+++ /dev/null
- program generator
- implicit none
- integer proba, conf, cm1, cm2, accept, nd
- integer krok, i, n, j, g, ii1, ilosc, ijl
- integer nnn, seed, proba1, proba2, proba3, proba0x,proba0y,proba0z
- integer ilosc_atomow1, ilosc_atomow2, korekta1, korekta2
- integer ile_reszt_mol1, ile_reszt_mol2, ir, peptide,numerr2(90000)
- integer numera1(90000),numerr1(90000),numera2(90000)
- integer glys1, glys2, glye1, glye2, ilee
- real*8 rand, r, boxx, boxy, boxz, dist2acm, dist1acm, b(4), t(3)
- real*8 minx1, miny1, minz1, maxx1, maxy1, maxz1
- real*8 minx2, miny2, minz2, maxx2, maxy2, maxz2
- real*8 distx1, disty1, distz1, distx2, disty2, distz2
- real*8 xcm1, ycm1, zcm1, xcm2, ycm2, zcm2
- real*8 dist1cm, dist1cmt, dist2cm, dist2cmt
- real*8 cm2xr, cm2yr, cm2zr,x2r(90000),y2r(90000),z2r(90000),dist12
- real*8 angle, c, s, x2new, y2new, z2new
- character*60 plik1, plik2, plik3, plik4
- character*54 linia
- real*8 x1(90000),y1(90000),z1(90000),x2(90000),y2(90000),z2(90000)
- real*8 dd, wymiar, cmxx(900), cmyy(900), cmzz(900),xt2(90000,3)
- real*8 xf(90000,3)
- character*1 chain
- character*3 r1s, r2s, r1e, r2e
- character*5 atoma1(90000), atoma2(90000)
- character*6 nazwaa1(90000), nazwar1(90000)
- character*6 nazwaa2(90000), nazwar2(90000)
- integer time_a(3)
-
- korekta1 = 1
- korekta2 = 1
-
-c write(*,*)"Sposob uruchamiania:"
-c write(*,*)"nazwa_programu nazwa_pliku_inp_pdb1
-c & nazwa_pliku_inp_pdb2 nazwa_pliku_out"
-c write(*,*)""
-
- nnn = iargc()
- if (nnn.lt.3) then
- write(*,*)"program input_pdb1 input_pdb2
- & [0-1] 0 for protein, 1 for peptide"
- stop
- endif
-
- call getarg(1,plik1)
- call getarg(2,plik2)
- call getarg(3,plik3)
- open(1,file=plik1,status="old")
- open(2,file=plik2,status="old")
- open(4,file='temp1')
- open(5,file='temp2')
- write(*,*) "All files read"
-
- read(plik3(1:1),'(i1)') peptide
-
- if (peptide.ne.0.and.peptide.ne.1) then
- write(*,*) "Third parameter must be 0 or 1,
- & where 0 is for a protein-protein docking,
- & and 1 is for protein-peptide docking."
- STOP
- endif
-
- write(*,*) "Option", peptide, "selected
- & (0 for protein, 1 for peptide)"
-
-
-c MOLEKULA 1
- do while (.true.)
- read(1,'(a54)',end=22) linia
- if (linia(1:4).eq.'ATOM'.and.linia(17:17).lt.'B') then
- write(4,'(a54)') linia
- endif
- if (linia(1:3).eq.'TER') then
-c write(2,'(a54)') linia
- goto 22
- endif
- enddo
-
-22 continue
- close(4)
- write(*,*) "Molecule 1 read"
-
-
-c MOLEKULA 2
- do while (.true.)
