include 'COMMON.CONTROL'
include 'COMMON.SBRIDGE'
include 'COMMON.IOUNITS'
+ include 'COMMON.SPLITELE'
logical file_exist
C Read force-field parameters except weights
call parmread
include 'COMMON.FFIELD'
include 'COMMON.INTERACT'
include 'COMMON.SETUP'
+ include 'COMMON.SPLITELE'
COMMON /MACHSW/ KDIAG,ICORFL,IXDR
character*8 diagmeth(0:3) /'Library','EVVRSP','Givens','Jacobi'/
character*80 ucase
C Set up the time limit (caution! The time must be input in minutes!)
read_cart=index(controlcard,'READ_CART').gt.0
call readi(controlcard,'CONSTR_DIST',constr_dist,0)
+ write (iout,*) "constr_dist",constr_dist
+ call readi(controlcard,'NSAXS',nsaxs,0)
+ call readi(controlcard,'SAXS_MODE',saxs_mode,0)
+ call reada(controlcard,'SCAL_RAD',scal_rad,1.0d0)
+ call reada(controlcard,'SAXS_CUTOFF',saxs_cutoff,1.0d0)
+ write (iout,*) "Number of SAXS restraints",NSAXS," SAXS_MODE",
+ & SAXS_MODE," SCAL_RAD",scal_rad,"SAXS_CUTOFF",saxs_cutoff
+ call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
call readi(controlcard,'SYM',symetr,1)
call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
unres_pdb = index(controlcard,'UNRES_PDB') .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"
call readi(controlcard,'IPRINT',iprint,0)
call readi(controlcard,'MAXGEN',maxgen,10000)
call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
i2ndstr=index(controlcard,'USE_SEC_PRED')
gradout=index(controlcard,'GRADOUT').gt.0
gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
+C DISTCHAINMAX become obsolete for periodic boundry condition
call reada(controlcard,'DISTCHAINMAX',distchainmax,5.0d0)
+C Reading the dimensions of box in x,y,z coordinates
+ call reada(controlcard,'BOXX',boxxsize,100.0d0)
+ call reada(controlcard,'BOXY',boxysize,100.0d0)
+ call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+c Cutoff range for interactions
+ call reada(controlcard,"R_CUT",r_cut,15.0d0)
+ call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+ call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
+ call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
+ if (lipthick.gt.0.0d0) then
+ bordliptop=(boxzsize+lipthick)/2.0
+ bordlipbot=bordliptop-lipthick
+C endif
+ if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0))
+ & write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
+ buflipbot=bordlipbot+lipbufthick
+ bufliptop=bordliptop-lipbufthick
+ if ((lipbufthick*2.0d0).gt.lipthick)
+ &write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
+ endif
+c write(iout,*) "bordliptop=",bordliptop
+c write(iout,*) "bordlipbot=",bordlipbot
+c write(iout,*) "bufliptop=",bufliptop
+c write(iout,*) "buflipbot=",buflipbot
+
+
if (me.eq.king .or. .not.out1file )
& write (iout,*) "DISTCHAINMAX",distchainmax
ntime_split0=ntime_split
call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
ntime_split0=ntime_split
- call reada(controlcard,"R_CUT",r_cut,2.0d0)
- call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+c call reada(controlcard,"R_CUT",r_cut,2.0d0)
+c call reada(controlcard,"LAMBDA",rlamb,0.3d0)
rest = index(controlcard,"REST").gt.0
tbf = index(controlcard,"TBF").gt.0
usampl = index(controlcard,"USAMPL").gt.0
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
+ if (preminim) then
+ dccart=(index(controlcard,'CART').gt.0)
+ call read_minim
+ endif
c if performing umbrella sampling, fragments constrained are read from the fragment file
nset=0
if(usampl) then
write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
if (rattle) write (iout,'(a60)')
& "Rattle algorithm used to constrain the virtual bonds"
+ if (preminim .or. iranconf.gt.0) then
+ write (iout,'(a60)')
+ & "Initial structure will be energy-minimized"
+ endif
endif
reset_fricmat=1000
if (lang.gt.0) then
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,'WLT',wliptran,0.0D0)
+ call reada(weightcard,'WSAXS',wsaxs,1.0D0)
if (index(weightcard,'SOFT').gt.0) ipot=6
C 12/1/95 Added weight for the multi-body term WCORR
call reada(weightcard,'WCORRH',wcorr,1.0D0)
weights(17)=wbond
weights(18)=scal14
weights(21)=wsccor
+ weights(25)=wsaxs
if(me.eq.king.or..not.out1file)
& write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
& wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
& 'General scaling factor of SC-p interactions:',scalscp
endif
r0_corr=cutoff_corr-delt_corr
- do i=1,20
+ do i=1,ntyp
aad(i,1)=scalscp*aad(i,1)
aad(i,2)=scalscp*aad(i,2)
bad(i,1)=scalscp*bad(i,1)
33 write (iout,'(a)') 'Error opening PDB file.'
