double precision app_(2,2),bpp_(2,2),rpp_(2,2)
integer ncont,icont(2,maxcont)
double precision econt(maxcont)
+ integer xshift,yshift,zshift
*
* Load the constants of peptide bond - peptide bond interactions.
* Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
xmedi=xi+0.5*dxi
ymedi=yi+0.5*dyi
zmedi=zi+0.5*dzi
+c write (iout,*) "i",xmedi,ymedi,zmedi
xmedi=mod(xmedi,boxxsize)
if (xmedi.lt.0) xmedi=xmedi+boxxsize
ymedi=mod(ymedi,boxysize)
if (ymedi.lt.0) ymedi=ymedi+boxysize
zmedi=mod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
+c write (iout,*) "i",xmedi,ymedi,zmedi
do 4 j=i+2,nct-1
if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) goto 4
ind=ind+1
xj=c(1,j)+0.5*dxj
yj=c(2,j)+0.5*dyj
zj=c(3,j)+0.5*dzj
+c write (iout,*) "j",xj,yj,zj
xj=mod(xj,boxxsize)
if (xj.lt.0) xj=xj+boxxsize
yj=mod(yj,boxysize)
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
- dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- write (iout,*) "i",i,xi,yi,zi," j",j,xj,yj,xj,"dist",
- & dsqrt(dist_init)
+c write (iout,*) "j",xj,yj,zj
+ dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+c write (iout,*) "dist",dsqrt(dist_init)
xj_safe=xj
yj_safe=yj
zj_safe=zj
xj=xj_safe+xshift*boxxsize
yj=yj_safe+yshift*boxysize
zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+c write (iout,*) "shift",xshift,yshift,zshift," dist_temp",
+c & dist_temp," dist_init",dist_init
if(dist_temp.lt.dist_init) then
dist_init=dist_temp
xj_temp=xj
endif
ees=ees+eesij
evdw=evdw+evdwij*sss
- write (iout,*) "i"," j",j," rij",dsqrt(rij)," eesij",eesij
+c write (iout,*) "i"," j",j," rij",dsqrt(rij)," eesij",eesij
4 continue
1 continue
if (lprint) then
+++ /dev/null
- subroutine map
- implicit none
- include 'DIMENSIONS'
- include 'COMMON.MAP'
- include 'COMMON.VAR'
- include 'COMMON.GEO'
- include 'COMMON.DERIV'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.CONTROL'
- include 'COMMON.TORCNSTR'
- double precision energia(0:n_ene)
- character*5 angid(4) /'PHI','THETA','ALPHA','OMEGA'/
- double precision ang_list(10)
- double precision g(maxvar),x(maxvar),gnorm,etot
- integer i,ii,iii,j,k,nf,nfun,iretcode,nmax,ntot
- integer uiparm(1)
- double precision urparm(1),fdum
- external fdum
- integer nn(10)
- write (iout,'(a,i3,a)')'Energy map constructed in the following ',
- & nmap,' groups of variables:'
- do i=1,nmap
- write (iout,'(2a,i3,a,i3)') angid(kang(i)),' of residues ',
- & res1(i),' to ',res2(i)
- enddo
- nmax=nstep(1)
- do i=2,nmap
- if (nmax.lt.nstep(i)) nmax=nstep(i)
- enddo
- ntot=nmax**nmap
- iii=0
- write (istat,'(1h#,a14,29a15)') (" ",k=1,nmap),
- & (ename(print_order(k)),k=1,nprint_ene),"ETOT","GNORM"
- do i=0,ntot-1
- ii=i
- do j=1,nmap
- nn(j)=mod(ii,nmax)+1
- ii=ii/nmax
- enddo
- do j=1,nmap
- if (nn(j).gt.nstep(j)) goto 10
- enddo
- iii=iii+1
-Cd write (iout,*) i,iii,(nn(j),j=1,nmap)
- do j=1,nmap
- ang_list(j)=ang_from(j)
- & +(nn(j)-1)*(ang_to(j)-ang_from(j))/nstep(j)
- do k=res1(j),res2(j)
- goto (1,2,3,4), kang(j)
- 1 phi(k)=deg2rad*ang_list(j)
- if (minim) phi0(k-res1(j)+1)=deg2rad*ang_list(j)
- goto 5
- 2 theta(k)=deg2rad*ang_list(j)
- goto 5
- 3 alph(k)=deg2rad*ang_list(j)
- goto 5
- 4 omeg(k)=deg2rad*ang_list(j)
- 5 continue
- enddo ! k
- enddo ! j
- call chainbuild
- if (minim) then
- call geom_to_var(nvar,x)
- call minimize(etot,x,iretcode,nfun)
- print *,'SUMSL return code is',iretcode,' eval ',nfun
-c call intout
- else
- call zerograd
- call geom_to_var(nvar,x)
- endif
- call etotal(energia(0))
- etot = energia(0)
- nf=1
- nfl=3
- call gradient(nvar,x,nf,g,uiparm,urparm,fdum)
- gnorm=0.0d0
- do k=1,nvar
- gnorm=gnorm+g(k)**2