- read(2,'(a54)',end=23) linia
- if (linia(1:4).eq.'ATOM'.and.linia(17:17).lt.'B') then
- write(5,'(a54)') linia
- endif
- if (linia(1:3).eq.'TER') then
-c write(2,'(a54)') linia
- goto 23
- endif
- enddo
-23 continue
- close(5)
- write(*,*) "Molecule 2 read"
-
- open(4,file='temp1')
- open(5,file='temp2')
-
- minx1=999.99
- miny1=999.99
- minz1=999.99
-
- maxx1=-999.99
- maxy1=-999.99
- maxz1=-999.99
-
-
- minx2=999.99
- miny2=999.99
- minz2=999.99
-
- maxx2=-999.99
- maxy2=-999.99
- maxz2=-999.99
-
-
-
-c MOLEKULA 1
- i=1
- xcm1=0
- ycm1=0
- zcm1=0
- ile_reszt_mol1=0
-
- do while (.true.)
- read(4,800,end=111)
- & atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),chain,numerr1(i),
- & x1(i),y1(i),z1(i)
-
-
-c write(*,300) minx, maxx, miny, maxy, minz, maxz
-
- if (x1(i).lt.minx1) minx1=x1(i)
- if (y1(i).lt.miny1) miny1=y1(i)
- if (z1(i).lt.minz1) minz1=z1(i)
-
- if (x1(i).gt.maxx1) maxx1=x1(i)
- if (y1(i).gt.maxy1) maxy1=y1(i)
- if (z1(i).gt.maxz1) maxz1=z1(i)
-
-c write(*,300) minx, maxx, miny, maxy, minz, maxz
-
-c write(*,*) nazwaa1(i)
- if (nazwaa1(i).eq.' CA ') then
- xcm1 = xcm1 + x1(i)
- ycm1 = ycm1 + y1(i)
- zcm1 = zcm1 + z1(i)
- ile_reszt_mol1 = ile_reszt_mol1 +1
- endif
-
- if (atoma1(i).eq.'TER ') goto 111
- if (atoma1(i).eq.'END ') goto 111
- if (i.eq.1) write(3,'(a6)') "REMARK"
-c write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),
-c & numerr1(i),x1(i),y1(i),z1(i)
-
-c write(*,*) i, x(i),y(i),z(i)
-
- i=i+1
- enddo
-111 continue
-
- distx1=maxx1-minx1
- disty1=maxy1-miny1
- distz1=maxz1-minz1
- ilosc_atomow1 = i-1
- xcm1 = xcm1 / (ile_reszt_mol1*1.0)
- ycm1 = ycm1 / (ile_reszt_mol1*1.0)
- zcm1 = zcm1 / (ile_reszt_mol1*1.0)
-
- do i=1,ilosc_atomow1
- x1(i)=x1(i)-xcm1
- y1(i)=y1(i)-ycm1
- z1(i)=z1(i)-zcm1
- enddo
-
- xcm1=0
- ycm1=0
- zcm1=0
-
- do i=1,ilosc_atomow1
- if (nazwaa1(i).eq.' CA ') then
- xcm1 = xcm1 + x1(i)
- ycm1 = ycm1 + y1(i)
- zcm1 = zcm1 + z1(i)
- endif
- enddo
- xcm1 = xcm1 / (ile_reszt_mol1*1.0)
- ycm1 = ycm1 / (ile_reszt_mol1*1.0)
- zcm1 = zcm1 / (ile_reszt_mol1*1.0)
-
- dist1cm=999.9
- dist1acm=0.0
- do i=1,ilosc_atomow1
-c write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),
-c & numerr1(i),x1(i)-xcm1,y1(i)-ycm1,z1(i)-zcm1
-
- dist1cmt = dsqrt(((xcm1-x1(i))**2)+
- & ((ycm1-y1(i))**2)+
- & ((zcm1-z1(i))**2))
-
-c write(*,*) dist1cmt, dist1cm, i, cm1
- if (dist1cm.gt.dist1cmt) then
- dist1cm=dist1cmt
- cm1=i
- endif
-
- enddo
-
- do i=1,ilosc_atomow1
- do j=i,ilosc_atomow1
- dist1cmt = dsqrt(((x1(j)-x1(i))**2)+
- & ((y1(j)-y1(i))**2)+
- & ((z1(j)-z1(i))**2))
- if (dist1acm.lt.dist1cmt) then
- dist1acm=dist1cmt
- endif
- enddo
- enddo
-
-
-c write(3,303) "TER"
-c write(3,304) "ENDMDL"
-
- write(*,*) "Molecule 1 calculated"
-
-c MOLEKULA 2
- i=1
- xcm2=0
- ycm2=0
- zcm2=0
- ile_reszt_mol2=0
-
- do while (.true.)
