+++ /dev/null
- subroutine readpdb
-C Read the PDB file and convert the peptide geometry into virtual-chain
-C geometry.
- implicit real*8 (a-h,o-z)
- 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.DISTFIT'
- include 'COMMON.SETUP'
- character*3 seq,atom,res
- character*80 card
- dimension sccor(3,20)
- double precision e1(3),e2(3),e3(3)
- logical fail
- integer rescode
- ibeg=1
- lsecondary=.false.
- nhfrag=0
- nbfrag=0
- do i=1,10000
- read (ipdbin,'(a80)',end=10) card
- if (card(:5).eq.'HELIX') then
- nhfrag=nhfrag+1
- lsecondary=.true.
- read(card(22:25),*) hfrag(1,nhfrag)
- read(card(34:37),*) hfrag(2,nhfrag)
- endif
- if (card(:5).eq.'SHEET') then
- nbfrag=nbfrag+1
- lsecondary=.true.
- read(card(24:26),*) bfrag(1,nbfrag)
- read(card(35:37),*) bfrag(2,nbfrag)
-crc----------------------------------------
-crc to be corrected !!!
- bfrag(3,nbfrag)=bfrag(1,nbfrag)
- bfrag(4,nbfrag)=bfrag(2,nbfrag)
-crc----------------------------------------
- endif
- if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
-C Fish out the ATOM cards.
- if (index(card(1:4),'ATOM').gt.0) then
- read (card(14:16),'(a3)') atom
- if (atom.eq.'CA' .or. atom.eq.'CH3') then
-C Calculate the CM of the preceding residue.
- if (ibeg.eq.0) then
- if (unres_pdb) then
- do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
- enddo
- else
- call sccenter(ires,iii,sccor)
- endif
- endif
-C Start new residue.
- read (card(24:26),*) ires
- read (card(18:20),'(a3)') res
- if (ibeg.eq.1) then
- ishift=ires-1
- if (res.ne.'GLY' .and. res.ne. 'ACE') then
- ishift=ishift-1
- itype(1)=21
- endif
- ibeg=0
- endif
- ires=ires-ishift
- if (res.eq.'ACE') then
- ity=10
- else
- itype(ires)=rescode(ires,res,0)
- endif
- read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-c if(me.eq.king.or..not.out1file)
-c & write (iout,'(2i3,2x,a,3f8.3)')
-c & ires,itype(ires),res,(c(j,ires),j=1,3)
- iii=1
- do j=1,3
- sccor(j,iii)=c(j,ires)
- enddo
- else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
- & atom.ne.'N ' .and. atom.ne.'C ') then
- 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
-C Calculate the CM of the last side chain.
- if (unres_pdb) then
- do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
- enddo
- else
- call sccenter(ires,iii,sccor)
- endif
- nres=ires
- nsup=nres
- nstart_sup=1
- if (itype(nres).ne.10) then
- nres=nres+1
- itype(nres)=21
- if (unres_pdb) then
-C 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)-3.8d0*e2(j)
- enddo
- else
- do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
- 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).eq.21) then
- nsup=nsup-1
- nstart_sup=2
- if (unres_pdb) then
-C 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)-3.8d0*e2(j)
- enddo
- else
- do j=1,3
- dcj=c(j,4)-c(j,3)
- c(j,1)=c(j,2)-dcj
- c(j,nres+1)=c(j,1)
- enddo
- endif
- endif
-C Calculate internal coordinates.
- if(me.eq.king.or..not.out1file)then
- write (iout,'(a)')
- & "Backbone and SC coordinates as read from the PDB"
- do ires=1,nres
- write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
- & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
- & (c(j,nres+ires),j=1,3)
- enddo
- endif
- call int_from_cart(.true.,.false.)
- 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
-c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
-c & vbld_inv(i+nres)
- enddo
-c call chainbuild
-C Copy the coordinates to reference coordinates
- do i=1,2*nres
- do j=1,3
- cref(j,i)=c(j,i)
- enddo
- enddo
-
-
- do j=1,nbfrag
- do i=1,4
- bfrag(i,j)=bfrag(i,j)-ishift
- enddo
- enddo
-
- do j=1,nhfrag
- do i=1,2
- hfrag(i,j)=hfrag(i,j)-ishift
- enddo
- enddo
-
- return
- end
-c---------------------------------------------------------------------------
- subroutine int_from_cart(lside,lprn)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
-c include "mpif.h"
- 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.SETUP'
- character*3 seq,atom,res
- character*80 card
- dimension sccor(3,20)
- integer rescode
- logical lside,lprn
- if(me.eq.king.or..not.out1file)then
- if (lprn) then
- write (iout,'(/a)')
- & 'Internal coordinates calculated from crystal structure.'
