refstr=(index(controlcard,'REFSTR').gt.0)
write (iout,*) "REFSTR",refstr
pdbref=(index(controlcard,'PDBREF').gt.0)
+ dyn_ss=(index(controlcard,'DYN_SS').gt.0)
iscode=index(controlcard,'ONE_LETTER')
tree=(index(controlcard,'MAKE_TREE').gt.0)
min_var=(index(controlcard,'MINVAR').gt.0)
plot_tree=(index(controlcard,'PLOT_TREE').gt.0)
punch_dist=(index(controlcard,'PUNCH_DIST').gt.0)
- call readi(controlcard,'NCUT',ncut,1)
+ call readi(controlcard,'NCUT',ncut,0)
+ call readi(controlcard,'NCLUST',nclust,5)
call readi(controlcard,'NSTART',nstart,0)
call readi(controlcard,'NEND',nend,0)
call reada(controlcard,'ECUT',ecut,10.0d0)
lgrp=(index(controlcard,'LGRP').gt.0)
caonly=(index(controlcard,'CA_ONLY').gt.0)
print_dist=(index(controlcard,'PRINT_DIST').gt.0)
- call multreada(controlcard,'CUTOFF',rcutoff,ncut,-1.0d0)
+ if (ncut.gt.0)
+ & call multreada(controlcard,'CUTOFF',rcutoff,ncut,-1.0d0)
call readi(controlcard,'IOPT',iopt,2)
lside = index(controlcard,"SIDE").gt.0
efree = index(controlcard,"EFREE").gt.0
call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
call reada(weightcard,'WSCCOR',wsccor,1.0D0)
+ call reada(weightcard,"D0CM",d0cm,3.78d0)
+ call reada(weightcard,"AKCM",akcm,15.1d0)
+ call reada(weightcard,"AKTH",akth,11.0d0)
+ call reada(weightcard,"AKCT",akct,12.0d0)
+ call reada(weightcard,"V1SS",v1ss,-1.08d0)
+ call reada(weightcard,"V2SS",v2ss,7.61d0)
+ call reada(weightcard,"V3SS",v3ss,13.7d0)
+ call reada(weightcard,"EBR",ebr,-5.50D0)
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)
+ do i=1,maxres-1
+ do j=i+1,maxres
+ dyn_ssbond_ij(i,j)=1.0d300
+ enddo
+ enddo
+ call reada(weightcard,"HT",Ht,0.0D0)
+ if (dyn_ss) then
+ ss_depth=ebr/wsc-0.25*eps(1,1)
+ Ht=Ht/wsc-0.25*eps(1,1)
+ akcm=akcm*wstrain/wsc
+ akth=akth*wstrain/wsc
+ akct=akct*wstrain/wsc
+ v1ss=v1ss*wstrain/wsc
+ v2ss=v2ss*wstrain/wsc
+ v3ss=v3ss*wstrain/wsc
+ else
+ ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ endif
+ write (iout,'(/a)') "Disulfide bridge parameters:"
+ write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
+ write (iout,'(a,f10.2)') 'S-S depth: ',ss_depth
+ write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
+ write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
+ write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
+ & ' v3ss:',v3ss
+ write (iout,'(2(a,f10.2))') 'ht:',ht,' eps:', eps(1,1)
if (wcorr4.gt.0.0d0) wcorr=wcorr4
weights(1)=wsc
weights(2)=wscp
do i=1,nres
itype(i)=rescode(i,sequence(i),iscode)
enddo
+ if (itype(2).eq.10.and.itype(1).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the first full residue, initial dummy deleted"
+ do i=1,nres
+ itype(i)=itype(i+1)
+ enddo
+ nres=nres-1
+ endif
+ if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the last full residue, terminal dummy deleted"
+ nres=nres-1
+ endif
print *,nres
print '(20i4)',(itype(i),i=1,nres)
enddo
enddo
endif
- call contact(.true.,ncont_ref,icont_ref)
+ call contact(print_contact_map,ncont_ref,icont_ref)
endif
c Read distance restraints
if (constr_dist.gt.0) then
enddo
endif
endif
+ 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.
+c write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU"
+ enddo
+ endif
+ print *, "Leaving brigde read"
return
end
c----------------------------------------------------------------------------