enddo
enddo
endif
+
+
+
+ if (.not.allocated(ichargecat)) allocate (ichargecat(ntyp_molec(5)))
+ if (oldion.eq.1) then
do i=1,ntyp_molec(5)
- read(iion,*) msc(i,5),restok(i,5)
+ read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
ip(5)=0.2
read (iion,*) (catprm(i,k),i=1,ncatprotparm)
enddo
print *, catprm
+ endif
+ allocate(catnuclprm(14,ntyp_molec(2),ntyp_molec(5)))
+ do i=1,ntyp_molec(5)
+ do j=1,ntyp_molec(2)
+ write(iout,*) i,j
+ read(iionnucl,*) (catnuclprm(k,j,i),k=1,14)
+ enddo
+ enddo
+ write(*,'(3(5x,a6)11(7x,a6))') "w1 ","w2 ","epslj ","pis1 ", &
+ "sigma0","epsi0 ","chi1 ","chip1 ","sig ","b1 ","b2 ", &
+ "b3 ","b4 ","chis1 "
+ do i=1,ntyp_molec(5)
+ do j=1,ntyp_molec(2)
+ write(*,'(3(f10.3,x),11(f12.6,x),a3,2a)') (catnuclprm(k,j,i),k=1,14), &
+ restyp(i,5),"-",restyp(j,2)
+ enddo
+ enddo
! read (iion,*) (vcatprm(k),k=1,ncatprotpram)
!----------------------------------------------------
allocate(a0thet(-ntyp:ntyp),theta0(-ntyp:ntyp))
enddo
enddo
endif
+#ifndef NEWCORR
+ do i=1,ntyp1
+ itype2loc(i)=itortyp(i)
+ enddo
+#endif
+
ELSE IF (TOR_MODE.eq.1) THEN
!C read valence-torsional parameters
do j=1,i
! write (*,*) "Im in ALAB", i, " ", j
read(isidep,*) &
- eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i), &
- (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j), &
- chis(i,j),chis(j,i), &
- nstate(i,j),(wstate(k,i,j),k=1,4), &
- dhead(1,1,i,j),dhead(1,2,i,j),dhead(2,1,i,j),dhead(2,2,i,j),&
- dtail(1,i,j),dtail(2,i,j), &
- epshead(i,j),sig0head(i,j), &
- rborn(i,j),rborn(j,i),(wqdip(k,i,j),k=1,2),wquad(i,j), &
- alphapol(i,j),alphapol(j,i), &
- (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j),debaykap(i,j)
-! print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i)
+ eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i), & !6 w tej linii
+ (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j), & !6 w tej linii
+ chis(i,j),chis(j,i), & !2 w tej linii
+ nstate(i,j),(wstate(k,i,j),k=1,4), & !5 w tej lini - 1 integer pierwszy
+ dhead(1,1,i,j),dhead(1,2,i,j),dhead(2,1,i,j),dhead(2,2,i,j),& ! 4 w tej linii
+ dtail(1,i,j),dtail(2,i,j), & ! 2 w tej lini
+ epshead(i,j),sig0head(i,j), & ! 2 w tej linii
+ rborn(i,j),rborn(j,i),(wqdip(k,i,j),k=1,2),wquad(i,j), & ! 5 w tej linii
+ alphapol(i,j),alphapol(j,i), & ! 2 w tej linii
+ (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j),debaykap(i,j) !8 w tej linii
+ IF ((LaTeX).and.(i.gt.24)) then
+ write (2,'(2a4,1h&,14(f8.2,1h&),23(f8.2,1h&))') restyp(i,1),restyp(j,1), &
+ eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i), & !6 w tej linii