- enddo
- etot=energia(0)
-
- gnorm=dsqrt(gnorm)
-c write (iout,'(6(1pe15.5))') (ang_list(k),k=1,nmap),etot,gnorm
- write (istat,'(30e15.5)') (ang_list(k),k=1,nmap),
- & (energia(print_order(ii)),ii=1,nprint_ene),etot,gnorm
-c write (iout,*) 'POINT',I,' ANGLES:',(ang_list(k),k=1,nmap)
-c call intout
-c call enerprint(energia)
- 10 continue
- enddo ! i
- return
- end
+++ /dev/null
- subroutine readpdb
-C Read the PDB file and convert the peptide geometry into virtual-chain
-C geometry.
- implicit none
- include 'DIMENSIONS'
- include 'DIMENSIONS.ZSCOPT'
- include 'COMMON.CONTROL'
- include 'COMMON.LOCAL'
- include 'COMMON.VAR'
- include 'COMMON.CHAIN'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.GEO'
- include 'COMMON.NAMES'
- include 'COMMON.SBRIDGE'
- character*3 seq,atom,res
- character*80 card
- double precision sccor(3,50)
- integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old
- double precision dcj
- integer rescode,kkk,lll,icha,cou,kupa,iprzes
- ibeg=1
- ishift1=0
- do
- read (ipdbin,'(a80)',end=10) card
- if (card(:3).eq.'END') then
- goto 10
- else if (card(:3).eq.'TER') then
-C End current chain
-c ires_old=ires+1
- ires_old=ires+2
- itype(ires_old-1)=ntyp1
- itype(ires_old)=ntyp1
- ibeg=2
-c write (iout,*) "Chain ended",ires,ishift,ires_old
- call sccenter(ires,iii,sccor)
- endif
-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
- call sccenter(ires,iii,sccor)
- endif
-C Start new residue.
-c write (iout,'(a80)') card
- read (card(23:26),*) 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)=ntyp1
- endif
-c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
- ibeg=0
- else if (ibeg.eq.2) then
-c Start a new chain
- ishift=-ires_old+ires-1
-c write (iout,*) "New chain started",ires,ishift
- ibeg=0
- endif
- ires=ires-ishift
-c write (2,*) "ires",ires," ishift",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)
- read(card(61:66),*) bfac(ires)
- write (iout,'(2i3,2x,a,3f8.3,5x,f8.3)')
- & ires,itype(ires),res,(c(j,ires),j=1,3),bfac(ires)
- 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(1:1).ne.'Q' .and. atom(1:2).ne.'1H' .and.
- & atom(1:2).ne.'2H' .and. atom(1:2).ne.'3H' .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 write (iout,'(a,i5)') ' Nres: ',ires
-C Calculate dummy residue coordinates inside the "chain" of a multichain
-C system
- nres=ires
- do i=2,nres-1
-c write (iout,*) i,itype(i)
-
- if (itype(i).eq.ntyp1) then
- if (itype(i+1).eq.ntyp1) then
-C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
-C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
-C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
-C if (unres_pdb) then
-C 2/15/2013 by Adam: corrected insertion of the last dummy residue
-C call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
-C if (fail) then
-C e2(1)=0.0d0
-C e2(2)=1.0d0
-C e2(3)=0.0d0
-C endif !fail
-C do j=1,3
-C c(j,i)=c(j,i-1)-1.9d0*e2(j)
-C enddo
-C else !unres_pdb
- do j=1,3
- dcj=(c(j,i-2)-c(j,i-3))/2.0
- c(j,i)=c(j,i-1)+dcj
- c(j,nres+i)=c(j,i)
- enddo
-C endif !unres_pdb
- else !itype(i+1).eq.ntyp1
-C if (unres_pdb) then
-C 2/15/2013 by Adam: corrected insertion of the first dummy residue
-C call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
-C if (fail) then
-C e2(1)=0.0d0
-C e2(2)=1.0d0
-C e2(3)=0.0d0
-C endif
-C do j=1,3
-C c(j,i)=c(j,i+1)-1.9d0*e2(j)
-C enddo
-C else !unres_pdb
- do j=1,3
- dcj=(c(j,i+3)-c(j,i+2))/2.0
- c(j,i)=c(j,i+1)-dcj
- c(j,nres+i)=c(j,i)
- enddo
-C endif !unres_pdb
- endif !itype(i+1).eq.ntyp1
- endif !itype.eq.ntyp1
- enddo
-C Calculate the CM of the last side chain.
