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
do i=1,nrep
iremd_m_total=iremd_m_total+remd_m(i)
enddo
- write (iout,*) 'Total number of replicas ',iremd_m_total
+ write (iout,*) 'Total number of replicas ',iremd_m_total
+ endif
endif
- endif
if(me.eq.king.or..not.out1file)
- & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
+ & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
return
end
c--------------------------------------------------------------------------
rest = index(controlcard,"REST").gt.0
tbf = index(controlcard,"TBF").gt.0
usampl = index(controlcard,"USAMPL").gt.0
+
mdpdb = index(controlcard,"MDPDB").gt.0
call reada(controlcard,"T_BATH",t_bath,300.0d0)
call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
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
C Body
C
C Read weights of the subsequent energy terms.
- call card_concat(weightcard)
- call reada(weightcard,'WLONG',wlong,1.0D0)
- call reada(weightcard,'WSC',wsc,wlong)
- call reada(weightcard,'WSCP',wscp,wlong)
- call reada(weightcard,'WELEC',welec,1.0D0)
- call reada(weightcard,'WVDWPP',wvdwpp,welec)
- call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
- call reada(weightcard,'WCORR4',wcorr4,0.0D0)
- call reada(weightcard,'WCORR5',wcorr5,0.0D0)
- call reada(weightcard,'WCORR6',wcorr6,0.0D0)
- call reada(weightcard,'WTURN3',wturn3,1.0D0)
- call reada(weightcard,'WTURN4',wturn4,1.0D0)
- call reada(weightcard,'WTURN6',wturn6,1.0D0)
- call reada(weightcard,'WSCCOR',wsccor,1.0D0)
- call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
- call reada(weightcard,'WBOND',wbond,1.0D0)
- call reada(weightcard,'WTOR',wtor,1.0D0)
- call reada(weightcard,'WTORD',wtor_d,1.0D0)
- call reada(weightcard,'WANG',wang,1.0D0)
- call reada(weightcard,'WSCLOC',wscloc,1.0D0)
- call reada(weightcard,'SCAL14',scal14,0.4D0)
- call reada(weightcard,'SCALSCP',scalscp,1.0d0)
- call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
- call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
- call reada(weightcard,'TEMP0',temp0,300.0d0)
- if (index(weightcard,'SOFT').gt.0) ipot=6
+ call card_concat(weightcard)
+ call reada(weightcard,'WLONG',wlong,1.0D0)
+ call reada(weightcard,'WSC',wsc,wlong)
+ call reada(weightcard,'WSCP',wscp,wlong)
+ call reada(weightcard,'WELEC',welec,1.0D0)
+ call reada(weightcard,'WVDWPP',wvdwpp,welec)
+ call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
+ call reada(weightcard,'WCORR4',wcorr4,0.0D0)
+ call reada(weightcard,'WCORR5',wcorr5,0.0D0)
+ call reada(weightcard,'WCORR6',wcorr6,0.0D0)
+ call reada(weightcard,'WTURN3',wturn3,1.0D0)
+ call reada(weightcard,'WTURN4',wturn4,1.0D0)
+ call reada(weightcard,'WTURN6',wturn6,1.0D0)
+ call reada(weightcard,'WSCCOR',wsccor,1.0D0)
+ call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
+ call reada(weightcard,'WBOND',wbond,1.0D0)
+ call reada(weightcard,'WTOR',wtor,1.0D0)
+ call reada(weightcard,'WTORD',wtor_d,1.0D0)
+ call reada(weightcard,'WANG',wang,1.0D0)
+ call reada(weightcard,'WSCLOC',wscloc,1.0D0)
+ call reada(weightcard,'SCAL14',scal14,0.4D0)
+ call reada(weightcard,'SCALSCP',scalscp,1.0d0)
+ call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
+ call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
+ call reada(weightcard,'TEMP0',temp0,300.0d0)
+ 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)
- if (wcorr4.gt.0.0d0) wcorr=wcorr4
- weights(1)=wsc
- weights(2)=wscp
- weights(3)=welec
- weights(4)=wcorr
- weights(5)=wcorr5
- weights(6)=wcorr6
- weights(7)=wel_loc
- weights(8)=wturn3
- weights(9)=wturn4
- weights(10)=wturn6
- weights(11)=wang
- weights(12)=wscloc
- weights(13)=wtor
- weights(14)=wtor_d
- weights(15)=wstrain
- weights(16)=wvdwpp
- weights(17)=wbond
- weights(18)=scal14
- weights(21)=wsccor
+ call reada(weightcard,'WCORRH',wcorr,1.0D0)
+ if (wcorr4.gt.0.0d0) wcorr=wcorr4
+ weights(1)=wsc
+ weights(2)=wscp
+ weights(3)=welec
+ weights(4)=wcorr
+ weights(5)=wcorr5
+ weights(6)=wcorr6
+ weights(7)=wel_loc
+ weights(8)=wturn3
+ weights(9)=wturn4
+ weights(10)=wturn6
+ weights(11)=wang
+ weights(12)=wscloc
+ weights(13)=wtor
+ weights(14)=wtor_d
+ weights(15)=wstrain
+ weights(16)=wvdwpp
+ weights(17)=wbond
+ weights(18)=scal14
+ weights(21)=wsccor
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 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
+ do i=1,nres
+ thetabound(1,i)=0
+ thetabound(2,i)=pi
+ 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,nthet_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
+ do i=1,ntheta_constr
+ ii = itheta_constr(i)
+ thetabound(1,ii) = phi0(i)-drange(i)
+ thetabound(2,ii) = phi0(i)+drange(i)
+ 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
i2=jhpb(i)-nres
it1=itype(i1)
it2=itype(i2)
- if (me.eq.king.or..not.out1file)
- & write (iout,'(2a,i3,3a,i3,a,3f10.3)')
+ write (iout,'(2a,i3,3a,i3,a,3f10.3)')
& restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
& ebr,forcon(i)
enddo
& write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)')
& 'Processor',myrank,': end reading molecular data.'
#endif
+ print *,"A TU?"
return
end
c--------------------------------------------------------------------------
include 'COMMON.SETUP'
C Read bridging residues.
read (inp,*) ns,(iss(i),i=1,ns)
-c print *,'ns=',ns
+ print *,'ns=',ns
if(me.eq.king.or..not.out1file)
& write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
C Check whether the specified bridging residues are cystines.
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)
c write (iout,*) "j",j," k",k
ddjk=dist(j,k)
if (constr_dist.eq.1) then
- nhpb=nhpb+1
- ihpb(nhpb)=j
- jhpb(nhpb)=k
+ nhpb=nhpb+1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
dhpb(nhpb)=ddjk
- forcon(nhpb)=wfrag_(i)
+ forcon(nhpb)=wfrag_(i)
else if (constr_dist.eq.2) then
if (ddjk.le.dist_cut) then
nhpb=nhpb+1
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
#endif
if (OKRandom) then
c r1 = prng_next(me)
- r1=ran_number(0.0D0,1.0D0)
+ r1=ran_number(0.0D0,1.0D0)
if(me.eq.king)
& write (iout,*) 'ran_num',r1
if (r1.lt.0.0d0) OKRandom=.false.
projects / unres.git / blobdiff