integer iscode,indpdb,outpdb,outmol2,icomparfunc,pdbint,
& ensembles,constr_dist,constr_homology,homol_nset,
- & iset
+ & iset,ihset
real*8 waga_homology
real*8 waga_dist, waga_angle, waga_theta, waga_d, dist_cut
logical refstr,pdbref,punch_dist,print_rms,caonly,verbose,
& merge_helices,bxfile,cxfile,histfile,entfile,zscfile,rmsrgymap,
& ensembles,with_dihed_constr,check_conf,histout,constr_dist,
& constr_homology,out1file,homol_nset
- common /homol/ waga_homology(MaxProcs/20),
- & waga_dist,waga_angle,waga_theta,waga_d,dist_cut,iset
+ common /homol/ waga_homology(maxR),
+ & waga_dist,waga_angle,waga_theta,waga_d,dist_cut,iset,ihset
- character*80 protfiles(maxfile_prot,2,MaxR,MaxT_h,Max_Parm),
+ character*128 protfiles(maxfile_prot,2,MaxR,MaxT_h,Max_Parm),
& bprotfiles
integer nfile_bin(MaxR,MaxT_h,Max_Parm),
& nfile_asc(MaxR,MaxT_h,Max_Parm),
integer MaxSlice
parameter (Max_Parm=32)
parameter (MaxQ=4,MaxQ1=MaxQ+2)
- parameter(MaxR=8,MaxT_h=32)
+ parameter(MaxR=32,MaxT_h=32)
parameter(MaxSlice=40)
integer MaxN
parameter (MaxN=100)
include "COMMON.FREE"
include "COMMON.SBRIDGE"
real*4 csingle(3,maxres2)
- character*64 nazwa,bprotfile_temp
+ character*64 nazwa
+ character*128 bprotfile_temp
character*3 liczba
integer i,is,ie,j,ii,jj,k,kk,l,ll,mm,if,m
integer nrec,nlines,iscor,islice
implicit none
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.CONTROL'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.PROT'
- character*64 nazwa,bprotfile_temp
+ character*64 nazwa
+ character*128 bprotfile_temp
real*4 rtime,rpotE,ruconst,rt_bath,rprop(maxQ)
double precision time
integer iret,itmp,itraj,ntraj
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
include 'DIMENSIONS.COMPAR'
+ include 'DIMENSIONS.FREE'
include 'COMMON.IOUNITS'
include 'COMMON.TIME1'
include 'COMMON.SBRIDGE'
double precision tt
integer snk_p(MaxR,MaxT_h,Max_parm)
logical lerr
- character*64 bprotfile_temp
+ character*128 bprotfile_temp
integer scount_t(0:maxprocs-1)
call opentmp(islice,ientout,bprotfile_temp)
iii=0
& wtor_d,wsccor,wbond
#endif
call etotal(energia(0),fT)
- if (constr_homology) energia(0)=energia(0)+
+ if (constr_homology.gt.0) energia(0)=energia(0)+
& waga_homology(iset)*energia(22)
- write (iout,*) "constr_homology",constr_homology," iset",iset,
- & " waga_homology",waga_homology(iset)
+c write (iout,*) "constr_homology",constr_homology," iset",iset,
+c & " waga_homology",waga_homology(iset)
#ifdef DEBUG
write (iout,*) "Conformation",i
call enerprint(energia(0),fT)
& 1.0d0/(1.987D-3*beta_h(ib,ipar))
#ifdef DEBUG
call enerprint(energia(0),fT)
+#endif
+#ifdef DEBUG
write (iout,'(4f10.5,2i5)') 0.0,energia(0),0.0,
& 1.0d0/(beta_h(ib,ipar)*1.987D-3),
& 0,0
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
#ifndef ISNAN
external proc_proc
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
- & +wbond*estr+wsccor*fact(1)*esccor+ehomology_constr
+ & +wbond*estr+wsccor*fact(1)*esccor!+ehomology_constr
& +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
& +wdfa_beta*edfabet
#else
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
- & +wbond*estr+wsccor*fact(1)*esccor+ehomology_constr
+ & +wbond*estr+wsccor*fact(1)*esccor!+ehomology_constr
& +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
& +wdfa_beta*edfabet
#endif
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.CONTROL'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
-
+ include 'DIMENSIONS.FREE'
integer nnn, i, j, k, ki, irec, l
integer katy, odleglosci, test7
real*8 odleg, odleg2, odleg3, kat, kat2, kat3, gdih(max_template)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.LOCAL'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.LOCAL'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
include 'COMMON.VAR'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
C The system gains extra energy.
ecorr=ecorr+ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
+#ifdef DEBUG
+ write (iout,*) "ecorr",i,j,i+1,j1,
+ & ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
+#undef DEBUG
n_corr=n_corr+1
else if (j1.eq.j) then
C Contacts I-J and I-(J+1) occur simultaneously.