stop
34 continue
-c write (iout,*) 'Begin reading pdb data'
-c call flush(iout)
+c print *,'Begin reading pdb data'
call readpdb
-c write (iout,*) 'Finished reading pdb data'
-c call flush(iout)
+ do i=1,2*nres
+ do j=1,3
+ crefjlee(j,i)=c(j,i)
+ enddo
+ enddo
+#ifdef DEBUG
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
+ & (crefjlee(j,i+nres),j=1,3)
+ enddo
+#endif
+c print *,'Finished reading pdb data'
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3,a,i3)')'nsup=',nsup,
& ' nstart_sup=',nstart_sup
maxsi=1000
do i=2,nres-1
iti=itype(i)
- if (iti.ne.10 .and. itype(i).ne.21) then
+ if (iti.ne.10 .and. itype(i).ne.ntyp1) then
nsi=0
fail=.true.
do while (fail.and.nsi.le.maxsi)
call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
nsi=nsi+1
enddo
+c AL 7/10/16
+c Calculalte only the coordinates of the current sidechain; no need to rebuild
+c whole chain
+ call locate_side_chain(i)
if(fail) write(iout,*)'Adding sidechain failed for res ',
& i,' after ',nsi,' trials'
endif
enddo
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+c call chainbuild
endif
endif
if (indpdb.eq.0) then
vbld_inv(i)=vblinv
enddo
do i=2,nres-1
- vbld(i+nres)=dsc(itype(i))
- vbld_inv(i+nres)=dsc_inv(itype(i))
+ vbld(i+nres)=dsc(iabs(itype(i)))
+ vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
c write (iout,*) "i",i," itype",itype(i),
c & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
enddo
c print '(20i4)',(itype(i),i=1,nres)
do i=1,nres
#ifdef PROCOR
- if (itype(i).eq.21 .or. itype(i+1).eq.21) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
#else
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
#endif
itel(i)=0
#ifdef PROCOR
- else if (itype(i+1).ne.20) then
+ else if (iabs(itype(i+1)).ne.20) then
#else
- else if (itype(i).ne.20) then
+ else if (iabs(itype(i)).ne.20) then
#endif
itel(i)=1
else
phibound(2,i)=pi
enddo
read (inp,*) ndih_constr
+ write (iout,*) "ndish_constr",ndih_constr
if (ndih_constr.gt.0) then
read (inp,*) ftors
read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
#endif
nct=nres
cd print *,'NNT=',NNT,' NCT=',NCT
- if (itype(1).eq.21) nnt=2
- if (itype(nres).eq.21) nct=nct-1
+ if (itype(1).eq.ntyp1) nnt=2
+ if (itype(nres).eq.ntyp1) nct=nct-1
if (pdbref) then
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3)') 'nsup=',nsup
call MPI_Finalize(MPI_COMM_WORLD,IERROR)
stop 'Error reading reference structure'
#endif
- 39 call chainbuild
+ 39 call chainbuild_extconf
call setup_var
czscore call geom_to_var(nvar,coord_exp_zs(1,1))
nstart_sup=nnt
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
- call hpb_partition
+c write (iout,*) "After read_dist_constr nhpb",nhpb
+ if ((AFMlog.gt.0).or.(selfguide.gt.0)) call read_afminp