+ (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j), & !6 w tej linii
+ chis(i,j),chis(j,i) !2 w tej linii
+ endif
+ print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i), wqdip(1,i,j)
+ END DO
+ END DO
+ do i=1,ntyp
+ do j=1,i
+ IF ((LaTeX).and.(i.gt.24)) then
+ write (2,'(2a4,1h&,14(f8.2,1h&),23(f8.2,1h&))') restyp(i,1),restyp(j,1), &
+ dhead(1,1,i,j),dhead(2,1,i,j),& ! 2 w tej linii
+ dtail(1,i,j),dtail(2,i,j), & ! 2 w tej lini
+ epshead(i,j),sig0head(i,j), & ! 2 w tej linii
+ rborn(i,j),rborn(j,i), & ! 3 w tej linii
+ alphapol(i,j),alphapol(j,i), & ! 2 w tej linii
+ (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j),debaykap(i,j) !8 w tej linii
+ endif
END DO
END DO
DO i = 1, ntyp
END DO
END DO
endif
+
+
! goto 50
!--------------------- GBV potential -----------------------------------
case(5)
! v1ss=0.0d0
! v2ss=0.0d0
! v3ss=0.0d0
+
+! Ions by Aga
+
+ allocate(alphapolcat(ntyp,ntyp),epsheadcat(ntyp,ntyp),sig0headcat(ntyp,ntyp))
+ allocate(alphapolcat2(ntyp,ntyp))
+ allocate(sigiso1cat(ntyp,ntyp),rborn1cat(ntyp,ntyp),rborn2cat(ntyp,ntyp),sigmap1cat(ntyp,ntyp))
+ allocate(sigmap2cat(ntyp,ntyp),sigiso2cat(ntyp,ntyp))
+ allocate(chis1cat(ntyp,ntyp),chis2cat(ntyp,ntyp),wquadcat(ntyp,ntyp),chipp1cat(ntyp,ntyp),chipp2cat(ntyp,ntyp))
+ allocate(epsintabcat(ntyp,ntyp))
+ allocate(dtailcat(2,ntyp,ntyp))
+ allocate(alphasurcat(4,ntyp,ntyp),alphisocat(4,ntyp,ntyp))
+ allocate(wqdipcat(2,ntyp,ntyp))
+ allocate(wstatecat(4,ntyp,ntyp))
+ allocate(dheadcat(2,2,ntyp,ntyp))
+ allocate(nstatecat(ntyp,ntyp))
+ allocate(debaykapcat(ntyp,ntyp))
+
+ if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,0:ntyp1))
+ if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,0:ntyp1))
+! if (.not.allocated(chicat)) allocate(chicat(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi1cat)) allocate(chi1cat(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
+
+
+ if (.not.allocated(ichargecat)) allocate (ichargecat(ntyp_molec(5)))
+! i to SC, j to jon, isideocat - nazwa pliku z ktorego czytam parametry
+ if (oldion.eq.0) then
+ if (.not.allocated(icharge)) then ! this mean you are oprating in old sc-sc mode
+ allocate(icharge(1:ntyp1))
+ read(iion,*) (icharge(i),i=1,ntyp)
+ else
+ read(iion,*) ijunk
+ endif
+
+ do i=1,ntyp_molec(5)
+ read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
+ print *,msc(i,5),restok(i,5)
+ enddo
+ ip(5)=0.2
+ ! mp(5)=0.2
+ ! pstok(5)=1.0
+!DIR$ NOUNROLL
+ do j=1,ntyp_molec(5)
+ do i=1,ntyp
+! do j=1,ntyp_molec(5)
+! write (*,*) "Im in ALAB", i, " ", j
+ read(iion,*) &
+ epscat(i,j),sigmacat(i,j), &