- call sccenter(ires,iii,sccor)
- nsup=nres
- nstart_sup=1
- if (itype(nres).ne.10) then
- nres=nres+1
- itype(nres)=ntyp1
- do j=1,3
- dcj=(c(j,nres-2)-c(j,nres-3))/2.0
- c(j,nres)=c(j,nres-1)+dcj
- c(j,2*nres)=c(j,nres)
- enddo
- 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.ntyp1) then
- nsup=nsup-1
- nstart_sup=2
- 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
-C Calculate internal coordinates.
- 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
- call int_from_cart(.true.,.false.)
- write (iout,*) "After int_from_cart"
- call flush(iout)
- 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,nres
- do j=1,3
- cref(j,i)=c(j,i)
- cref(j,i+nres)=c(j,i+nres)
- enddo
- enddo
- 100 format (//' alpha-carbon coordinates ',
- & ' centroid coordinates'/
- 1 ' ', 6X,'X',11X,'Y',11X,'Z',
- & 10X,'X',11X,'Y',11X,'Z')
- 110 format (a,'(',i3,')',6f12.5)
-
- ishift_pdb=ishift
- return
- end
-c---------------------------------------------------------------------------
- subroutine int_from_cart(lside,lprn)
- implicit none
- include 'DIMENSIONS'
- include 'DIMENSIONS.ZSCOPT'
- include 'COMMON.LOCAL'
- include 'COMMON.VAR'
- include 'COMMON.CHAIN'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.GEO'
- include 'COMMON.NAMES'
- character*3 seq,atom,res
- character*80 card
- double precision sccor(3,50)
- integer rescode
- double precision dist,alpha,beta,di
- integer i,j,iti
- logical lside,lprn
- if (lprn) then
- write (iout,'(/a)')
- & 'Internal coordinates calculated from crystal structure.'
- if (lside) then
- write (iout,'(8a)') ' Res ',' dvb',' Theta',
- & ' Phi',' Dsc_id',' Dsc',' Alpha',
- & ' Omega'
- else
- write (iout,'(4a)') ' Res ',' dvb',' Theta',
- & ' Phi'
- endif
- endif
- do i=2,nres
- iti=itype(i)
-c write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
- if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and.
- & (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
- write (iout,'(a,i4)') 'Bad Cartesians for residue',i
- stop
- endif
- 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
- if (itype(1).eq.ntyp1) then
- do j=1,3
- c(j,1)=c(j,2)+(c(j,3)-c(j,4))
- enddo
- endif
- if (itype(nres).eq.ntyp1) then
- do j=1,3
- c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
- enddo
- endif
- if (lside) then
- do i=2,nres-1
- do j=1,3
- c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
- enddo
- iti=itype(i)
- di=dist(i,nres+i)
- if (iti.ne.10) then
- alph(i)=alpha(nres+i,i,maxres2)
- omeg(i)=beta(nres+i,i,maxres2,i+1)
- endif
- if (lprn)
- & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
- & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,
- & rad2deg*alph(i),rad2deg*omeg(i)
- enddo
- else if (lprn) then
- do i=2,nres
- iti=itype(i)
- 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 sccenter(ires,nscat,sccor)
- implicit none
- include 'DIMENSIONS'
- include 'COMMON.CHAIN'
- integer ires,nscat,i,j
- double precision sccor(3,50),sccmj
- 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
projects / unres.git / commitdiff