if(me.eq.king.or..not.out1file)
& write (iout,*) 'Contact order:',co
if (pdbref) then
enddo
endif
endif
+ write (iout,*) "calling read_saxs_consrtr",nsaxs
+ if (nsaxs.gt.0) call read_saxs_constr
+
+
+ if (constr_homology.gt.0) then
+ call read_constr_homology
+ if (indpdb.gt.0 .or. pdbref) then
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=crefjlee(j,i)
+ cref(j,i,1)=crefjlee(j,i)
+ enddo
+ enddo
+ endif
+#ifdef DEBUG
+ write (iout,*) "Array C"
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(c(j,i),j=1,3),
+ & (c(j,i+nres),j=1,3)
+ enddo
+ write (iout,*) "Array Cref"
+ do i=1,nres
+ write (iout,'(i5,3f8.3,5x,3f8.3)') i,(cref(j,i,1),j=1,3),
+ & (cref(j,i+nres,1),j=1,3)
+ enddo
+#endif
+ call int_from_cart1(.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ do i=1,nres-1
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
+ enddo
+ enddo
+ do i=2,nres-1
+ do j=1,3
+ dc(j,i+nres)=c(j,i+nres)-c(j,i)
+ dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
+ enddo
+ enddo
+ else
+ homol_nset=0
+ endif
+
+
+ if (nhpb.gt.0) call hpb_partition
+c write (iout,*) "After read_dist_constr nhpb",nhpb
+c call flush(iout)
if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
& .and. modecalc.ne.8 .and. modecalc.ne.9 .and.
& modecalc.ne.10) then
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).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)
enddo
return
else
+ write (iout,*) "Calling read_ang"
call read_angles(inp,*36)
+ write (iout,*) "Calling chainbuild"
+ call chainbuild_extconf
endif
goto 37
36 write (iout,'(a)') 'Error reading angle file.'
enddo
do i=2,nres-1
omeg(i)=-120d0*deg2rad
+ if (itype(i).le.0) omeg(i)=-omeg(i)
enddo
+c from old chainbuild
+C
+C Define the origin and orientation of the coordinate system and locate the
+C first three CA's and SC(2).
+C
+ call orig_frame
+*
+* Build the alpha-carbon chain.
+*
+ do i=4,nres
+ call locate_next_res(i)
+ enddo
+C
+C First and last SC must coincide with the corresponding CA.
+C
+ do j=1,3
+ dc(j,nres+1)=0.0D0
+ dc_norm(j,nres+1)=0.0D0
+ dc(j,nres+nres)=0.0D0
+ dc_norm(j,nres+nres)=0.0D0
+ c(j,nres+1)=c(j,1)
+ c(j,nres+nres)=c(j,nres)
+ enddo
+C
+C Define the origin and orientation of the coordinate system and locate the
+C first three CA's and SC(2).
+C
+ call orig_frame
+*
+* Build the alpha-carbon chain.
+*
+ do i=4,nres
+ call locate_next_res(i)
+ enddo
+C
+C First and last SC must coincide with the corresponding CA.
+C
+ do j=1,3
+ dc(j,nres+1)=0.0D0
+ dc_norm(j,nres+1)=0.0D0
+ dc(j,nres+nres)=0.0D0
+ dc_norm(j,nres+nres)=0.0D0
+ c(j,nres+1)=c(j,1)
+ c(j,nres+nres)=c(j,nres)
+ enddo
+
+c
else
if(me.eq.king.or..not.out1file)
& write (iout,'(a)') 'Random-generated initial geometry.'