+! chicat(i,j),chicat(j,i),chippcat(i,j),chippcat(j,i), &
+ chi1cat(i,j),chi2cat(i,j),chipp1cat(i,j),chipp2cat(i,j), &
+
+ (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&
+! chiscat(i,j),chiscat(j,i), &
+ chis1cat(i,j),chis2cat(i,j), &
+
+ nstatecat(i,j),(wstatecat(k,i,j),k=1,4), & !5 w tej lini - 1 integer pierwszy
+ dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&
+ dtailcat(1,i,j),dtailcat(2,i,j), &
+ epsheadcat(i,j),sig0headcat(i,j), &
+!wdipcat = w1 , w2
+! rborncat(i,j),rborncat(j,i),&
+ rborn1cat(i,j),rborn2cat(i,j),&
+ (wqdipcat(k,i,j),k=1,2), &
+ alphapolcat(i,j),alphapolcat2(j,i), &
+ (alphisocat(k,i,j),k=1,4),sigiso1cat(i,j),sigiso2cat(i,j),epsintabcat(i,j),debaykapcat(i,j)
+
+ if (chi1cat(i,j).gt.0.9) write (*,*) "WTF ANISO", i,j, chi1cat(i,j)
+! print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i)
+! if (i.eq.1) then
+! write (iout,*) 'i= ', i, ' j= ', j
+! write (iout,*) 'epsi0= ', epscat(1,j)
+! write (iout,*) 'sigma0= ', sigmacat(1,j)
+! write (iout,*) 'chi(i,j)= ', chicat(1,j)
+! write (iout,*) 'chi(j,i)= ', chicat(j,1)
+! write (iout,*) 'chip(i,j)= ', chippcat(1,j)
+! write (iout,*) 'chip(j,i)= ', chippcat(j,1)
+! write (iout,*) 'alphasur1= ', alphasurcat(1,1,j)
+! write (iout,*) 'alphasur2= ', alphasurcat(2,1,j)
+! write (iout,*) 'alphasur3= ', alphasurcat(3,1,j)
+! write (iout,*) 'alphasur4= ', alphasurcat(4,1,j)
+! write (iout,*) 'sig1= ', sigmap1cat(1,j)
+! write (iout,*) 'chis(i,j)= ', chiscat(1,j)
+! write (iout,*) 'chis(j,i)= ', chiscat(j,1)
+! write (iout,*) 'dhead= ', dheadcat(1,1,1,j)
+! write (iout,*) 'a1= ', rborncat(j,1)
+! write (iout,*) 'a2= ', rborncat(1,j)
+! write (iout,*) 'epsin= ', epsintabcat(1,j), epsintabcat(j,1)
+! write (iout,*) 'alphapol1= ', alphapolcat(1,j)
+! write (iout,*) 'w1= ', wqdipcat(1,1,j)
+! write (iout,*) 'w2= ', wqdipcat(2,1,j)
+! endif
+
+!
+! If ((i.eq.1).and.(j.eq.27)) then
+! write (iout,*) 'SEP'
+! Write (iout,*) 'w1= ', wqdipcat(1,1,27)
+! Write (iout,*) 'w2= ', wqdipcat(2,1,27)
+! endif
+
+ END DO
+ END DO
+ allocate(aa_aq_cat(-ntyp:ntyp,ntyp),bb_aq_cat(-ntyp:ntyp,ntyp))
+ do i=1,ntyp
+ do j=1,ntyp_molec(5)
+ epsij=epscat(i,j)
+ rrij=sigmacat(i,j)
+ rrij=rrij**expon
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_aq_cat(i,j)=epsij*rrij*rrij
+ bb_aq_cat(i,j)=-sigeps*epsij*rrij
+ enddo
+ enddo
+
+ do i=1,ntyp
+ do j=1,ntyp_molec(5)
+ if (i.eq.10) then
+ write (iout,*) 'i= ', i, ' j= ', j
+ write (iout,*) 'epsi0= ', epscat(i,j)
+ write (iout,*) 'sigma0= ', sigmacat(i,j)
+ write (iout,*) 'chi1= ', chi1cat(i,j)
+ write (iout,*) 'chi1= ', chi2cat(i,j)
+ write (iout,*) 'chip1= ', chipp1cat(i,j)