- read(5,800,end=112)
- & atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),chain,numerr2(i),
- & x2(i),y2(i),z2(i)
-
-c write(*,300) minx, maxx, miny, maxy, minz, maxz
-
- if (x2(i).lt.minx2) minx2=x2(i)
- if (y2(i).lt.miny2) miny2=y2(i)
- if (z2(i).lt.minz2) minz2=z2(i)
-
- if (x2(i).gt.maxx2) maxx2=x2(i)
- if (y2(i).gt.maxy2) maxy2=y2(i)
- if (z2(i).gt.maxz2) maxz2=z2(i)
-
-c write(*,300) minx, maxx, miny, maxy, minz, maxz
-
-c write(*,*) nazwaa1(i)
- if (nazwaa2(i).eq.' CA ') then
- xcm2 = xcm2 + x2(i)
- ycm2 = ycm2 + y2(i)
- zcm2 = zcm2 + z2(i)
- ile_reszt_mol2 = ile_reszt_mol2 + 1
- endif
-
- if (atoma2(i).eq.'TER ') goto 111
- if (atoma2(i).eq.'END ') goto 111
-c if (i.eq.1) write(3,'(a6)') "REMARK"
-c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
-c & numerr2(i),x2(i),y2(i),z2(i)
-c write(*,*) i, x(i),y(i),z(i)
-
- i=i+1
- enddo
-112 continue
-
- distx2=maxx2-minx2
- disty2=maxy2-miny2
- distz2=maxz2-minz2
- ilosc_atomow2 = i-1
-
- xcm2 = xcm2 / (ile_reszt_mol2*1.0)
- ycm2 = ycm2 / (ile_reszt_mol2*1.0)
- zcm2 = zcm2 / (ile_reszt_mol2*1.0)
-
- do i=1,ilosc_atomow2
- x2(i)=x2(i)-xcm2
- y2(i)=y2(i)-ycm2
- z2(i)=z2(i)-zcm2
-c write(*,*) x2(i),y2(i),z2(i)
- xt2(i,1)=x2(i)
- xt2(i,2)=y2(i)
- xt2(i,3)=z2(i)
-c write(*,*) xt2(i,1), xt2(i,2), xt2(i,3)
- enddo
-
- xcm2=0
- ycm2=0
- zcm2=0
- do i=1,ilosc_atomow2
- if (nazwaa2(i).eq.' CA ') then
- xcm2 = xcm2 + x2(i)
- ycm2 = ycm2 + y2(i)
- zcm2 = zcm2 + z2(i)
- endif
- enddo
- xcm2 = xcm2 / (ile_reszt_mol2*1.0)
- ycm2 = ycm2 / (ile_reszt_mol2*1.0)
- zcm2 = zcm2 / (ile_reszt_mol2*1.0)
-
-
- dist2cm=999.9
- dist2acm=0.0
- do i=1,ilosc_atomow2
-c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
-c & numerr2(i),x2(i)-xcm2,y2(i)-ycm2,z2(i)-zcm2
-
- dist2cmt = dsqrt(((xcm2-x2(i))**2)+
- & ((ycm2-y2(i))**2)+
- & ((zcm2-z2(i))**2))
-
-c write(*,*) dist2cmt, dist2cm, i, cm2
- if (dist2cm.gt.dist2cmt) then
- dist2cm=dist2cmt
- cm2=i
- endif
-
- enddo
-
-
- do i=1,ilosc_atomow2
- do j=i,ilosc_atomow2
- dist2cmt = dsqrt(((x2(j)-x2(i))**2)+
- & ((y2(j)-y2(i))**2)+
- & ((z2(j)-z2(i))**2))
- if (dist2acm.lt.dist2cmt) then
- dist2acm=dist2cmt
- endif
- enddo
- enddo
-
-
-c write(3,303) "TER"
-
- glys1=0
- glys2=0
- glye1=0
- glye2=0
- r1s=nazwar1(1)
- r2s=nazwar2(1)
- r1e=nazwar1(ile_reszt_mol1)
- r2e=nazwar2(ile_reszt_mol2)
-
- if (r1s.eq."GLY") then
- glys1=1
- write(*,*) "Chain 1 is starting from Gly ", r1s, glys1
- endif
-
- if (r2s.eq."GLY") then
- glys2=1
- write(*,*) "Chain 2 is starting from Gly ", r2s, glys2
- endif
-
- if (r1e.eq."GLY") then
- glye1=1
- write(*,*) "Chain 1 is ending at Gly ", r1e, glye1
- endif
-
-
- if (r2e.eq."GLY") then
- glye2=1
- write(*,*) "Chain 2 is ending from Gly ", r2e, glye2
- endif
-
-
-c checking for Gly
- ilee=4