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc(j,i+nres)=c(j,i+nres)-c(j,i)
dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
nvar=ntheta+nphi
nside=0
do i=2,nres-1
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
nside=nside+1
ialph(i,1)=nvar+nside
ialph(nside,2)=i
include 'DIMENSIONS'
include 'COMMON.MINIM'
include 'COMMON.IOUNITS'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SETUP'
character*80 ucase
character*320 minimcard
call card_concat(minimcard)
print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
+#ifdef MPI
+ if (.not. out1file .or. me.eq.king) then
+#endif
write (iout,'(/80(1h*)/20x,a/80(1h*))')
& 'Options in energy minimization:'
write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)')
& 'MaxMin:',MaxMin,' MaxFun:',MaxFun,
& 'MinMin:',MinMin,' MinFun:',MinFun,
& ' TolF:',TolF,' RTolF:',RTolF
+#ifdef MPI
+ endif
+#endif
return
end
c----------------------------------------------------------------------------
open (ibond,file=bondname,status='old',readonly,shared)
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',readonly,shared)
+#ifndef CRYST_THETA
+ call getenv_loc('THETPARPDB',thetname_pdb)
+ open (ithep_pdb,file=thetname_pdb,status='old',readonly,shared)
+#endif
call getenv_loc('ROTPAR',rotname)
open (irotam,file=rotname,status='old',readonly,shared)
+#ifndef CRYST_SC
+ call getenv_loc('ROTPARPDB',rotname_pdb)
+ open (irotam_pdb,file=rotname_pdb,status='old',readonly,shared)
+#endif
call getenv_loc('TORPAR',torname)
open (itorp,file=torname,status='old',readonly,shared)
call getenv_loc('TORDPAR',tordname)
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',action='read')
c print *,"Processor",myrank," opened file ITHEP"
+#ifndef CRYST_THETA
+ call getenv_loc('THETPARPDB',thetname_pdb)
+ open (ithep_pdb,file=thetname_pdb,status='old',action='read')
+#endif
call getenv_loc('ROTPAR',rotname)
open (irotam,file=rotname,status='old',action='read')
c print *,"Processor",myrank," opened file IROTAM"
+#ifndef CRYST_SC
+ call getenv_loc('ROTPARPDB',rotname_pdb)
+ open (irotam_pdb,file=rotname_pdb,status='old',action='read')
+#endif
call getenv_loc('TORPAR',torname)
open (itorp,file=torname,status='old',action='read')
c print *,"Processor",myrank," opened file ITORP"
open (ibond,file=bondname,status='old')
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old')
+#ifndef CRYST_THETA
+ call getenv_loc('THETPARPDB',thetname_pdb)
+ open (ithep_pdb,file=thetname_pdb,status='old')
+#endif
call getenv_loc('ROTPAR',rotname)
open (irotam,file=rotname,status='old')
+#ifndef CRYST_SC
+ call getenv_loc('ROTPARPDB',rotname_pdb)
+ open (irotam_pdb,file=rotname_pdb,status='old')
+#endif
call getenv_loc('TORPAR',torname)
open (itorp,file=torname,status='old')
call getenv_loc('TORDPAR',tordname)
open (ielep,file=elename,status='old')
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old')
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
& readonly)
open (itordp,file=tordname,status='old',readonly)
call getenv_loc('SCCORPAR',sccorname)
open (isccor,file=sccorname,status='old',readonly)
+#ifndef CRYST_THETA
+ call getenv_loc('THETPARPDB',thetname_pdb)
+c print *,"thetname_pdb ",thetname_pdb
+ open (ithep_pdb,file=thetname_pdb,status='old',action='read')
+c print *,ithep_pdb," opened"
+#endif
call getenv_loc('FOURIER',fouriername)
open (ifourier,file=fouriername,status='old',readonly)
call getenv_loc('ELEPAR',elename)
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',readonly)
+#ifndef CRYST_SC
+ call getenv_loc('ROTPARPDB',rotname_pdb)
+ open (irotam_pdb,file=rotname_pdb,status='old',action='read')
+#endif
#endif
#ifndef OLDSCP
C
& thetname(:ilen(thetname))