+ write (iout,*) 'chip2= ', chipp2cat(i,j)
+ write (iout,*) 'alphasur1= ', alphasurcat(1,i,j)
+ write (iout,*) 'alphasur2= ', alphasurcat(2,i,j)
+ write (iout,*) 'alphasur3= ', alphasurcat(3,i,j)
+ write (iout,*) 'alphasur4= ', alphasurcat(4,i,j)
+ write (iout,*) 'sig1= ', sigmap1cat(i,j)
+ write (iout,*) 'sig2= ', sigmap2cat(i,j)
+ write (iout,*) 'chis1= ', chis1cat(i,j)
+ write (iout,*) 'chis1= ', chis2cat(i,j)
+ write (iout,*) 'nstatecat(i,j)= ', nstatecat(i,j)
+ write (iout,*) 'wstatecat(k,i,j),k=1= ',wstatecat(1,i,j)
+ write (iout,*) 'dhead= ', dheadcat(1,1,i,j)
+ write (iout,*) 'dhead2= ', dheadcat(1,2,i,j)
+ write (iout,*) 'a1= ', rborn1cat(i,j)
+ write (iout,*) 'a2= ', rborn2cat(i,j)
+ write (iout,*) 'epsin= ', epsintabcat(i,j), epsintabcat(j,i)
+ write (iout,*) 'alphapol1= ', alphapolcat(i,j)
+ write (iout,*) 'alphapol2= ', alphapolcat2(i,j)
+ write (iout,*) 'w1= ', wqdipcat(1,i,j)
+ write (iout,*) 'w2= ', wqdipcat(2,i,j)
+ write (iout,*) 'debaykapcat(i,j)= ', debaykapcat(i,j)
+ endif
+
+ If ((i.eq.1).and.(j.eq.27)) then
+ write (iout,*) 'SEP'
+ Write (iout,*) 'w1= ', wqdipcat(1,1,27)
+ Write (iout,*) 'w2= ', wqdipcat(2,1,27)
+ endif
+
+ enddo
+ enddo
+
+ endif
+
if(me.eq.king) then
write (iout,'(/a)') "Disulfide bridge parameters:"
! enddo
! else
do j=1,3
- dcj=(c(j,nres-2)-c(j,nres-3))/2.0
- c(j,nres)=c(j,nres-1)+dcj
+ dcj=(c(j,nres-nres_molec(5)-2)-c(j,nres-nres_molec(5)-3))/2.0
+ c(j,nres)=c(j,nres-nres_molec(5)-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
! endif
endif
do j=1,3
! c(j,1)=c(j,2)-1.9d0*e2(j)
- c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
+ c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/sqrt(2.0d0)
enddo
else
do j=1,3
istype(i)=istype_temp(i)
enddo
enddo
+ if ((itype(1,1).eq.ntyp1).and.itype(2,5).ne.0) then
+! I have only ions now dummy atoms in the system
+ molnum(1)=5
+ itype(1,5)=itype(2,5)
+ itype(1,1)=0
+ do i=2,nres
+ itype(i,5)=itype(i+1,5)
+ enddo
+ itype(nres,5)=0
+ nres=nres-1
+ nres_molec(1)=nres_molec(1)-1
+ endif
! if (itype(1,1).eq.ntyp1) then
! nsup=nsup-1
! nstart_sup=2
enddo
endif
-! print *,seqalingbegin,nres
+ print *,seqalingbegin,nres
if(.not.allocated(vbld)) then
allocate(vbld(2*nres))
do i=1,2*nres
allocate(dc_norm(3,0:2*nres+2))
dc_norm(:,:)=0.d0
endif
-
+ write(iout,*) "before int_from_cart"
call int_from_cart(.true.,.false.)
call sc_loc_geom(.false.)
+ write(iout,*) "after int_from_cart"
+
+
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
enddo
+ write(iout,*) "after thetaref"
! do i=1,2*nres
! vbld_inv(i)=0.d0
! vbld(i)=0.d0
! enddo
! enddo
!
