pdbref=(index(controlcard,'PDBREF').gt.0)
refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
indpdb=index(controlcard,'PDBSTART')
- extconf=(index(controlcard,'EXTCONF').gt.0)
AFMlog=(index(controlcard,'AFM'))
selfguide=(index(controlcard,'SELFGUIDE'))
c print *,'AFMlog',AFMlog,selfguide,"KUPA"
indphi=index(controlcard,'PHI')
indback=index(controlcard,'BACK')
iranconf=index(controlcard,'RAND_CONF')
+ start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0)
+ extconf=(index(controlcard,'EXTCONF').gt.0)
+ if (start_from_model) then
+ iranconf=0
+ extconf=.false.
+ endif
i2ndstr=index(controlcard,'USE_SEC_PRED')
gradout=index(controlcard,'GRADOUT').gt.0
gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
integer ilen
external ilen
integer iperm,tperm
- integer i,j,ii,k,l,itrial,itmp,i1,i2,it1,it2
+ integer i,j,ii,k,l,itrial,itmp,i1,i2,it1,it2,nres_temp
double precision sumv
C
C Read PDB structure if applicable
do i=1,nres-1
write (iout,*) i,itype(i),itel(i)
enddo
- print *,'Call Read_Bridge.'
+c print *,'Call Read_Bridge.'
endif
nnt=1
nct=nres
chain_border1(1,i)=chain_border(1,i)-1
chain_border1(2,i)=chain_border(2,i)+1
enddo
- chain_border1(1,nchain)=chain_border(1,nchain)-1
+ if (nchain.gt.1) chain_border1(1,nchain)=chain_border(1,nchain)-1
chain_border1(2,nchain)=nres
write(iout,*) "nres",nres," nchain",nchain
do i=1,nchain
if (.not. (wdfa_dist.eq.0.0 .and. wdfa_tor.eq.0.0 .and.
& wdfa_nei.eq.0.0 .and. wdfa_beta.eq.0.0)) then
call init_dfa_vars
- print*, 'init_dfa_vars finished!'
+c print*, 'init_dfa_vars finished!'
call read_dfa_info
- print*, 'read_dfa_info finished!'
+c print*, 'read_dfa_info finished!'
endif
#endif
if (pdbref) then
endif
endif
c print *, "A TU"
- write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
+c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
call flush(iout)
if (constr_dist.gt.0) call read_dist_constr
- write (iout,*) "After read_dist_constr nhpb",nhpb
+c write (iout,*) "After read_dist_constr nhpb",nhpb
if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
call hpb_partition
call NMRpeak_partition
enddo
else
homol_nset=0
+ if (start_from_model) then
+ nmodel_start=0
+ do
+ read(inp,'(a)',end=332,err=332) pdbfile
+ if (me.eq.king .or. .not. out1file)
+ & write (iout,'(a,5x,a)') 'Opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=336)
+ goto 335
+ 336 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ call flush(iout)
+ stop
+ 335 continue
+ unres_pdb=.false.
+ nres_temp=nres
+ call readpdb
+ close(ipdbin)
+ if (nres.ge.nres_temp) then
+ nmodel_start=nmodel_start+1
+ pdbfiles_chomo(nmodel_start)=pdbfile
+ do i=1,2*nres
+ do j=1,3
+ chomo(j,i,nmodel_start)=c(j,i)
+ enddo
+ enddo
+ else
+ if (me.eq.king .or. .not. out1file)
+ & write (iout,'(a,2i5,1x,a)')
+ & "Different number of residues",nres_temp,nres,
+ & " model skipped."
+ endif
+ nres=nres_temp
+ enddo
+ 332 continue
+ if (nmodel_start.eq.0) then
+ if (me.eq.king .or. .not. out1file)
+ & write (iout,'(a)')
+ & "No valid starting model found START_FROM_MODELS is OFF"
+ start_from_model=.false.
+ endif
+ write (iout,*) "nmodel_start",nmodel_start
+ endif
endif
& modecalc.ne.10) then
C If input structure hasn't been supplied from the PDB file read or generate
C initial geometry.
- if (iranconf.eq.0 .and. .not. extconf) then
+ if (iranconf.eq.0 .and. .not. extconf .and. .not.
