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)
+ write (iout,*) "Number of SAXS restraints",NSAXS," SAXS_MODE",
+ & SAXS_MODE," SCAL_RAD",scal_rad
call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
call readi(controlcard,'SYM',symetr,1)
call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
if ((lipbufthick*2.0d0).gt.lipthick)
&write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
endif
- write(iout,*) "bordliptop=",bordliptop
- write(iout,*) "bordlipbot=",bordlipbot
- write(iout,*) "bufliptop=",bufliptop
- write(iout,*) "buflipbot=",buflipbot
+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 )
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,
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
- call chainbuild
+c call chainbuild
endif
endif
if (indpdb.eq.0) then
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)
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
+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
enddo
endif
endif
+ write (iout,*) "calling read_saxs_consrtr",nsaxs
+ if (nsaxs.gt.0) call read_saxs_constr
if (constr_homology.gt.0) then
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.'
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.'
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 (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)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
call getenv_loc('LIPTRANPAR',liptranname)
- open (iliptranpar,file=liptranname,status='old',action='read')
+ 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')
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)
include 'DIMENSIONS'
read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0)
if(.not.read2sigma.and.start_from_model) then
- write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA'
+ 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) write(iout,*) 'START_FROM_MODELS is ON'
+ 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
- write(iout,*) 'START_FROM_MODELS is OFF'
- write(iout,*) 'remove restart keyword from input'
+ 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)
lim_odl=0
lim_dih=0
c
- write(iout,*) 'nnt=',nnt,'nct=',nct
+c write(iout,*) 'nnt=',nnt,'nct=',nct
c
do i = nnt,nct
do k=1,constr_homology
do k=1,constr_homology
read(inp,'(a)') pdbfile
-c Next stament causes error upon compilation (?)
-c if(me.eq.king.or. .not. out1file)
-c write (iout,'(2a)') 'PDB data will be read from file ',
-c & pdbfile(:ilen(pdbfile))
- write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
+ 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
rescore(k,i_tmp)=rescore_tmp
rescore2(k,i_tmp)=rescore2_tmp
rescore3(k,i_tmp)=rescore3_tmp
- write(iout,'(a7,i5,3f10.5,i5)') "rescore",
+ 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