+! do i=1,2*nres
+! do j=1,3
+! chomo(j,i,k)=c(j,i)
+! enddo
+! enddo
+! write(iout,*) "after chomo"
+
if(.not.allocated(cref)) allocate(cref(3,2*nres+2,maxperm)) !(3,maxres2+2,maxperm)
if(.not.allocated(chain_rep)) allocate(chain_rep(3,2*nres+2,maxsym)) !(3,maxres2+2,maxsym)
if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
integer i
-
+ usampl=.false. ! the default value of usample should be 0
+! write(iout,*) "KURWA2",usampl
nglob_csa=0
eglob_csa=1d99
nmin_csa=0
call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
call reada(controlcard,'DRMS',drms,0.1D0)
+ call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
+ read_homol_frag = index(controlcard,"READ_HOMOL_FRAG").gt.0
+ out_template_coord = index(controlcard,"OUT_TEMPLATE_COORD").gt.0
+ out_template_restr = index(controlcard,"OUT_TEMPLATE_RESTR").gt.0
if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
protein=index(controlcard,"PROTEIN").gt.0
ions=index(controlcard,"IONS").gt.0
+ call readi(controlcard,'OLDION',oldion,1)
nucleic=index(controlcard,"NUCLEIC").gt.0
write (iout,*) "with_theta_constr ",with_theta_constr
AFMlog=(index(controlcard,'AFM'))
! elemode = 0 is orignal UNRES electrostatics
! elemode = 1 is "Momo" potentials in progress
! elemode = 2 is in development EVALD
+
+
write (iout,*) TUBEmode,"TUBEMODE"
if (TUBEmode.gt.0) then
call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
endif
! CUTOFFF ON ELECTROSTATICS
- call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
+ call reada(controlcard,"R_CUT_ELE",r_cut_ele,25.0d0)
call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
write(iout,*) "R_CUT_ELE=",r_cut_ele
! Lipidic parameters
! enddo
buff_shield=1.0d0
endif
+ itime_mat=0
return
end subroutine read_control
!-----------------------------------------------------------------------------
rest = index(controlcard,"REST").gt.0
tbf = index(controlcard,"TBF").gt.0
usampl = index(controlcard,"USAMPL").gt.0
+! write(iout,*) "KURWA",usampl
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)
print_compon = index(controlcard,"PRINT_COMPON").gt.0
rattle = index(controlcard,"RATTLE").gt.0
preminim=(index(controlcard,'PREMINIM').gt.0)
+ forceminim=(index(controlcard,'FORCEMINIM').gt.0)
write (iout,*) "PREMINIM ",preminim
dccart=(index(controlcard,'CART').gt.0)
if (preminim) call read_minim
open (itube,file=tubename,status='old')
call getenv_loc('IONPAR',ionname)
open (iion,file=ionname,status='old')
+ call getenv_loc('IONPAR_NUCL',ionnuclname)
+ open (iionnucl,file=ionnuclname,status='old')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
readonly)
open (itube,file=tubename,status='old',action='read')
call getenv_loc('IONPAR',ionname)
open (iion,file=ionname,status='old',action='read')
+ call getenv_loc('IONPAR_NUCL',ionnuclname)
+ open (iionnucl,file=ionnuclname,status='old',action='read')
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
return
end subroutine write_stat_thread
!-----------------------------------------------------------------------------
+ subroutine readpdb_template(k)
+! Read the PDB file for read_constr_homology with read2sigma
+! and convert the peptide geometry into virtual-chain geometry.