cd ees0pij=1.0D0
cd ees0mkl=0.0D0
cd ees0mij=1.0D0
-c write (iout,*)'Contacts have occurred for peptide groups',i,j,
-c & ' and',k,l
-c write (iout,*)'Contacts have occurred for peptide groups',
-c & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
-c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
+cd write (iout,*)'Contacts have occurred for peptide groups',i,j,
+cd & ' and',k,l
+cd write (iout,*)'Contacts have occurred for peptide groups',
+cd & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
+cd & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
C Calculate the multi-body contribution to energy.
ecorr=ecorr+ekont*ees
if (calc_grad) then
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
#ifdef MPI
include 'mpif.h'
#endif
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.VAR'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.CONTROL'
include 'COMMON.CHAIN'
include 'COMMON.IOUNITS'
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
#ifdef MPI
include 'mpif.h'
#endif
call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
call readi(controlcard,"HOMOL_NSET",homol_nset,1)
+ call readi(controlcard,"IHSET",ihset,1)
if (homol_nset.gt.1)then
call card_concat(controlcard,.true.)
read(controlcard,*) (waga_homology(i),i=1,homol_nset)
read (ientin,*,end=1401) rescore_tmp
c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
-c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
+c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
1301 continue
enddo
1401 continue
c write (iout,*) "distal = ",distal
c write (iout,*) "odl(",k,ii,") =",odl(k,ii)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
-c & "rescore(",k,j,") =",rescore(k,j)
+c & "rescore(",k,j,") =",rescore(k,j)
c
c Calculation of sigma from res sim
c
if (odl(k,ii).le.dist_cut) then
sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) ! other exprs possible
c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)
+c write (iout,*) "c sigma_odl",k,ii,sigma_odl(k,ii)
else
#ifdef OLDSIGMA
sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
#else
sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
& dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+c write (iout,*) "d sigma_odl",k,ii,sigma_odl(k,ii),
+c & odl(k,ii),dist_cut
#endif
c Following expr replaced by a positive exp argument
c sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
enddo
endif
+ call flush_(iout)
c -----------------------------------------------------------------
return
end
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'DIMENSIONS.COMPAR'
include 'COMMON.IOUNITS'
include 'COMMON.TIME1'
implicit none
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.CONTROL'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
implicit none
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'DIMENSIONS.COMPAR'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'COMMON.FRAG'
include 'COMMON.LOCAL'
include 'COMMON.VAR'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
#ifdef MPI
include "mpif.h"
#endif
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
#ifdef MPI
include "mpif.h"
#endif
include "COMMON.NAMES"
include "COMMON.FREE"
include "COMMON.OBCINKA"
- character*64 nazwa
+ character*128 nazwa
character*16000 controlcard
integer i,ii,ib,iR,iparm,ilen,iroof,nthr,npars
external ilen,iroof
include "COMMON.PROTFILES"
include "COMMON.PROT"
include "COMMON.FREE"
- character*64 bprotfile_temp
+ character*128 bprotfile_temp
character*3 liczba,liczba2
character*2 liczba1
integer iunit,islice
include "COMMON.SBRIDGE"
include "COMMON.OBCINKA"
real*4 csingle(3,maxres2)
- character*64 nazwa,bprotfile_temp
+ character*64 nazwa
+ character*128 bprotfile_temp
character*3 liczba
character*2 liczba1
integer i,j,ii,jj(maxslice),k,kk(maxslice),l,
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
include 'DIMENSIONS.COMPAR'
include 'COMMON.IOUNITS'
include 'COMMON.TIME1'
edihcnstr=enetb(20,i,iparm)
ehomology_constr=enetb(22,i,iparm)
if (homol_nset.gt.1)
- & ehomology_constr=waga_homology(homol_nset)*ehomology_constr
+ & ehomology_constr=waga_homology(ihset)*ehomology_constr
edfadis=enetb(23,i,iparm)
edfator=enetb(24,i,iparm)
edfanei=enetb(25,i,iparm)
edihcnstr=enetb(20,t,iparm)
ehomology_constr=enetb(22,t,iparm)
if (homol_nset.gt.1)
- & ehomology_constr=waga_homology(homol_nset)*ehomology_constr
+ & ehomology_constr=waga_homology(ihset)*ehomology_constr
edfadis=enetb(23,t,iparm)
edfator=enetb(24,t,iparm)
edfanei=enetb(25,t,iparm)
include "COMMON.SBRIDGE"
include "COMMON.OBCINKA"
real*4 csingle(3,maxres2)
- character*64 nazwa,bprotfile_temp
+ character*64 nazwa
+ character*128 bprotfile_temp
integer i,j,k,l,ii,jj(maxslice),kk(maxslice),ll(maxslice),
& mm(maxslice)
integer iscor,islice,islice1,slice