- if(glys1.eq.1) ilee=ilee-1
- if(glys2.eq.1) ilee=ilee-1
- if(glye1.eq.1) ilee=ilee-1
- if(glye2.eq.1) ilee=ilee-1
- write(*,*) "How many dummy atoms:", ilee
- write(*,*) ""
-
-
- write(*,*) "Molecule 2 calculated"
- write(*,*) "Number of atoms:", ilosc_atomow1, ilosc_atomow2
-
- write(*,*) "Min and max coordinates in the systems"
- write(*,300) minx1, maxx1, miny1, maxy1, minz1, maxz1
- write(*,300) minx2, maxx2, miny2, maxy2, minz2, maxz2
-
- write(*,*) "Distances in axes x, y, z"
- write(*,301) distx1, disty1, distz1
- write(*,301) distx2, disty2, distz2
-
- boxx = (distx1 + distx2)*1.5 + 20.0
- boxy = (disty1 + disty2)*1.5 + 20.0
- boxz = (distz1 + distz2)*1.5 + 20.0
-
-c write(*,*) "Boxsize [x, y, z]"
-c write(*,301) boxx, boxy, boxz
-
- write(*,*) "Maximum distances:"
- write(*,*) dist1acm, dist2acm
-
- write(*,*) "Boxsize (suggested)"
- write(*,*) (dist1acm+dist2acm)*1.2+20
- open(61,file='boxsize.txt')
- write(61,302) ((dist1acm+dist2acm)*1.2+20)
- close (61)
-
- write(*,*) "Center of masses:"
- write(*,301) xcm1, ycm1, zcm1
- write(*,301) xcm2, ycm2, zcm2
-
- write(*,*) "Center of masses atoms:"
- write(*,800) atoma1(cm1),numera1(cm1),nazwaa1(cm1),nazwar1(cm1),
- & " ",numerr1(cm1),x1(cm1),y1(cm1),z1(cm1)
- write(*,800) atoma2(cm2),numera2(cm2),nazwaa2(cm2),nazwar2(cm2),
- & " ",numerr2(cm2),x2(cm2),y2(cm2),z2(cm2)
-
-
- write(*,*) "Number of amino-acid residues in two proteins:"
- write(*,*) ile_reszt_mol1, ile_reszt_mol2
-
-
-c ---------------------------------------------------------------------
-c KONIEC WCZYTYWANIA
-c ---------------------------------------------------------------------
-
- korekta1 = numerr1(1)
- write(*,*) "Original number of the first residue in
- & the first protein:"
- write(*,*) numerr1(1)
-
- write(*,*) "Correction of the first residue in the first protein:"
- write(*,*) korekta1
-
-
-c wymiar=(distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2)
-c wymiar=wymiar/12.0
-c wymiar=10.0
-
-c write(*,*) "Minimum required distance between centers of mass:"
-c write(*,*) wymiar
-
- boxx = (7+distx1 + dist2acm)/2.0
- boxy = (7+disty1 + dist2acm)/2.0
- boxz = (7+distz1 + dist2acm)/2.0
- write(*,*) "Rotation space (+/-):", boxx, boxy, boxz
-
-
- do ii1=1,24
-
- proba = 1
- proba0x = 1
- proba0y = 1
- proba0z = 1
- proba1 = 1
- proba2 = 1
- proba3 = 1
- conf = 1
-
-
- if (ii1.lt.10) then
- write (plik3, "(A6,I1,a4)") "model0", ii1, ".pdb"
- else
- write (plik3, "(A5,I2,a4)") "model", ii1, ".pdb"
- endif
-
- write(*,*) "Conformation will be saved to file:", plik3
-
-c plik3a = plik3//ilosc
- open(3,file=plik3)
-
-
- do i=1,ilosc_atomow1
- write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),"A",
- & (numerr1(i)-korekta1+1),
- & x1(i),y1(i),z1(i)
- enddo
- write(3,303) "TER"