write (iout,*) "Rotamer parameter file : ",
& rotname(:ilen(rotname))
+ write (iout,*) "Thetpdb parameter file : ",
+ & thetname_pdb(:ilen(thetname_pdb))
write (iout,*) "Threading database : ",
& patname(:ilen(patname))
if (lentmp.ne.0)
include 'COMMON.CHAIN'
include 'COMMON.IOUNITS'
include 'COMMON.MD'
+ include 'COMMON.CONTROL'
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
+ totTafm=totT
do i=1,2*nres
read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
enddo
do i=1,2*nres
read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
enddo
- if(usampl) then
+ if(usampl.or.homol_nset.gt.1) then
read (irest2,*) iset
endif
close(irest2)
include 'COMMON.IOUNITS'
include 'COMMON.MD'
include 'COMMON.CONTROL'
+ integer iset1
read(inp,*) nset,nfrag,npair,nfrag_back
if(me.eq.king.or..not.out1file)
& write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
& " nfrag_back",nfrag_back
- do iset=1,nset
- read(inp,*) mset(iset)
+ do iset1=1,nset
+ read(inp,*) mset(iset1)
do i=1,nfrag
- read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
- & qinfrag(i,iset)
+ read(inp,*) wfrag(i,iset1),ifrag(1,i,iset1),ifrag(2,i,iset1),
+ & qinfrag(i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
- & ifrag(2,i,iset), qinfrag(i,iset)
+ & write(iout,*) "R ",i,wfrag(i,iset1),ifrag(1,i,iset1),
+ & ifrag(2,i,iset1), qinfrag(i,iset1)
enddo
do i=1,npair
- read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
- & qinpair(i,iset)
+ read(inp,*) wpair(i,iset1),ipair(1,i,iset1),ipair(2,i,iset1),
+ & qinpair(i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
- & ipair(2,i,iset), qinpair(i,iset)
+ & write(iout,*) "R ",i,wpair(i,iset1),ipair(1,i,iset1),
+ & ipair(2,i,iset1), qinpair(i,iset1)
enddo
do i=1,nfrag_back
- read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
- & wfrag_back(3,i,iset),
- & ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+ read(inp,*) wfrag_back(1,i,iset1),wfrag_back(2,i,iset1),
+ & wfrag_back(3,i,iset1),
+ & ifrag_back(1,i,iset1),ifrag_back(2,i,iset1)
if(me.eq.king.or..not.out1file)
- & write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
- & wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+ & write(iout,*) "A",i,wfrag_back(1,i,iset1),
+ & wfrag_back(2,i,iset1),
+ & wfrag_back(3,i,iset1),ifrag_back(1,i,iset1),
+ & ifrag_back(2,i,iset1)
enddo
enddo
return
end
+C---------------------------------------------------------------------------
+ subroutine read_afminp
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.SBRIDGE'
+ character*320 afmcard
+c print *, "wchodze"
+ call card_concat(afmcard)
+ call readi(afmcard,"BEG",afmbeg,0)
+ call readi(afmcard,"END",afmend,0)
+ call reada(afmcard,"FORCE",forceAFMconst,0.0d0)
+ call reada(afmcard,"VEL",velAFMconst,0.0d0)
+ print *,'FORCE=' ,forceAFMconst
+CCCC NOW PROPERTIES FOR AFM
+ distafminit=0.0d0
+ do i=1,3
+ distafminit=(c(i,afmend)-c(i,afmbeg))**2+distafminit
+ enddo
+ distafminit=dsqrt(distafminit)
+ print *,'initdist',distafminit
+ return
+ end
+
+c-------------------------------------------------------------------------------
+ subroutine read_saxs_constr
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.SBRIDGE'
+ double precision cm(3)
+c read(inp,*) nsaxs
+ write (iout,*) "Calling read_saxs nsaxs",nsaxs
+ call flush(iout)
+ if (saxs_mode.eq.0) then
+c SAXS distance distribution
+ do i=1,nsaxs
+ read(inp,*) distsaxs(i),Psaxs(i)
+ enddo
+ Cnorm = 0.0d0
+ do i=1,nsaxs
+ Cnorm = Cnorm + Psaxs(i)
+ enddo
+ write (iout,*) "Cnorm",Cnorm
+ do i=1,nsaxs
+ Psaxs(i)=Psaxs(i)/Cnorm
+ enddo
+ write (iout,*) "Normalized distance distribution from SAXS"
+ do i=1,nsaxs
+ write (iout,'(f8.2,e15.5)') distsaxs(i),Psaxs(i)
+ enddo
+ else
+c SAXS "spheres".
