implicit none
!-----------------------------------------------------------------------------
! Max. number of AA residues
- integer,parameter :: maxres=6000!1200
+ integer,parameter :: maxres=6500!1200
! Appr. max. number of interaction sites
integer,parameter :: maxres2=2*maxres
! parameter (maxres6=6*maxres)
!-----------------------------------------------------------------------------
! readrtns_CSA.F
!-----------------------------------------------------------------------------
+#ifndef XDRFPDB
subroutine read_bridge
! Read information about disulfide bridges.
use geometry_data, only: nres
print *,"ENTER READ"
! Read bridging residues.
read (inp,*) ns
- print *,"ns",ns
+ write(iout,*) "ns",ns
+ call flush(iout)
if (ns.gt.0) then
allocate(iss(ns))
read (inp,*) (iss(i),i=1,ns)
subroutine read_angles(kanal,*)
use geometry_data
- ! use energy
- ! use control
+
+! use energy
+! use control
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.GEO'
!-----------------------------------------------------------------------------
subroutine read_dist_constr
use MPI_data
- ! use control
+! use control
use geometry, only: dist
use geometry_data
use control_data
if(.not.allocated(dhpb1)) allocate(dhpb1(maxdim))
if(.not.allocated(forcon)) allocate(forcon(maxdim))
if(.not.allocated(fordepth)) allocate(fordepth(maxdim))
+ if(.not.allocated(ibecarb)) allocate(ibecarb(maxdim))
if ((genconstr.gt.0).and.(constr_dist.eq.11)) then
call gen_dist_constr2
go to 1712
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)
+!EL fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1)
+ fordepth(nhpb+1)=fordepth(nhpb+1)**(0.25d0)
+ forcon(nhpb+1)=forcon(nhpb+1)**(0.25d0)
else
!C print *,"in else"
read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i), &
!-----------------------------------------------------------------------------
subroutine gen_dist_constr2
use MPI_data
- ! use control
+! use control
use geometry, only: dist
use geometry_data
use control_data
10 find_group=.false.
return
end function find_group
+#endif
!-----------------------------------------------------------------------------
logical function iblnk(charc)
character(len=1) :: charc
return
end function iblnk
!-----------------------------------------------------------------------------
+#ifndef XDRFPDB
integer function ilen(string)
character*(*) :: string
!EL logical :: iblnk
numm(1:1)=huj(inum2+1:inum2+1)
return
end subroutine numstr
+#endif
!-----------------------------------------------------------------------------
function ucase(string)
integer :: i, k, idiff
use geometry_data, only: c,nres
use energy_data
- ! use control
+! use control
use compare_data
use MD_data
! implicit real*8 (a-h,o-z)
! include 'COMMON.MD'
!el character(len=50) :: tytul
character*(*) :: tytul
- character(len=1),dimension(10) :: chainid= (/'A','B','C','D','E','F','G','H','I','J'/)
+ character(len=1),dimension(10) :: chainid= (/'A','B','C','D','E','F','G','H','I','J'/)
+#ifdef XDRFPDB
+ integer,dimension(maxres) :: ica !(maxres)
+#else
integer,dimension(nres) :: ica !(maxres)
- integer iti1
+#endif
+ integer :: iti1
!el local variables
integer :: j,iti,itj,itk,itl,i,iatom,ichain,ires,iunit
real(kind=8) :: etot
integer :: nres2
nres2=2*nres
-
+#ifdef XDRFPDB
+ if(.not.allocated(molnum)) allocate(molnum(maxres))
+ molnum(:)=1
+ if(.not.allocated(vtot)) allocate(vtot(maxres*2)) !(maxres2)
+#else
if(.not.allocated(vtot)) allocate(vtot(nres2)) !(maxres2)
+#endif
write (iunit,'(3a,1pe15.5)') 'REMARK ',tytul,' ENERGY ',etot
!model write (iunit,'(a5,i6)') 'MODEL',1
+#ifndef XDRFPDB
if (nhfrag.gt.0) then
do j=1,nhfrag
iti=itype(hfrag(1,j),1)
enddo
endif
-
+#endif
if (nss.gt.0) then
do i=1,nss
if (dyn_ss) then
if (i.lt.nnt) then
if (iti.eq.ntyp1_molec(molnum(i)).and.(molnum(i+1).eq.5)) cycle
endif
- if (iti.eq.ntyp1) then
+ if (iti.eq.ntyp1_molec(molnum(i))) then
ichain=ichain+1
! ires=0
write (iunit,'(a)') 'TER'
ires=ires+1
iatom=iatom+1
ica(i)=iatom
