endif
+ if (with_theta_constr) then
+!C with_theta_constr is keyword allowing for occurance of theta constrains
+ read (inp,*) ntheta_constr
+!C ntheta_constr is the number of theta constrains
+ if (ntheta_constr.gt.0) then
+!C read (inp,*) ftors
+ allocate(itheta_constr(ntheta_constr))
+ allocate(theta_constr0(ntheta_constr))
+ allocate(theta_drange(ntheta_constr),for_thet_constr(ntheta_constr))
+ read (inp,*) (itheta_constr(i),theta_constr0(i), &
+ theta_drange(i),for_thet_constr(i), &
+ i=1,ntheta_constr)
+!C the above code reads from 1 to ntheta_constr
+!C itheta_constr(i) residue i for which is theta_constr
+!C theta_constr0 the global minimum value
+!C theta_drange is range for which there is no energy penalty
+!C for_thet_constr is the force constant for quartic energy penalty
+!C E=k*x**4
+ if(me.eq.king.or..not.out1file)then
+ write (iout,*) &
+ 'There are',ntheta_constr,' constraints on phi angles.'
+ do i=1,ntheta_constr
+ write (iout,'(i5,3f8.3)') itheta_constr(i),theta_constr0(i), &
+ theta_drange(i), &
+ for_thet_constr(i)
+ enddo
+ endif
+ do i=1,ntheta_constr
+ theta_constr0(i)=deg2rad*theta_constr0(i)
+ theta_drange(i)=deg2rad*theta_drange(i)
+ enddo
+!C if(me.eq.king.or..not.out1file)
+!C & write (iout,*) 'FTORS',ftors
+!C do i=1,ntheta_constr
+!C ii = itheta_constr(i)
+!C thetabound(1,ii) = phi0(i)-drange(i)
+!C thetabound(2,ii) = phi0(i)+drange(i)
+!C enddo
+ endif ! ntheta_constr.gt.0
+ endif! with_theta_constr
+
nnt=1
#ifdef MPI
if (me.eq.king) then
write (iout,'(a)') 'Boundaries in phi angle sampling:'
do i=1,nres
write (iout,'(a3,i5,2f10.1)') &
- restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
+ restyp(itype(i,1),1),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
enddo
#ifdef MP
endif
#endif
nct=nres
-!d print *,'NNT=',NNT,' NCT=',NCT
- if (itype(1).eq.ntyp1) nnt=2
- if (itype(nres).eq.ntyp1) nct=nct-1
+ print *,'NNT=',NNT,' NCT=',NCT
+ if (itype(1,molnum(1)).eq.ntyp1_molec(molnum(1))) nnt=2
+ if (itype(nres,molnum(nres)).eq.ntyp1_molec(molnum(nres))) nct=nct-1
if (pdbref) then
if(me.eq.king.or..not.out1file) &
write (iout,'(a,i3)') 'nsup=',nsup
nstart_seq=nnt
if (nsup.le.(nct-nnt+1)) then
do i=0,nct-nnt+1-nsup
- if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
+ if (seq_comp(itype(nnt+i,1),itype_pdb(nstart_sup),nsup)) then
nstart_seq=nnt+i
goto 111
endif
stop
else
do i=0,nsup-(nct-nnt+1)
- if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1)) &
+ if (seq_comp(itype(nnt,1),itype_pdb(nstart_sup+i),nct-nnt+1)) &
then
nstart_sup=nstart_sup+i
nsup=nct-nnt+1
call flush(iout)
if (constr_dist.gt.0) call read_dist_constr
write (iout,*) "After read_dist_constr nhpb",nhpb
+ if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
call hpb_partition
if(me.eq.king.or..not.out1file) &
write (iout,*) 'Contact order:',co
icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
enddo
if(me.eq.king.or..not.out1file) &
- write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',&
+ write (2,*) i,' ',restyp(itype(icont_ref(1,i),1),1),' ',&
icont_ref(1,i),' ',&
- restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
+ restyp(itype(icont_ref(2,i),1),1),' ',icont_ref(2,i)
enddo
endif
endif
((c(l,k+nres),l=1,3),k=nnt,nct)
write (iout,*) "Exit READ_CART"
write (iout,'(8f10.5)') &
- ((c(l,k),l=1,3),k=1,nres),&
+ ((c(l,k),l=1,3),k=1,nres)
+ write (iout,'(8f10.5)') &
((c(l,k+nres),l=1,3),k=nnt,nct)
call int_from_cart1(.true.)
write (iout,*) "Finish INT_TO_CART"
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
do j=1,3
dc(j,i+nres)=c(j,i+nres)-c(j,i)
dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
do i=2,nres-1
alph(i)=110d0*deg2rad
enddo
-!elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
do i=2,nres-1
omeg(i)=-120d0*deg2rad
- if (itype(i).le.0) omeg(i)=-omeg(i)
+ if (itype(i,1).le.0) omeg(i)=-omeg(i)
enddo
else
if(me.eq.king.or..not.out1file) &
call read_threadbase
endif
call setup_var
-!elwrite (iout,*)"alph(i)*deg2rad",(alph(i), i=1,nres)
if (me.eq.king .or. .not. out1file) &
call intout
-!elwrite (iout,*)"alph(i)*rad2deg",(alph(i)*rad2deg, i=1,nres)
if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
write (iout,'(/a,i3,a)') &
'The chain contains',ns,' disulfide-bridging cysteines.'
do i=1,nss
i1=ihpb(i)-nres
i2=jhpb(i)-nres
- it1=itype(i1)
- it2=itype(i2)
+ it1=itype(i1,1)
+ it2=itype(i2,1)
if (me.eq.king.or..not.out1file) &
write (iout,'(2a,i3,3a,i3,a,3f10.3)') &
- restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),&
+ restyp(it1,1),'(',i1,') -- ',restyp(it2,1),'(',i2,')',dhpb(i),&
ebr,forcon(i)
enddo
write (iout,'(a)')
projects / unres4.git / blobdiff