+ do i=1,nsaxs
+ read (inp,'(30x,3f8.3)') (Csaxs(j,i),j=1,3)
+ enddo
+ do j=1,3
+ cm(j)=0.0d0
+ enddo
+ do i=1,nsaxs
+ do j=1,3
+ cm(j)=cm(j)+Csaxs(j,i)
+ enddo
+ enddo
+ do j=1,3
+ cm(j)=cm(j)/nsaxs
+ enddo
+ do i=1,nsaxs
+ do j=1,3
+ Csaxs(j,i)=Csaxs(j,i)-cm(j)
+ enddo
+ enddo
+ write (iout,*) "SAXS sphere coordinates"
+ do i=1,nsaxs
+ write (iout,'(i5,3f10.5)') i,(Csaxs(j,i),j=1,3)
+ enddo
+ endif
+ return
+ end
c-------------------------------------------------------------------------------
subroutine read_dist_constr
implicit real*8 (a-h,o-z)
c do i=1,npair_
c write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
c enddo
+ if (.not.refstr .and. nfrag.gt.0) then
+ write (iout,*)
+ & "ERROR: no reference structure to compute distance restraints"
+ write (iout,*)
+ & "Restraints must be specified explicitly (NDIST=number)"
+ stop
+ endif
+ if (nfrag.lt.2 .and. npair.gt.0) then
+ write (iout,*) "ERROR: Less than 2 fragments specified",
+ & " but distance restraints between pairs requested"
+ stop
+ endif
call flush(iout)
do i=1,nfrag_
if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
return
end
c-------------------------------------------------------------------------------
+
+ subroutine read_constr_homology
+
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.MD'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+c
+c For new homol impl
+c
+ include 'COMMON.VAR'
+c
+
+c double precision odl_temp,sigma_odl_temp,waga_theta,waga_d,
+c & dist_cut
+c common /przechowalnia/ odl_temp(maxres,maxres,max_template),
+c & sigma_odl_temp(maxres,maxres,max_template)
+ character*2 kic2
+ character*24 model_ki_dist, model_ki_angle
+ character*500 controlcard
+ integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
+ logical lprn /.true./
+ integer ilen
+ external ilen
+ logical liiflag
+c
+c FP - Nov. 2014 Temporary specifications for new vars
+c
+ double precision rescore_tmp,x12,y12,z12,rescore2_tmp,
+ & rescore3_tmp
+ double precision, dimension (max_template,maxres) :: rescore
+ double precision, dimension (max_template,maxres) :: rescore2
+ double precision, dimension (max_template,maxres) :: rescore3
+ character*24 pdbfile,tpl_k_rescore
+c -----------------------------------------------------------------
+c Reading multiple PDB ref structures and calculation of retraints
+c not using pre-computed ones stored in files model_ki_{dist,angle}
+c FP (Nov., 2014)
+c -----------------------------------------------------------------
+c
+c
+c Alternative: reading from input
+ call card_concat(controlcard)
+ call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0)
+ call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0)
+ call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new
+ call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new
+ call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
+ call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
+ call readi(controlcard,"HOMOL_NSET",homol_nset,1)
+ read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
+ start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0)
+ if(.not.read2sigma.and.start_from_model) then
+ 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.
+ 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
+ if (homol_nset.gt.1)then
+ call card_concat(controlcard)
+ read(controlcard,*) (waga_homology(i),i=1,homol_nset)
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "iset homology_weight "
+ do i=1,homol_nset
+ write(iout,*) i,waga_homology(i)
+ enddo
+ endif
+ iset=mod(kolor,homol_nset)+1
+ else
+ iset=1
+ waga_homology(1)=1.0
+ endif
+
+cd write (iout,*) "nnt",nnt," nct",nct
+cd call flush(iout)
+
+
+ lim_odl=0
+ lim_dih=0
+c
+c write(iout,*) 'nnt=',nnt,'nct=',nct
+c
+ do i = nnt,nct
+ do k=1,constr_homology
+ idomain(k,i)=0
+ enddo
+ enddo
+
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ ii_in_use(ii)=0
+ enddo
+ enddo
+
+ do k=1,constr_homology
+
+ read(inp,'(a)') pdbfile
+ if(me.eq.king .or. .not. out1file)
+ & write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ stop
+ 34 continue
+c print *,'Begin reading pdb data'
+c
+c Files containing res sim or local scores (former containing sigmas)
+c
+
+ write(kic2,'(bz,i2.2)') k
+
+ tpl_k_rescore="template"//kic2//".sco"
+
+ unres_pdb=.false.