-c write(3,304) "ENDMDL"
-
- if (peptide.eq.1) then
- wymiar=((distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2))/4
- endif
-
- if (peptide.eq.0) then
- wymiar=((distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2))/7
- endif
-
- if (ii1.eq.1) then
- write(*,*) "Initial minimum distance between centers of mass:",
- & wymiar
- endif
-
-c ROTATIONS OF THE SECOND MOLECULE
- nd=4
- t(1)=0.0
- t(2)=0.0
- t(3)=0.0
- call ranorND(b,nd,ilosc_atomow2,ii1)
-c do i=1,4
-c write(*,*) b(i)
-c enddo
- call rot_trans(xt2,t,b,xf,ilosc_atomow2)
- do i=1,ilosc_atomow2
- x2(i)=xf(i,1)
- y2(i)=xf(i,2)
- z2(i)=xf(i,3)
- enddo
-c END OF ROTATIONS
-
-
- do while (.true.)
- if (conf.gt.1) goto 133
-
-#ifdef GFORTRAN
- seed = time()*proba
-#else
- call itime(time_a)
- seed = (60*time_a(2)+time_a(3))*proba
-#endif
- call srand(seed)
- r = rand(0)
-c write(*,*)rand(0),rand(0),rand(0)
-c write(*,*)rand(0),rand(0),rand(0)
-
- cm2xr = (rand(0)*2*boxx)-(boxx)
- cm2yr = (rand(0)*2*boxy)-(boxy)
- cm2zr = (rand(0)*2*boxz)-(boxz)
-c write(*,*) cm2xr, cm2yr, cm2zr
-c write(*,300)rand(0),rand(0),rand(0)
-
-c write(*,*) ABS(cm2xr+xcm1), (dist1acm+dist2acm+3)
-
-c if (ABS(cm2xr+xcm1).gt.((dist1acm+dist2acm+5)*0.8)) then
-c proba0x=proba0x+1
-c goto 200
-c endif
-
-c if (ABS(cm2yr+ycm1).gt.((dist1acm+dist2acm+5)*0.8)) then
-c proba0y=proba0y+1
-c goto 200
-c endif
-
-c if (ABS(cm2zr+zcm1).gt.((dist1acm+dist2acm+5)*0.8)) then
-c proba0z=proba0z+1
-c goto 200
-c endif
-
-
- do i=1,ilosc_atomow2
- x2r(i)=x2(i)-cm2xr
- y2r(i)=y2(i)-cm2yr
- z2r(i)=z2(i)-cm2zr
- enddo
-
-
-c SPRAWDZANIE CZY NIE JEST ZBYT PODOBNE DO JUZ WYLOSOWANEGO
- cmxx(ii1)=cm2xr
- cmyy(ii1)=cm2yr
- cmzz(ii1)=cm2zr
-
- if (ii1.gt.1) then
-
- do ir=1,ii1-1
- dd=sqrt((cm2xr-cmxx(ir))**2+(cm2yr-cmyy(ir))**2+
- & (cm2zr-cmzz(ir))**2)
-
-c write(*,*) "Center of mass is", dd, "A away from", ir
-c write(*,*) "Minimum distance required:", wymiar, "A"
-
-c write(*,*) ii1, ir, proba3, dd, wymiar
-
- if (dd.lt.wymiar) then
- proba3=proba3+1
- if (proba3.gt.1.and.peptide.eq.1) wymiar=wymiar*0.99992
- if (proba3.gt.1.and.peptide.eq.0) wymiar=wymiar*0.99992
-c write(*,*) proba3, wymiar
- goto 200
- endif
-
- enddo
- endif
-
-
-
-
-c SPRAWDZANIE ODLEGLOSCI
- accept=0
- do i=1,ilosc_atomow2
-c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
-c & numerr2(i),x2(i)-xcm2,y2(i)-ycm2,z2(i)-zcm2
-
- do j=1,ilosc_atomow1
- dist12 = sqrt(((x2r(i)-x1(j))**2)+
- & ((y2r(i)-y1(j))**2)+
- & ((z2r(i)-z1(j))**2))
-c write(*,*) dist12, cm2xr, cm2yr, cm2zr
- if (dist12.lt.2.5) then
- proba1=proba1+1
- goto 200
- endif
-
- if (dist12.le.3.5) accept=1
-c if (dist12.le.3.5) accept=1
-c if (dist12.gt.3.5) proba2=proba2+1
- enddo
- enddo
-
-c write(*,*) "No overlaps", proba
- if (accept.eq.0) goto 200
