include 'COMMON.INTERACT'
include 'COMMON.SETUP'
include 'COMMON.SPLITELE'
+ include 'COMMON.SHIELD'
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)
+C this variable with_theta_constr is the variable which allow to read and execute the
+C constrains on theta angles WITH_THETA_CONSTR is the keyword
+ with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
+ write (iout,*) "with_theta_constr ",with_theta_constr
call readi(controlcard,'SYM',symetr,1)
call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
selfguide=(index(controlcard,'SELFGUIDE'))
print *,'AFMlog',AFMlog,selfguide,"KUPA"
call readi(controlcard,'IPRINT',iprint,0)
+C SHIELD keyword sets if the shielding effect of side-chains is used
+C 0 denots no shielding is used all peptide are equally despite the
+C solvent accesible area
+C 1 the newly introduced function
+C 2 reseved for further possible developement
+ call readi(controlcard,'SHIELD',shield_mode,0)
+C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "shield_mode",shield_mode
+C endif
call readi(controlcard,'MAXGEN',maxgen,10000)
call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
call readi(controlcard,"KDIAG",kdiag,0)
write(iout,*) "bordlipbot=",bordlipbot
write(iout,*) "bufliptop=",bufliptop
write(iout,*) "buflipbot=",buflipbot
-
-
+ write (iout,*) "SHIELD MODE",shield_mode
+ if (shield_mode.gt.0) then
+ pi=3.141592d0
+C VSolvSphere the volume of solving sphere
+C print *,pi,"pi"
+C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
+C there will be no distinction between proline peptide group and normal peptide
+C group in case of shielding parameters
+ VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+ write (iout,*) VSolvSphere,VSolvSphere_div
+C long axis of side chain
+ do i=1,ntyp
+ long_r_sidechain(i)=vbldsc0(1,i)
+ short_r_sidechain(i)=sigma0(i)
+ enddo
+ buff_shield=1.0d0
+ endif
if (me.eq.king .or. .not.out1file )
& write (iout,*) "DISTCHAINMAX",distchainmax
integer rescode
double precision x(maxvar)
character*256 pdbfile
- character*320 weightcard
+ character*400 weightcard
character*80 weightcard_t,ucase
dimension itype_pdb(maxres)
common /pizda/ itype_pdb
call reada(weightcard,"V2SS",v2ss,7.61d0)
call reada(weightcard,"V3SS",v3ss,13.7d0)
call reada(weightcard,"EBR",ebr,-5.50D0)
+ call reada(weightcard,"ATRISS",atriss,0.301D0)
+ call reada(weightcard,"BTRISS",btriss,0.021D0)
+ call reada(weightcard,"CTRISS",ctriss,1.001D0)
+ call reada(weightcard,"DTRISS",dtriss,1.001D0)
+ write (iout,*) "ATRISS=", atriss
+ write (iout,*) "BTRISS=", btriss
+ write (iout,*) "CTRISS=", ctriss
+ write (iout,*) "DTRISS=", dtriss
dyn_ss=(index(weightcard,'DYN_SS').gt.0)
do i=1,maxres
dyn_ss_mask(i)=.false.
v2ss=v2ss*wstrain/wsc
v3ss=v3ss*wstrain/wsc
else
- ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ if (wstrain.ne.0.0) then
+ ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ else
+ ss_depth=0.0
+ endif
endif
if(me.eq.king.or..not.out1file) then
33 write (iout,'(a)') 'Error opening PDB file.'
stop
34 continue
-c print *,'Begin reading pdb data'
+c write (iout,*) 'Begin reading pdb data'
+c call flush(iout)
call readpdb
-c print *,'Finished reading pdb data'
+c write (iout,*) 'Finished reading pdb data'
+c call flush(iout)
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3,a,i3)')'nsup=',nsup,
& ' nstart_sup=',nstart_sup
enddo
read (inp,*) ndih_constr
if (ndih_constr.gt.0) then
- read (inp,*) ftors
- read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
+C read (inp,*) ftors
+ read (inp,*) (idih_constr(i),phi0(i),drange(i),ftors(i),
+ & i=1,ndih_constr)
if(me.eq.king.or..not.out1file)then
write (iout,*)
& 'There are',ndih_constr,' constraints on phi 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
endif
do i=1,ndih_constr
phi0(i)=deg2rad*phi0(i)
drange(i)=deg2rad*drange(i)
enddo
- if(me.eq.king.or..not.out1file)
- & write (iout,*) 'FTORS',ftors
+C if(me.eq.king.or..not.out1file)
+C & write (iout,*) 'FTORS',ftors
do i=1,ndih_constr
ii = idih_constr(i)
phibound(1,ii) = phi0(i)-drange(i)
phibound(2,ii) = phi0(i)+drange(i)
enddo
endif
+C first setting the theta boundaries to 0 to pi
+C this mean that there is no energy penalty for any angle occuring this can be applied
+C for generate random conformation but is not implemented in this way
+C do i=1,nres
+C thetabound(1,i)=0
+C thetabound(2,i)=pi
+C enddo
+C begin reading theta constrains this is quartic constrains allowing to
+C have smooth second derivative
+ 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
+ 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
+ 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
+C
+C with_dihed_constr = index(controlcard,"WITH_DIHED_CONSTR").gt.0
+C write (iout,*) "with_dihed_constr ",with_dihed_constr
nnt=1
#ifdef MPI
if (me.eq.king) then
enddo
call contact(.true.,ncont_ref,icont_ref,co)
endif
-c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
+ endif
+ print *, "A TU"
+ 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
& restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
enddo
endif
- endif
+C endif
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
omeg(i)=-120d0*deg2rad
if (itype(i).le.0) omeg(i)=-omeg(i)
enddo
+ call chainbuild_extconf
else
if(me.eq.king.or..not.out1file)
& write (iout,'(a)') 'Random-generated initial geometry.'
& write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)')
& 'Processor',myrank,': end reading molecular data.'
#endif
+ print *,"A TU?"
return
end
c--------------------------------------------------------------------------
integer ifrag_(2,100),ipair_(2,100)
double precision wfrag_(100),wpair_(100)
character*500 controlcard
-c write (iout,*) "Calling read_dist_constr"
+ print *, "WCHODZE"
+ write (iout,*) "Calling read_dist_constr"
c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
c call flush(iout)
call card_concat(controlcard)
enddo
endif
enddo
+ print *,ndist_
do i=1,ndist_
- read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
+ if (constr_dist.eq.11) then
+ read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+ & ibecarb(i),forcon(nhpb+1),fordepth(nhpb+1)
+ fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1)
+ else
+C print *,"in else"
+ read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+ & ibecarb(i),forcon(nhpb+1)
+ endif
if (forcon(nhpb+1).gt.0.0d0) then
nhpb=nhpb+1
- dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+ if (ibecarb(i).gt.0) then
+ ihpb(i)=ihpb(i)+nres
+ jhpb(i)=jhpb(i)+nres
+ endif
+ if (dhpb(nhpb).eq.0.0d0)
+ & dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+ endif
+C read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
+C if (forcon(nhpb+1).gt.0.0d0) then
+C nhpb=nhpb+1
+C dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
#ifdef MPI
if (.not.out1file .or. me.eq.king)
& write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
& nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
#endif
- endif
+
enddo
call flush(iout)
return
projects / unres.git / blobdiff