+ & start_from_model) then
if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
& write (iout,'(a)') 'Initial geometry will be read in.'
if (read_cart) then
read(inp,'(8f10.5)',end=36,err=36)
& ((c(l,k),l=1,3),k=1,nres),
& ((c(l,k+nres),l=1,3),k=nnt,nct)
- write (iout,*) "Exit READ_CART"
+c write (iout,*) "Exit READ_CART"
c write (iout,'(8f10.5)')
c & ((c(l,k),l=1,3),k=1,nres),
c & ((c(l,k+nres),l=1,3),k=nnt,nct)
integer i,j
C Read bridging residues.
read (inp,*) ns,(iss(i),i=1,ns)
- print *,'ns=',ns
+c 5/24/2020 Adam: Added a table to translate residue numbers to cysteine
+c numbers
+ icys=0
+ do i=1,ns
+ icys(iss(i))=i
+ enddo
+c print *,'ns=',ns
if(me.eq.king.or..not.out1file)
& write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
C Check whether the specified bridging residues are cystines.
include 'COMMON.CONTROL'
include 'COMMON.DBASE'
include 'COMMON.THREAD'
+ include 'COMMON.SPLITELE'
include 'COMMON.TIME1'
integer i,j,itype_pdb(maxres)
common /pizda/ itype_pdb
+ double precision dd
double precision dist
character*2 iden
cd print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
cd write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
cd & ' seq_pdb', restyp(itype_pdb(i))
do j=i+2,nstart_sup+nsup-1
+c 5/24/2020 Adam: Cutoff included to reduce array size
+ dd = dist(i,j)
+ if (dd.gt.r_cut_int) cycle
nhpb=nhpb+1
ihpb(nhpb)=i+nstart_seq-nstart_sup
jhpb(nhpb)=j+nstart_seq-nstart_sup
forcon(nhpb)=weidis
- dhpb(nhpb)=dist(i,j)
+ dhpb(nhpb)=dd
enddo
enddo
cd write (iout,'(a)') 'Distance constraints:'
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
totTafm=totT
- do i=1,2*nres
+ do i=0,2*nres-1
read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
enddo
- do i=1,2*nres
+ do i=0,2*nres-1
read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
enddo
if(usampl) then
call readi(afmcard,"END",afmend,0)
call reada(afmcard,"FORCE",forceAFMconst,0.0d0)
call reada(afmcard,"VEL",velAFMconst,0.0d0)
- print *,'FORCE=' ,forceAFMconst
+c print *,'FORCE=' ,forceAFMconst
CCCC NOW PROPERTIES FOR AFM
distafminit=0.0d0
do i=1,3
character*24 model_ki_dist, model_ki_angle
character*500 controlcard
integer ki,i,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec,
- & ik,iistart
+ & ik,iistart,nres_temp
integer ilen
external ilen
logical liiflag,lfirst
if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
& write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA'
start_from_model=.false.
+ iranconf=(indpdb.le.0)
endif
if(start_from_model .and. (me.eq.king .or. .not. out1file))
& write(iout,*) 'START_FROM_MODELS is ON'
- if(start_from_model .and. rest) then
- if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
- write(iout,*) 'START_FROM_MODELS is OFF'
- write(iout,*) 'remove restart keyword from input'
- endif
- endif
+c if(start_from_model .and. rest) then
+c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+c write(iout,*) 'START_FROM_MODELS is OFF'
+c write(iout,*) 'remove restart keyword from input'
+c endif
+c endif
+ if (start_from_model) nmodel_start=constr_homology
if (homol_nset.gt.1)then
call card_concat(controlcard)
read(controlcard,*) (waga_homology(i),i=1,homol_nset)
tpl_k_rescore="template"//kic2//".sco"
unres_pdb=.false.
+ nres_temp=nres
if (read2sigma) then
call readpdb_template(k)
else
call readpdb
endif
+ nres_chomo(k)=nres
+ nres=nres_temp
c
c Distance restraints
c
c ... --> odl(k,ii)
C Copy the coordinates from reference coordinates (?)
- do i=1,2*nres
+ do i=1,2*nres_chomo(k)
do j=1,3
c(j,i)=cref(j,i)
c write (iout,*) "c(",j,i,") =",c(j,i)
& ik,ll,ii,kk,iistart,iishift,lim_xx
double precision distal
logical lprn /.true./
+ integer nres_temp
integer ilen
external ilen
logical liiflag
stop
34 continue
unres_pdb=.false.
+ nres_temp=nres
call readpdb_template(k)
+ nres_chomo(k)=nres
+ nres=nres_temp
do i=1,nres
rescore(k,i)=0.2d0
rescore2(k,i)=1.0d0
c
c ... --> odl(k,ii)
C Copy the coordinates from reference coordinates (?)
+ nres_temp=nres
+ nres=nres_chomo(k)
do i=1,2*nres
do j=1,3
c(j,i)=chomo(j,i,k)
thetaref(i)=theta(i)
phiref(i)=phi(i)
enddo
+ nres=nres_temp
if (waga_dist.ne.0.0d0) then
ii=0
do i = nnt,nct-2
projects / unres.git / blobdiff