timlim=60.0D0*timlim
safety = 60.0d0*safety
modecalc=0
+ call readi(controlcard,"INTER_LIST_UPDATE",imatupdate,100)
call reada(controlcard,"T_BATH",t_bath,300.0d0)
minim=(index(controlcard,'MINIMIZE').gt.0)
dccart=(index(controlcard,'CART').gt.0)
overlapsc=(index(controlcard,'OVERLAP').gt.0)
overlapsc=.not.overlapsc
- searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
- searchsc=.not.searchsc
+ searchsc=(index(controlcard,'SEARCHSC').gt.0 .and.
+ & index(controlcard,'NOSEARCHSC').eq.0)
sideadd=(index(controlcard,'SIDEADD').gt.0)
energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
mremd_dec=(index(controlcard,'MREMD_DEC').gt.0)
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
call reada(controlcard,'BOXX',boxxsize,100.0d0)
call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ write(iout,*) "Periodic box dimensions",boxxsize,boxysize,boxzsize
c Cutoff range for interactions
- call reada(controlcard,"R_CUT",r_cut,15.0d0)
+ call reada(controlcard,"R_CUT_INT",r_cut_int,25.0d0)
+ call reada(controlcard,"R_CUT_RESPA",r_cut_respa,2.0d0)
call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+ write (iout,*) "Cutoff on interactions",r_cut_int
+ write (iout,*)
+ & "Cutoff in switching short and long range interactions in RESPA",
+ & r_cut_respa
+ write (iout,*) "lambda in switch function",rlamb
call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
if (lipthick.gt.0.0d0) then
& "Initial time step of numerical integration:",d_time,
& " natural units"
write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
+ write (iout,'(a60,f10.5,a)') "Cutoff on interactions",r_cut_int,
+ & " A"
+ write(iout,'(a60,i5)')"Frequency of updating interaction list",
+ & imatupdate
if (RESPA) then
write (iout,'(2a,i4,a)')
& "A-MTS algorithm used; initial time step for fast-varying",
& " short-range forces split into",ntime_split," steps."
write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",
- & r_cut," lambda",rlamb
+ & r_cut_respa," lambda",rlamb
endif
write (iout,'(2a,f10.5)')
& "Maximum acceleration threshold to reduce the time step",
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,itemp
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
+c itemp=nres
+c nres=nres_temp
+c call gen_rand_conf(itemp,*115)
+c nmodel_start=nmodel_start+1
+c do i=1,2*nres
+c do j=1,3
+c chomo(j,i,nmodel_start)=c(j,i)
+c enddo
+c enddo
+c goto 116
+ 115 if (me.eq.king .or. .not. out1file)
+ & write (iout,'(a,2i5,1x,a)')
+ & "Different number of residues",nres_temp,nres,
+ & " model skipped."
+ endif
+ 116 continue
+ 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"
+ if (nnt.gt.1) c(:,nres+1)=c(:,1)
+ if (nct.lt.nres) c(:,2*nres)=c(:,nres)
+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)
call cartprint
+ do j=1,3
+ dc(j,0)=c(j,1)
+ enddo
do i=1,nres-1
do j=1,3
dc(j,i)=c(j,i+1)-c(j,i)
enddo
call bond_regular
call chainbuild_extconf
- else
+ else if (.not. start_from_model) then
if(me.eq.king.or..not.out1file)
& write (iout,'(a)') 'Random-generated initial geometry.'
call bond_regular
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.
nphi=nres-3
nvar=ntheta+nphi
nside=0
- write (iout,*) "SETUP_VAR ialph"
do i=2,nres-1
if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
- nside=nside+1
+ nside=nside+1
ialph(i,1)=nvar+nside
- ialph(nside,2)=i
+ ialph(nside,2)=i
endif
enddo
if (indphi.gt.0) then
else
nvar=nvar+2*nside
endif
- write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1)
return
end
c----------------------------------------------------------------------------
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,iishift
+ & ik,iistart,nres_temp
integer ilen
external ilen
- logical liiflag
+ logical liiflag,lfirst
+ integer i01,i10
c
c FP - Nov. 2014 Temporary specifications for new vars
c
double precision, dimension (max_template,maxres) :: rescore2
double precision, dimension (max_template,maxres) :: rescore3
double precision distal
- character*24 pdbfile,tpl_k_rescore
+ character*24 tpl_k_rescore
+ character*256 pdbfile
c -----------------------------------------------------------------
c Reading multiple PDB ref structures and calculation of retraints
c not using pre-computed ones stored in files model_ki_{dist,angle}
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)
do k=1,constr_homology
read(inp,'(a)') pdbfile
+ pdbfiles_chomo(k)=pdbfile
if(me.eq.king .or. .not. out1file)
& write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
& pdbfile(:ilen(pdbfile))
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)
enddo
lim_odl=ii
endif
+c write (iout,*) "Distance restraints set"
+c call flush(iout)
c
c Theta, dihedral and SC retraints
c
enddo
lim_dih=nct-nnt-2
endif
+c write (iout,*) "Dihedral angle restraints set"
+c call flush(iout)
if (waga_theta.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_theta,status='old')
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
+c write (iout,*) "Angle restraints set"
+c call flush(iout)
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
enddo
endif
enddo
+c write (iout,*) "SC restraints set"
+c call flush(iout)
c
c remove distance restraints not used in any model from the list
c shift data in all arrays
c
+c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct
if (waga_dist.ne.0.0d0) then
ii=0
liiflag=.true.