+! implicit none
+! include 'DIMENSIONS'
+! include 'COMMON.LOCAL'
+! include 'COMMON.VAR'
+! include 'COMMON.CHAIN'
+! include 'COMMON.INTERACT'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.GEO'
+! include 'COMMON.NAMES'
+! include 'COMMON.CONTROL'
+! include 'COMMON.FRAG'
+! include 'COMMON.SETUP'
+ use compare_data, only:nhfrag,nbfrag
+ integer :: i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity, &
+ ishift_pdb,ires_ca
+ logical lprn /.false./,fail
+ real(kind=8), dimension (3):: e1,e2,e3
+ real(kind=8) :: dcj,efree_temp
+ character*3 seq,res
+ character*5 atom
+ character*80 card
+ real(kind=8), dimension (3,20) :: sccor
+! integer rescode
+ integer, dimension (:), allocatable :: iterter
+ if(.not.allocated(iterter))allocate(iterter(nres))
+ do i=1,nres
+ iterter(i)=0
+ enddo
+ ibeg=1
+ ishift1=0
+ ishift=0
+ write (2,*) "UNRES_PDB",unres_pdb
+ ires=0
+ ires_old=0
+ iii=0
+ lsecondary=.false.
+ nhfrag=0
+ nbfrag=0
+ do
+ read (ipdbin,'(a80)',end=10) card
+ if (card(:3).eq.'END') then
+ goto 10
+ else if (card(:3).eq.'TER') then
+! End current chain
+ ires_old=ires+2
+ itype(ires_old-1,1)=ntyp1
+ iterter(ires_old-1)=1
+ itype(ires_old,1)=ntyp1
+ iterter(ires_old)=1
+ ibeg=2
+! write (iout,*) "Chain ended",ires,ishift,ires_old
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ endif
+! Fish out the ATOM cards.
+ if (index(card(1:4),'ATOM').gt.0) then
+ read (card(12:16),*) atom
+! write (iout,*) "! ",atom," !",ires
+! if (atom.eq.'CA' .or. atom.eq.'CH3') then
+ read (card(23:26),*) ires
+ read (card(18:20),'(a3)') res
+! write (iout,*) "ires",ires,ires-ishift+ishift1,
+! & " ires_old",ires_old
+! write (iout,*) "ishift",ishift," ishift1",ishift1
+! write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+ if (ires-ishift+ishift1.ne.ires_old) then
+! Calculate the CM of the preceding residue.
+ if (ibeg.eq.0) then
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires_old)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires_old,iii,sccor)
+ endif
+ iii=0
+ endif
+! Start new residue.
+ if (res.eq.'Cl-' .or. res.eq.'Na+') then
+ ires=ires_old
+ cycle
+ else if (ibeg.eq.1) then
+! write (iout,*) "BEG ires",ires
+ ishift=ires-1
+ if (res.ne.'GLY' .and. res.ne. 'ACE') then
+ ishift=ishift-1
+ itype(1,1)=ntyp1
+ endif
+ ires=ires-ishift+ishift1
+ ires_old=ires
+! write (iout,*) "ishift",ishift," ires",ires,
+! & " ires_old",ires_old
+! write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
+ ibeg=0
+ else if (ibeg.eq.2) then
+! Start a new chain
+ ishift=-ires_old+ires-1
+ ires=ires_old+1
+! write (iout,*) "New chain started",ires,ishift
+ ibeg=0
+ else
+ ishift=ishift-(ires-ishift+ishift1-ires_old-1)
+ ires=ires-ishift+ishift1
+ ires_old=ires
+ endif
+ if (res.eq.'ACE' .or. res.eq.'NHE') then
+ itype(ires,1)=10
+ else
+ itype(ires,1)=rescode(ires,res,0,1)
+ endif
+ else
+ ires=ires-ishift+ishift1
+ endif
+! write (iout,*) "ires_old",ires_old," ires",ires
+! if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+! ishift1=ishift1+1
+! endif
+! write (2,*) "ires",ires," res ",res," ity",ity
+ if (atom.eq.'CA' .or. atom.eq.'CH3' .or. &
+ res.eq.'NHE'.and.atom(:2).eq.'HN') then
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+! write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
+#ifdef DEBUG
+ write (iout,'(2i3,2x,a,3f8.3)') &
+ ires,itype(ires,1),res,(c(j,ires),j=1,3)
+#endif
+ iii=iii+1
+ do j=1,3
+ sccor(j,iii)=c(j,ires)
+ enddo
+ if (ishift.ne.0) then
+ ires_ca=ires+ishift-ishift1
+ else
+ ires_ca=ires
+ endif