-c write(*,*) "No overlaps, contact", conf, proba
-c write(3,305) "MODEL", conf
-c conf = conf+1
-
-
-
- write(*,*) "Conformation", ii1, "Is accepted after",
- & proba0x+proba0y+proba0z,
- & proba1, proba2, proba3, proba, "attempts. ",
- & "Dist between CoM of previous=", wymiar
-
-c Dodatkowe info
- write(*,*)"Extr",ABS(cm2xr+xcm1), ABS(cm2yr+ycm1), ABS(cm2zr+zcm1)
-
-
- conf=conf+1
-c write (*,*)
-
-
-
-
-
- korekta2 = numerr2(1)-1
-c write(*,*) "Original number of the first residue in
-c & the second protein:"
-c write(*,*) numerr2(1)
-
-c write(*,*)"Correction of the first residue in the second protein:"
-c write(*,*) korekta2
- do i=1,ilosc_atomow2
- write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),"B",
- & (numerr2(i)+ile_reszt_mol1-korekta2),
- & x2r(i),y2r(i),z2r(i)
- enddo
- write(3,303) "TER"
-c write(3,304) "ENDMDL"
-c write(3,305) "MODEL", conf
- write(3,303) "END"
-
- 200 continue
- proba = proba + 1
- enddo
- 133 continue
-
- close (3)
-
-c call sleep(1)
-
-
- if (ii1.lt.10) then
- write (plik4, "(A9,I1,a4)") "template0", ii1, ".sco"
- else
- write (plik4, "(A8,I2,a4)") "template", ii1, ".sco"
- endif
-
- open (7,file=plik4)
-
-
- if (peptide.eq.1) then
- do ijl=1,(ile_reszt_mol1+ile_reszt_mol2+ilee)
- if (glys1.eq.0) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
- if (glys1.eq.1) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+1))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
- enddo
- endif
-
-
- if (peptide.eq.0) then
- do ijl=1,(ile_reszt_mol1+ile_reszt_mol2+ilee)
-c write(*,*) "ijl"
-c no Gly
- if (glys1.eq.0.and.glye1.eq.0.and.glys2.eq.0) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1+3).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+3))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
- if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+4))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-
-c chain 1 first Gly
- if (glys1.eq.1.and.glye1.eq.0.and.glys2.eq.0) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1+2).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
- if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-c chain 1 last Gly
- if (glys1.eq.0.and.glye1.eq.1.and.glys2.eq.0) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1+2).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
- if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-c chain 1 first Gly and chain 1 last Gly
- if (glys1.eq.1.and.glye1.eq.1.and.glys2.eq.0) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+1))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1+1).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
- if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-c chain 2 first Gly