+ if (read2sigma) then
+ call readpdb_template(k)
+ else
+ call readpdb
+ endif
+c
+c Distance restraints
+c
+c ... --> odl(k,ii)
+C Copy the coordinates from reference coordinates (?)
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=cref(j,i,1)
+c write (iout,*) "c(",j,i,") =",c(j,i)
+ enddo
+ enddo
+c
+c From read_dist_constr (commented out 25/11/2014 <-> res sim)
+c
+c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
+ open (ientin,file=tpl_k_rescore,status='old')
+ if (nnt.gt.1) rescore(k,1)=0.0d0
+ do irec=nnt,nct ! loop for reading res sim
+ if (read2sigma) then
+ read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
+ & rescore3_tmp,idomain_tmp
+ i_tmp=i_tmp+nnt-1
+ idomain(k,i_tmp)=idomain_tmp
+ rescore(k,i_tmp)=rescore_tmp
+ rescore2(k,i_tmp)=rescore2_tmp
+ rescore3(k,i_tmp)=rescore3_tmp
+ if (.not. out1file .or. me.eq.king)
+ & write(iout,'(a7,i5,3f10.5,i5)') "rescore",
+ & i_tmp,rescore2_tmp,rescore_tmp,
+ & rescore3_tmp,idomain_tmp
+ else
+ idomain(k,irec)=1
+ read (ientin,*,end=1401) rescore_tmp
+
+c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
+ rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
+c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
+ endif
+ enddo
+ 1401 continue
+ close (ientin)
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ do i = nnt,nct-2
+ do j=i+2,nct
+
+ x12=c(1,i)-c(1,j)
+ y12=c(2,i)-c(2,j)
+ z12=c(3,i)-c(3,j)
+ distal=dsqrt(x12*x12+y12*y12+z12*z12)
+c write (iout,*) k,i,j,distal,dist2_cut
+
+ if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+ & .and. distal.le.dist2_cut ) then
+
+ ii=ii+1
+ ii_in_use(ii)=1
+ l_homo(k,ii)=.true.
+
+c write (iout,*) "k",k
+c write (iout,*) "i",i," j",j," constr_homology",
+c & constr_homology
+ ires_homo(ii)=i
+ jres_homo(ii)=j
+ odl(k,ii)=distal
+ if (read2sigma) then
+ sigma_odl(k,ii)=0
+ do ik=i,j
+ sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
+ enddo
+ sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
+ if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
+ & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+ else
+ if (odl(k,ii).le.dist_cut) then
+ sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
+ else
+#ifdef OLDSIGMA
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
+#else
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+#endif
+ endif
+ endif
+ sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
+ else
+ ii=ii+1
+ l_homo(k,ii)=.false.
+ endif
+ enddo
+ enddo
+ lim_odl=ii
+ endif
+c
+c Theta, dihedral and SC retraints
+c
+ if (waga_angle.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_dih,status='old')
+c do irec=1,maxres-3 ! loop for reading sigma_dih
+c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
+c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
+c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_dih(k,i+nnt-1)
+c enddo
+c1402 continue
+c close (ientin)
+ do i = nnt+3,nct
+ if (idomain(k,i).eq.0) then
+ sigma_dih(k,i)=0.0
+ cycle
+ endif
+ dih(k,i)=phiref(i) ! right?
+c read (ientin,*) sigma_dih(k,i) ! original variant
+c write (iout,*) "dih(",k,i,") =",dih(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+c & "rescore(",k,i-1,") =",rescore(k,i-1),
+c & "rescore(",k,i-2,") =",rescore(k,i-2),
+c & "rescore(",k,i-3,") =",rescore(k,i-3)
+
+ sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2)+rescore(k,i-3))/4.0
+c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
+c write (iout,*) "Raw sigmas for dihedral angle restraints"
+c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
+c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
+c Instead of res sim other local measure of b/b str reliability possible
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+
+ if (waga_theta.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_theta,status='old')
+c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
+c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
+c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_theta(k,i+nnt-1)
+c enddo
+c1403 continue
+c close (ientin)
+
+ do i = nnt+2,nct ! right? without parallel.