+ lfirst=.true.
do i=nnt,nct-2
do j=i+2,nct
ii=ii+1
- if (ii_in_use(ii).eq.0.and.liiflag) then
+c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+c & .and. distal.le.dist2_cut ) then
+c write (iout,*) "i",i," j",j," ii",ii
+c call flush(iout)
+ if (ii_in_use(ii).eq.0.and.liiflag.or.
+ & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then
liiflag=.false.
- iistart=ii
+ i10=ii
+ if (lfirst) then
+ lfirst=.false.
+ iistart=ii
+ else
+ if(i10.eq.lim_odl) i10=i10+1
+ do ki=0,i10-i01-1
+ ires_homo(iistart+ki)=ires_homo(ki+i01)
+ jres_homo(iistart+ki)=jres_homo(ki+i01)
+ ii_in_use(iistart+ki)=ii_in_use(ki+i01)
+ do k=1,constr_homology
+ odl(k,iistart+ki)=odl(k,ki+i01)
+ sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01)
+ l_homo(k,iistart+ki)=l_homo(k,ki+i01)
+ enddo
+ enddo
+ iistart=iistart+i10-i01
+ endif
endif
- if (ii_in_use(ii).ne.0.and..not.liiflag.or.
- & .not.liiflag.and.ii.eq.lim_odl) then
- if (ii.eq.lim_odl) then
- iishift=ii-iistart+1
- else
- iishift=ii-iistart
- endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag) then
+ i01=ii
liiflag=.true.
- do ki=iistart,lim_odl-iishift
- ires_homo(ki)=ires_homo(ki+iishift)
- jres_homo(ki)=jres_homo(ki+iishift)
- ii_in_use(ki)=ii_in_use(ki+iishift)
- do k=1,constr_homology
- odl(k,ki)=odl(k,ki+iishift)
- sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
- l_homo(k,ki)=l_homo(k,ki+iishift)
- enddo
- enddo
- ii=ii-iishift
- lim_odl=lim_odl-iishift
endif
enddo
enddo
+ lim_odl=iistart-1
endif
-
+c write (iout,*) "Removing distances completed"
+c call flush(iout)
endif ! .not. klapaucjusz
if (constr_homology.gt.0) call homology_partition
+c write (iout,*) "After homology_partition"
+c call flush(iout)
if (constr_homology.gt.0) call init_int_table
-c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
-c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+c write (iout,*) "After init_int_table"
+c call flush(iout)
+c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
c
c Print restraints
c
& ik,ll,ii,kk,iistart,iishift,lim_xx
double precision distal
logical lprn /.true./
+ integer nres_temp
integer ilen
external ilen
logical liiflag
double precision rescore_tmp,x12,y12,z12,rescore2_tmp
double precision, dimension (max_template,maxres) :: rescore
double precision, dimension (max_template,maxres) :: rescore2
- character*24 pdbfile,tpl_k_rescore
+ character*24 tpl_k_rescore
+ character*256 pdbfile
c
c For new homol impl
call getenv("FRAGFILE",fragfile)
open(ientin,file=fragfile,status="old",err=10)
read(ientin,*) constr_homology,nclust
+ nmodel_start=constr_homology
l_homo = .false.
sigma_theta=0.0
sigma_d=0.0
read(ientin,'(a)') pdbfile
write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
& pdbfile(:ilen(pdbfile))
+ pdbfiles_chomo(k)=pdbfile
open(ipdbin,file=pdbfile,status='old',err=33)
goto 34
33 write (iout,'(a,5x,a)') 'Error opening PDB file',
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)
enddo
enddo
call int_from_cart(.true.,.false.)
- call sc_loc_geom(.true.)
+ call sc_loc_geom(.false.)
do i=1,nres
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