- if (glys1.eq.0.and.glye1.eq.0.and.glys2.eq.1) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1+2).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
- if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-c chain 1 first Gly chain 2 first Gly
- if (glys1.eq.1.and.glye1.eq.0.and.glys2.eq.1) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+1))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1+1).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
- if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-c chain 1 last Gly chain 2 first Gly
- if (glys1.eq.0.and.glye1.eq.1.and.glys2.eq.1) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
-c if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
-c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1+1).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
- if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-c all Gly
- if (glys1.eq.1.and.glye1.eq.1.and.glys2.eq.1) then
- if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
- if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
- & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
-c if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
-c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- if (ijl.gt.(ile_reszt_mol1).and.
- & ijl.le.(ile_reszt_mol2+ile_reszt_mol1))
- & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
-c if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+1))
-c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
- endif
-
-
-
- enddo
- endif
-
-
- close (7)
-
-c koniec petli po ilosci struktur
- enddo
-
-c do i=1,20
-c write(*,*) i, cmxx(i), cmyy(i), cmzz(i)
-c dd=(cm2xr-cmxx(ir))**2+(cm2yr-cmyy(ir))**2+(cm2zr-cmyy(ir))**2
-c enddo
-
-c do i=1,20
-c do j=1,20
-c dd=sqrt((cmxx(i)-cmxx(j))**2+(cmyy(i)-cmyy(j))**2+
-c & (cmzz(i)-cmzz(j))**2)
-c write(*,*) i,j,dd
-c enddo
-c enddo
-
-
- 300 format(6f8.2)
- 301 format(3f8.2)
- 302 format(f8.2)
- 800 format(a4,2X,i5,1X,a4,1X,a3,1X,a1,i4,4X,3f8.3)
- 303 format(a3)
- 304 format(a6)
- 305 format(a5,1X,i8)
- end
-
-
-
-
- SUBROUTINE SRAND(ISEED)
-C
-C This subroutine sets the integer seed to be used with the
-C companion RAND function to the value of ISEED. A flag is
-C set to indicate that the sequence of pseudo-random numbers
-C for the specified seed should start from the beginning.
-C
- COMMON /SEED/JSEED,IFRST
-C
- JSEED = ISEED
- IFRST = 0
-C
- RETURN
- END
- REAL FUNCTION RAND()
-C
-C This function returns a pseudo-random number for each invocation.
-C It is a FORTRAN 77 adaptation of the "Integer Version 2" minimal
-C standard number generator whose Pascal code appears in the article:
-C
-C Park, Steven K. and Miller, Keith W., "Random Number Generators:
-C Good Ones are Hard to Find", Communications of the ACM,
-C October, 1988.