+c do i = i=1,nres ! alternative for bounds acc to readpdb?
+c do i=ithet_start,ithet_end ! with FG parallel.
+ if (idomain(k,i).eq.0) then
+ sigma_theta(k,i)=0.0
+ cycle
+ endif
+ thetatpl(k,i)=thetaref(i)
+c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+c & "rescore(",k,i-1,") =",rescore(k,i-1),
+c & "rescore(",k,i-2,") =",rescore(k,i-2)
+c read (ientin,*) sigma_theta(k,i) ! 1st variant
+ sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2))/3.0
+c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+
+c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+c rescore(k,i-2) ! right expression ?
+c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
+ enddo
+ endif
+
+ if (waga_d.gt.0.0d0) then
+c open (ientin,file=tpl_k_sigma_d,status='old')
+c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
+c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
+c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
+c & sigma_d(k,i+nnt-1)
+c enddo
+c1404 continue
+
+ do i = nnt,nct ! right? without parallel.
+c do i=2,nres-1 ! alternative for bounds acc to readpdb?
+c do i=loc_start,loc_end ! with FG parallel.
+ if (itype(i).eq.10) cycle
+ if (idomain(k,i).eq.0 ) then
+ sigma_d(k,i)=0.0
+ cycle
+ endif
+ xxtpl(k,i)=xxref(i)
+ yytpl(k,i)=yyref(i)
+ zztpl(k,i)=zzref(i)
+c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
+c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
+c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
+c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
+ sigma_d(k,i)=rescore3(k,i) ! right expression ?
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+
+c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
+c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
+c read (ientin,*) sigma_d(k,i) ! 1st variant
+ enddo
+ endif
+ enddo
+c
+c remove distance restraints not used in any model from the list
+c shift data in all arrays
+c
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ liiflag=.true.
+ do i=nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ if (ii_in_use(ii).eq.0.and.liiflag) then
+ liiflag=.false.
+ iistart=ii
+ 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
+ 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
+ endif
+ if (constr_homology.gt.0) call homology_partition
+ 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
+c Print restraints
+c
+ if (.not.lprn) return
+cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write (iout,*) "Distance restraints from templates"
+ do ii=1,lim_odl
+ write(iout,'(3i5,100(2f8.2,1x,l1,4x))')
+ & ii,ires_homo(ii),jres_homo(ii),
+ & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii),
+ & ki=1,constr_homology)
+ enddo
+ write (iout,*) "Dihedral angle restraints from templates"
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*dih(ki,i),
+ & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
+ enddo
+ write (iout,*) "Virtual-bond angle restraints from templates"
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*thetatpl(ki,i),
+ & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
+ enddo
+ write (iout,*) "SC restraints from templates"
+ do i=nnt,nct
+ write(iout,'(i5,100(4f8.2,4x))') i,
+ & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
+ & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
+ enddo
+ endif
+c -----------------------------------------------------------------
+ return
+ end
+c----------------------------------------------------------------------
+
#ifdef WINIFL
subroutine flush(iu)
return
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+#ifdef AMD64
+ integer*8 iseedi8
+#endif
#ifdef MPI
include 'mpif.h'
logical OKRandom, prng_restart
if (fg_rank.eq.0) then
seed=seed*(me+1)+1
#ifdef AMD64
- if(me.eq.king)
- & write (iout,*) 'MPI: node= ', me, ' iseed= ',iseed
- OKRandom = prng_restart(me,iseed)
+ iseedi8=dint(seed)
+ if(me.eq.king .or. .not. out1file)
+ & write (iout,*) 'MPI: node= ', me, ' iseed= ',iseedi8
+ write (*,*) 'MPI: node= ', me, ' iseed= ',iseedi8
+ OKRandom = prng_restart(me,iseedi8)
#else
do i=1,4
tmp=65536.0d0**(4-i)
if (OKRandom) then
c r1 = prng_next(me)
r1=ran_number(0.0D0,1.0D0)
- if(me.eq.king)
+ if(me.eq.king .or. .not. out1file)
& write (iout,*) 'ran_num',r1
if (r1.lt.0.0d0) OKRandom=.false.
endif
projects / unres.git / blobdiff