character*320 controlcard,ucase
dimension itype_pdb(maxres)
logical seq_comp
+ double precision secprob(3,maxdih_constr),phihel,phibet
call card_concat(controlcard,.true.)
call reada(controlcard,'SCAL14',scal14,0.4d0)
call reada(controlcard,'SCALSCP',scalscp,1.0d0)
write (iout,'(20i4)') (itype(i),i=1,nres)
do i=1,nres-1
#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
itel(i)=2
endif
enddo
+ write (iout,*) "ITEL"
+ do i=1,nres-1
+ write (iout,*) i,itype(i),itel(i)
+ enddo
call read_bridge
+ nnt=1
+ nct=nres
+ if (itype(1).eq.ntyp1) nnt=2
+ if (itype(nres).eq.ntyp1) nct=nct-1
+ write(iout,*) 'NNT=',NNT,' NCT=',NCT
if (with_dihed_constr) then
read (inp,*) ndih_constr
+ write (iout,*) "ndih_constr",ndih_constr
if (ndih_constr.gt.0) then
- read (inp,*) ftors
- write (iout,*) 'FTORS',ftors
- read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
+ raw_psipred=.false.
+C read (inp,*) ftors
+C write (iout,*) 'FTORS',ftors
+ read (inp,*) (idih_constr(i),phi0(i),drange(i),ftors(i),
+ & i=1,ndih_constr)
write (iout,*)
- & 'There are',ndih_constr,' constraints on phi angles.'
+ & 'There are',ndih_constr,' restraints on gamma angles.'
do i=1,ndih_constr
- write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
+ write (iout,'(i5,3f8.3)') idih_constr(i),phi0(i),drange(i),
+ & ftors(i)
enddo
do i=1,ndih_constr
phi0(i)=deg2rad*phi0(i)
drange(i)=deg2rad*drange(i)
enddo
- endif
+ else if (ndih_constr.lt.0) then
+ raw_psipred=.true.
+ call card_concat(controlcard,.true.)
+ call reada(controlcard,"PHIHEL",phihel,50.0D0)
+ call reada(controlcard,"PHIBET",phibet,180.0D0)
+ call reada(controlcard,"SIGMAHEL",sigmahel,30.0d0)
+ call reada(controlcard,"SIGMABET",sigmabet,40.0d0)
+ call reada(controlcard,"WDIHC",wdihc,0.591d0)
+ write (iout,*) "Weight of the dihedral restraint term",wdihc
+ read(inp,'(9x,3f7.3)')
+ & (secprob(1,i),secprob(2,i),secprob(3,i),i=nnt,nct)
+ write (iout,*) "The secprob array"
+ do i=nnt,nct
+ write (iout,'(i5,3f8.3)') i,(secprob(j,i),j=1,3)
+ enddo
+ ndih_constr=0
+ do i=nnt+3,nct
+ if (itype(i-3).ne.ntyp1 .and. itype(i-2).ne.ntyp1
+ & .and. itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1) then
+ ndih_constr=ndih_constr+1
+ idih_constr(ndih_constr)=i
+ sumv=0.0d0
+ do j=1,3
+ vpsipred(j,ndih_constr)=secprob(j,i-1)*secprob(j,i-2)
+ sumv=sumv+vpsipred(j,ndih_constr)
+ enddo
+ do j=1,3
+ vpsipred(j,ndih_constr)=vpsipred(j,ndih_constr)/sumv
+ enddo
+ phibound(1,ndih_constr)=phihel*deg2rad
+ phibound(2,ndih_constr)=phibet*deg2rad
+ sdihed(1,ndih_constr)=sigmahel*deg2rad
+ sdihed(2,ndih_constr)=sigmabet*deg2rad
+ endif
+ enddo
+ write (iout,*)
+ & 'There are',ndih_constr,
+ & ' bimodal restraints on gamma angles.'
+ do i=1,ndih_constr
+ write(iout,'(i5,1x,a4,i5,1h-,a4,i5,4f8.3,3f10.5)') i,
+ & restyp(itype(idih_constr(i)-2)),idih_constr(i)-2,
+ & restyp(itype(idih_constr(i)-1)),idih_constr(i)-1,
+ & phibound(1,i)*rad2deg,sdihed(1,i)*rad2deg,
+ & phibound(2,i)*rad2deg,sdihed(2,i)*rad2deg,
+ & (vpsipred(j,i),j=1,3)
+ enddo
endif
- nnt=1
- nct=nres
- if (itype(1).eq.21) nnt=2
- if (itype(nres).eq.21) nct=nct-1
- write(iout,*) 'NNT=',NNT,' NCT=',NCT
+ 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
+ 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
+C 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
+C 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
call setup_var
call init_int_table
if (ns.gt.0) then
write (iout,'(/a,i3,a)') 'The chain contains',ns,
& ' disulfide-bridging cysteines.'
write (iout,'(20i4)') (iss(i),i=1,ns)
+ if (dyn_ss) then
+ write(iout,*)"Running with dynamic disulfide-bond formation"
+ else
write (iout,'(/a/)') 'Pre-formed links are:'
do i=1,nss
i1=ihpb(i)-nres
& dhpb(i),ebr,forcon(i)
enddo
endif
+ endif
write (iout,'(a)')
+ write (iout,*) "setting ss mask dyn_ss",dyn_ss
+ if (ns.gt.0.and.dyn_ss) then
+ do i=nss+1,nhpb
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ write (iout,*) "i",i," iss",iss(i),
+ & " mask",dyn_ss_mask(iss(i))
+ enddo
+ endif
return
end
c-----------------------------------------------------------------------------
write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
C Check whether the specified bridging residues are cystines.
do i=1,ns
- if (itype(iss(i)).ne.1) then
+ if (iabs(itype(iss(i))).ne.1) then
write (iout,'(2a,i3,a)')
- & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & 'Do you REALLY think that the residue ',
+ & restyp(itype(iss(i))),i,
& ' can form a disulfide bridge?!!!'
write (*,'(2a,i3,a)')
- & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & 'Do you REALLY think that the residue ',
+ & restyp(itype(iss(i))),i,
& ' can form a disulfide bridge?!!!'
stop
endif
projects / unres.git / blobdiff