- if (lside) then
- write (iout,'(8a)') ' Res ',' dvb',' Theta',
- & ' Gamma',' Dsc_id',' Dsc',' Alpha',
- & ' Beta '
- else
- write (iout,'(4a)') ' Res ',' dvb',' Theta',
- & ' Gamma'
- endif
- endif
- endif
- do i=1,nres-1
- iti=itype(i)
- if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
- write (iout,'(a,i4)') 'Bad Cartesians for residue',i
-ctest stop
- endif
- vbld(i+1)=dist(i,i+1)
- vbld_inv(i+1)=1.0d0/vbld(i+1)
- if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
- if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
- enddo
-c if (unres_pdb) then
-c if (itype(1).eq.21) then
-c theta(3)=90.0d0*deg2rad
-c phi(4)=180.0d0*deg2rad
-c vbld(2)=3.8d0
-c vbld_inv(2)=1.0d0/vbld(2)
-c endif
-c if (itype(nres).eq.21) then
-c theta(nres)=90.0d0*deg2rad
-c phi(nres)=180.0d0*deg2rad
-c vbld(nres)=3.8d0
-c vbld_inv(nres)=1.0d0/vbld(2)
-c endif
-c endif
- if (lside) then
- do i=2,nres-1
- do j=1,3
- c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
- & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
- enddo
- iti=itype(i)
- di=dist(i,nres+i)
-C 9/29/12 Adam: Correction for zero SC-SC bond length
- if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
- & di=dsc(itype(i))
- vbld(i+nres)=di
- if (itype(i).ne.10) then
- vbld_inv(i+nres)=1.0d0/di
- else
- vbld_inv(i+nres)=0.0d0
- endif
- if (iti.ne.10) then
- alph(i)=alpha(nres+i,i,maxres2)
- omeg(i)=beta(nres+i,i,maxres2,i+1)
- endif
- if(me.eq.king.or..not.out1file)then
- if (lprn)
- & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
- & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
- & rad2deg*alph(i),rad2deg*omeg(i)
- endif
- enddo
- else if (lprn) then
- do i=2,nres
- iti=itype(i)
- if(me.eq.king.or..not.out1file)
- & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
- & rad2deg*theta(i),rad2deg*phi(i)
- enddo
- endif
- return
- end
-c-------------------------------------------------------------------------------
- subroutine sc_loc_geom(lprn)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
-c include "mpif.h"
- 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.SETUP'
- double precision x_prime(3),y_prime(3),z_prime(3)
- logical lprn
- do i=1,nres-1
- do j=1,3
- dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
- enddo
- enddo
- do i=2,nres-1
- if (itype(i).ne.10) then
- do j=1,3
- dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
- enddo
- else
- do j=1,3
- dc_norm(j,i+nres)=0.0d0
- enddo
- endif
- enddo
- do i=2,nres-1
- costtab(i+1) =dcos(theta(i+1))
- sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
- cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
- sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
- cosfac2=0.5d0/(1.0d0+costtab(i+1))
- cosfac=dsqrt(cosfac2)
- sinfac2=0.5d0/(1.0d0-costtab(i+1))
- sinfac=dsqrt(sinfac2)
- it=itype(i)
- if (it.ne.10) then
-c
-C Compute the axes of tghe local cartesian coordinates system; store in
-c x_prime, y_prime and z_prime
-c
- do j=1,3
- x_prime(j) = 0.00
- y_prime(j) = 0.00
- z_prime(j) = 0.00
- enddo
- do j = 1,3
- x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
- y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
- enddo
- call vecpr(x_prime,y_prime,z_prime)
-c
-C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
-C to local coordinate system. Store in xx, yy, zz.
-c
- xx=0.0d0
- yy=0.0d0
- zz=0.0d0
- do j = 1,3
- xx = xx + x_prime(j)*dc_norm(j,i+nres)
- yy = yy + y_prime(j)*dc_norm(j,i+nres)
- zz = zz + z_prime(j)*dc_norm(j,i+nres)
- enddo
-
- xxref(i)=xx
- yyref(i)=yy
- zzref(i)=zz
- else
- xxref(i)=0.0d0
- yyref(i)=0.0d0
- zzref(i)=0.0d0
- endif
- enddo
- if (lprn) then
- do i=2,nres
- iti=itype(i)
- if(me.eq.king.or..not.out1file)
- & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
- & yyref(i),zzref(i)
- enddo
- endif
- return
- end
-c---------------------------------------------------------------------------
- subroutine sccenter(ires,nscat,sccor)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CHAIN'
- dimension sccor(3,20)
- do j=1,3
- sccmj=0.0D0
- do i=1,nscat
- sccmj=sccmj+sccor(j,i)
- enddo
- dc(j,ires)=sccmj/nscat
- enddo
- return
- end
-c---------------------------------------------------------------------------
- subroutine bond_regular
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.VAR'
- include 'COMMON.LOCAL'
- include 'COMMON.CALC'
- include 'COMMON.INTERACT'
- include 'COMMON.CHAIN'
- do i=1,nres-1
- vbld(i+1)=vbl
- vbld_inv(i+1)=1.0d0/vbld(i+1)
- vbld(i+1+nres)=dsc(itype(i+1))
- vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
-c print *,vbld(i+1),vbld(i+1+nres)
- enddo
- return
- end
projects / unres.git / blobdiff