-C
- PARAMETER (MPLIER=16807,MODLUS=2147483647,MOBYMP=127773,
- + MOMDMP=2836)
-C
- COMMON /SEED/JSEED,IFRST
- INTEGER HVLUE, LVLUE, TESTV, NEXTN
- SAVE NEXTN
-C
- IF (IFRST .EQ. 0) THEN
- NEXTN = JSEED
- IFRST = 1
- ENDIF
-C
- HVLUE = NEXTN / MOBYMP
- LVLUE = MOD(NEXTN, MOBYMP)
- TESTV = MPLIER*LVLUE - MOMDMP*HVLUE
- IF (TESTV .GT. 0) THEN
- NEXTN = TESTV
- ELSE
- NEXTN = TESTV + MODLUS
- ENDIF
- RAND = REAL(NEXTN)/REAL(MODLUS)
-C
- RETURN
- END
- BLOCKDATA RANDBD
- COMMON /SEED/JSEED,IFRST
-C
- DATA JSEED,IFRST/123456789,0/
-C
- END
-
- Subroutine ranorND(b,nd,ilosc_atomow2,ii1)
- double precision b
-C generates a random vector on a unit sphere onC an ND-dimensional space.
-C algorithm 40 page 410.
-C the algorithm assumes that the formula for bz is valid, i.e
-C bz=(1.0-2.0*ransq),
-C and also that, ransq can be computed as as the sum of the independent random
-C numbers to the second power (expression 3).
- dimension ran(nd-1), b(nd)
- integer seed
-c write(*,*) "In Subroutine ranorND(b,nd), nd=", nd
-c write(*,*) "ilosc_atomow2=", ilosc_atomow2
-c do j=1,ilosc_atomow2
- ransq=2
- seed = time()*ii1
- call srand(seed)
- do while (ransq.ge.1)
-c write(*,*) ransq
- rsq=0.0
- do i=1,nd-1
- ran(i)=1.0-2.0*rand(0)
-c write(*,*) i, ran(i)
- rsq=ran(i)*ran(i)+rsq ! (3)
-c write(*,*) i, rsq
- enddo
- ransq=rsq
-c write(*,*) j, ransq
- enddo
- ranh=2.0*sqrt(1.0-ransq)
-c write(*,*) j, ranh, ransq
- do i=1,nd-1
- b(i)=ran(i)*ranh
-c write(*,*) ran(i), ranh
- enddo
- b(nd)=(1.0-2.0*ransq)
-c write(*,*) b(1,j), b(2,j), b(3,j), b(4,j)
-c enddo
- return
- end
-
- subroutine rot_trans(xt2,t,q,xf,ilosc_atomow2)
-C x coordinates, t translation vector, q quaternion
- double precision xt2(90000,3),xf(90000,3)
- double precision t(3),q(4)
- integer i
- write(*,*) "Rotation vector:", q(1), q(2), q(3), q(4)
- r11= q(1)*q(1)+q(2)*q(2)-q(3)*q(3)-q(4)*q(4)
- r22= q(1)*q(1)-q(2)*q(2)+q(3)*q(3)-q(4)*q(4)
- r33= q(1)*q(1)-q(2)*q(2)-q(3)*q(3)+q(4)*q(4)
- r12= 2*(q(2)*q(3)-q(1)*q(4))
- r21= 2*(q(2)*q(3)+q(1)*q(4))
- r13= 2*(q(2)*q(4)+q(1)*q(3))
- r31= 2*(q(2)*q(4)-q(1)*q(3))
- r23= 2*(q(3)*q(4)-q(1)*q(2))
- r32= 2*(q(3)*q(4)+q(1)*q(2))
-
-c write(*,*) r11, r22, r33, r12, r21, r13, r31, r23, r32
-
- do i=1,ilosc_atomow2
- xf(i,1)= r11*xt2(i,1)+r12*xt2(i,2)+r13*xt2(i,3) + t(1)
- xf(i,2)= r21*xt2(i,1)+r22*xt2(i,2)+r23*xt2(i,3) + t(2)
- xf(i,3)= r31*xt2(i,1)+r32*xt2(i,2)+r33*xt2(i,3) + t(3)
-c write(*,*) i, xt2(i,1), xt2(i,2), xt2(i,3)
-c write(*,*) i, xf(i,1), xf(i,2), xf(i,3)
- enddo
-
- return
- end
-