+! write (*,*) card(23:27),ires,itype(ires)
+ else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.&
+ atom.ne.'N' .and. atom.ne.'C' .and.&
+ atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.&
+ atom.ne.'OXT' .and. atom(:2).ne.'3H') then
+! write (iout,*) "sidechain ",atom
+ iii=iii+1
+ read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+ endif
+ endif
+ enddo
+ 10 if(me.eq.king.or..not.out1file) &
+ write (iout,'(a,i5)') ' Nres: ',ires
+! Calculate dummy residue coordinates inside the "chain" of a multichain
+! system
+ nres=ires
+ do i=2,nres-1
+! write (iout,*) i,itype(i),itype(i+1)
+ if (itype(i,1).eq.ntyp1.and.iterter(i).eq.1) then
+ if (itype(i+1,1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
+! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+! first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+! second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+ if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif !fail
+ do j=1,3
+ c(j,i)=c(j,i-1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ else !itype(i+1).eq.ntyp1
+ if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,i)=c(j,i+1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ endif !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
+ enddo
+! Calculate the CM of the last side chain.
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ nsup=nres
+ nstart_sup=1
+ if (itype(nres,1).ne.10) then
+ nres=nres+1
+ itype(nres,1)=ntyp1
+ if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
+ enddo
+ else
+ do j=1,3
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,nres)=c(j,nres-1)+dcj
+ c(j,2*nres)=c(j,nres)
+ enddo
+ endif
+ endif
+ do i=2,nres-1
+ do j=1,3
+ c(j,i+nres)=dc(j,i)
+ enddo
+ enddo
+ do j=1,3
+ c(j,nres+1)=c(j,1)
+ c(j,2*nres)=c(j,nres)
+ enddo
+ if (itype(1,1).eq.ntyp1) then
+ nsup=nsup-1
+ nstart_sup=2
+ if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(2,3,4,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,1)=c(j,2)-1.9d0*e2(j)
+ enddo
+ else
+ do j=1,3
+ dcj=(c(j,4)-c(j,3))/2.0
+ c(j,1)=c(j,2)-dcj
+ c(j,nres+1)=c(j,1)
+ enddo
+ endif
+ endif
+! Copy the coordinates to reference coordinates
+! do i=1,2*nres
+! do j=1,3
+! cref(j,i)=c(j,i)
+! enddo
+! enddo
+! Calculate internal coordinates.
+ if (out_template_coord) then
+ write (iout,'(/a)') &
+ "Cartesian coordinates of the reference structure"
+ write (iout,'(a,3(3x,a5),5x,3(3x,a5))') &
+ "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
+ do ires=1,nres
+ write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')&
+ restyp(itype(ires,1),1),ires,(c(j,ires),j=1,3),&
+ (c(j,ires+nres),j=1,3)
+ enddo
+ endif
+! Calculate internal coordinates.
+ call int_from_cart(.true.,out_template_coord)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ do i=1,nres-1
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
+ enddo
+ enddo
+ do i=2,nres-1
+ do j=1,3
+ dc(j,i+nres)=c(j,i+nres)-c(j,i)
+ dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
+ enddo
+! write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
+! & vbld_inv(i+nres)
+ enddo
+ do i=1,nres
+ do j=1,3
+ cref(j,i,1)=c(j,i)
+ cref(j,i+nres,1)=c(j,i+nres)
+ enddo
+ enddo
+ do i=1,2*nres
+ do j=1,3
+ chomo(j,i,k)=c(j,i)
+ enddo
+ enddo
+
+ return
+ end subroutine readpdb_template
+!-----------------------------------------------------------------------------
#endif
!-----------------------------------------------------------------------------
end module io_config
projects / unres4.git / blobdiff