- if (molnum(i).ne.5) then
+ if (molnum(i).eq.1) then
+
write (iunit,10) iatom,restyp(iti,molnum(i)),chainid(ichain),&
ires,(c(j,i),j=1,3),vtot(i)
+ elseif(molnum(i).eq.2) then
+ if (istype(i).eq.0) istype(i)=1
+ write (iunit,40) iatom,sugartyp(istype(i)),restyp(iti,2), &
+ chainid(ichain),ires,(c(j,i),j=1,3),vtot(i)
else
write (iunit,60) iatom,restyp(iti,molnum(i)),chainid(ichain),&
ires,(c(j,i),j=1,3),vtot(i)
endif
if ((iti.ne.10).and.(molnum(i).ne.5)) then
iatom=iatom+1
- write (iunit,20) iatom,restyp(iti,1),chainid(ichain),&
+ if (molnum(i).eq.1) then
+ write (iunit,20) iatom,restyp(iti,1),chainid(ichain),&
ires,(c(j,nres+i),j=1,3),&
vtot(i+nres)
+ else if (molnum(i).eq.2) then
+ if (istype(i).eq.0) istype(i)=1
+ write (iunit,50) iatom,sugartyp(istype(i)),restyp(iti,2), &
+ chainid(ichain),ires,(c(j,nres+i),j=1,3),vtot(i+nres)
+ endif
+
endif
endif
enddo
10 FORMAT ('ATOM',I7,' CA ',A3,1X,A1,I4,4X,3F8.3,f15.3)
20 FORMAT ('ATOM',I7,' CB ',A3,1X,A1,I4,4X,3F8.3,f15.3)
+ 40 FORMAT ("ATOM",I7," C5' ",1X,2A1,1X,A1,I4,4X,3F8.3,f15.3)
+ 50 FORMAT ("ATOM",I7," C1' ",1X,2A1,1X,A1,I4,4X,3F8.3,f15.3)
+
30 FORMAT ('CONECT',8I5)
60 FORMAT ('HETATM',I5,' CA ',A3,1X,A1,I4,4X,3F8.3,f15.3)
return
end subroutine pdbout
+#ifndef XDRFPDB
!-----------------------------------------------------------------------------
subroutine MOL2out(etot,tytul)
! Prints the Cartesian coordinates of the alpha-carbons in the Tripos mol2
! format.
use geometry_data, only: c
use energy_data
- ! use control
+! use control
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.CHAIN'
use geometry_data
use energy_data, only: itype
- ! use control
+! use control
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.IOUNITS'
#endif
use geometry_data
use energy_data
- ! use control
+! use control
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.IOUNITS'
#endif
use geometry_data, only: c
- ! use geometry
+! use geometry
use energy_data
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
nextp=.true.
return
end function nextp
+#endif
+!-----------------------------------------------------------------------------
+! rescode.f
+!-----------------------------------------------------------------------------
+ integer function rescode(iseq,nam,itype,molecule)
+
+! use io_base, only: ucase
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+! include 'COMMON.NAMES'
+! include 'COMMON.IOUNITS'
+ character(len=3) :: nam !,ucase
+ integer :: iseq,itype,i
+ integer :: molecule
+ print *,molecule,nam
+ if (molecule.eq.1) then
+ if (itype.eq.0) then
+
+ do i=-ntyp1_molec(molecule),ntyp1_molec(molecule)
+ if (ucase(nam).eq.restyp(i,molecule)) then
+ rescode=i
+ return
+ endif
+ enddo
+
+ else
+
+ do i=-ntyp1_molec(molecule),ntyp1_molec(molecule)
+ if (nam(1:1).eq.onelet(i)) then
+ rescode=i
+ return
+ endif
+ enddo
+
+ endif
+ else if (molecule.eq.2) then
+ do i=1,ntyp1_molec(molecule)
+ print *,nam(1:1),restyp(i,molecule)(1:1)
+ if (nam(2:2).eq.restyp(i,molecule)(1:1)) then
+ rescode=i
+ return
+ endif
+ enddo
+ else if (molecule.eq.3) then
+ write(iout,*) "SUGAR not yet implemented"
+ stop
+ else if (molecule.eq.4) then
+ write(iout,*) "Explicit LIPID not yet implemented"
+ stop
+ else if (molecule.eq.5) then
+ do i=1,ntyp1_molec(molecule)
+ print *,i,restyp(i,molecule)(1:2)
+ if (ucase(nam(1:2)).eq.restyp(i,molecule)(1:2)) then
+ rescode=i
+ return
+ endif
+ enddo
+ else
+ write(iout,*) "molecule not defined"
+ endif
+ write (iout,10) iseq,nam
+ stop
+ 10 format ('**** Error - residue',i4,' has an unresolved name ',a3)
+ end function rescode
+ integer function sugarcode(sugar,ires)
+ character sugar
+ integer ires
+ if (sugar.eq.'D') then
+ sugarcode=1
+ else if (sugar.eq.' ') then
+ sugarcode=2
+ else
+ write (iout,*) 'UNKNOWN sugar type for residue',ires,' ',sugar
+ stop
+ endif
+ return
+ end function sugarcode
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
end module io_base
projects / unres4.git / blobdiff