3 integer proba, conf, cm1, cm2, accept, nd
4 integer krok, i, n, j, g, ii1, ilosc, ijl
5 integer nnn, seed, proba1, proba2, proba3, proba0x,proba0y,proba0z
6 integer ilosc_atomow1, ilosc_atomow2, korekta1, korekta2
7 integer ile_reszt_mol1, ile_reszt_mol2, ir, peptide,numerr2(90000)
8 integer numera1(90000),numerr1(90000),numera2(90000)
9 integer glys1, glys2, glye1, glye2, ilee
10 integer no_models, seed1, seed11, seed12, seed13
12 real*8 r, boxx, boxy, boxz, dist2acm, dist1acm, b(4), t(3)
13 real*8 minx1, miny1, minz1, maxx1, maxy1, maxz1
14 real*8 minx2, miny2, minz2, maxx2, maxy2, maxz2
15 real*8 distx1, disty1, distz1, distx2, disty2, distz2
16 real*8 xcm1, ycm1, zcm1, xcm2, ycm2, zcm2
17 real*8 dist1cm, dist1cmt, dist2cm, dist2cmt
18 real*8 cm2xr, cm2yr, cm2zr,x2r(90000),y2r(90000),z2r(90000),dist12
19 real*8 angle, c, s, x2new, y2new, z2new
20 character*60 plik1, plik2, plik3, plik4, arg4, arg5
22 real*8 x1(90000),y1(90000),z1(90000),x2(90000),y2(90000),z2(90000)
23 real*8 dd, wymiar, cmxx(900), cmyy(900), cmzz(900),xt2(90000,3)
26 character*3 r1s, r2s, r1e, r2e
27 character*5 atoma1(90000), atoma2(90000)
28 character*6 nazwaa1(90000), nazwar1(90000)
29 character*6 nazwaa2(90000), nazwar2(90000)
34 c write(*,*)"Sposob uruchamiania:"
35 c write(*,*)"nazwa_programu nazwa_pliku_inp_pdb1
36 c & nazwa_pliku_inp_pdb2 nazwa_pliku_out"
41 write(*,*)"program input_pdb1 input_pdb2
42 & [0-1] number_of_models seed_number
43 & 0 for protein, 1 for peptide"
52 open(1,file=plik1,status="old")
53 open(2,file=plik2,status="old")
56 write(*,*) "All files read"
58 read(plik3(1:1),'(i1)') peptide
59 read(arg4,'(i2)') no_models
60 read(arg5,'(i19)') seed1
62 if (peptide.ne.0.and.peptide.ne.1) then
63 write(*,*) "Third parameter must be 0 or 1,
64 & where 0 is for a protein-protein docking,
65 & and 1 is for protein-peptide docking."
69 write(*,*) "Option", peptide, "selected
70 & (0 for protein, 1 for peptide)"
75 read(1,'(a54)',end=22) linia
76 if (linia(1:4).eq.'ATOM'.and.linia(17:17).lt.'B') then
77 write(4,'(a54)') linia
79 if (linia(1:3).eq.'TER') then
80 c write(2,'(a54)') linia
87 write(*,*) "Molecule 1 read"
92 read(2,'(a54)',end=23) linia
93 if (linia(1:4).eq.'ATOM'.and.linia(17:17).lt.'B') then
94 write(5,'(a54)') linia
96 if (linia(1:3).eq.'TER') then
97 c write(2,'(a54)') linia
103 write(*,*) "Molecule 2 read"
136 & atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),chain,numerr1(i),
140 c write(*,300) minx, maxx, miny, maxy, minz, maxz
142 if (x1(i).lt.minx1) minx1=x1(i)
143 if (y1(i).lt.miny1) miny1=y1(i)
144 if (z1(i).lt.minz1) minz1=z1(i)
146 if (x1(i).gt.maxx1) maxx1=x1(i)
147 if (y1(i).gt.maxy1) maxy1=y1(i)
148 if (z1(i).gt.maxz1) maxz1=z1(i)
150 c write(*,300) minx, maxx, miny, maxy, minz, maxz
152 c write(*,*) nazwaa1(i)
153 if (nazwaa1(i).eq.' CA ') then
157 ile_reszt_mol1 = ile_reszt_mol1 +1
160 if (atoma1(i).eq.'TER ') goto 111
161 if (atoma1(i).eq.'END ') goto 111
162 if (i.eq.1) write(3,'(a6)') "REMARK"
163 c write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),
164 c & numerr1(i),x1(i),y1(i),z1(i)
166 c write(*,*) i, x(i),y(i),z(i)
176 xcm1 = xcm1 / (ile_reszt_mol1*1.0)
177 ycm1 = ycm1 / (ile_reszt_mol1*1.0)
178 zcm1 = zcm1 / (ile_reszt_mol1*1.0)
191 if (nazwaa1(i).eq.' CA ') then
197 xcm1 = xcm1 / (ile_reszt_mol1*1.0)
198 ycm1 = ycm1 / (ile_reszt_mol1*1.0)
199 zcm1 = zcm1 / (ile_reszt_mol1*1.0)
204 c write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),
205 c & numerr1(i),x1(i)-xcm1,y1(i)-ycm1,z1(i)-zcm1
207 dist1cmt = dsqrt(((xcm1-x1(i))**2)+
211 c write(*,*) dist1cmt, dist1cm, i, cm1
212 if (dist1cm.gt.dist1cmt) then
221 dist1cmt = dsqrt(((x1(j)-x1(i))**2)+
222 & ((y1(j)-y1(i))**2)+
223 & ((z1(j)-z1(i))**2))
224 if (dist1acm.lt.dist1cmt) then
232 c write(3,304) "ENDMDL"
234 write(*,*) "Molecule 1 calculated"
245 & atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),chain,numerr2(i),
248 c write(*,300) minx, maxx, miny, maxy, minz, maxz
250 if (x2(i).lt.minx2) minx2=x2(i)
251 if (y2(i).lt.miny2) miny2=y2(i)
252 if (z2(i).lt.minz2) minz2=z2(i)
254 if (x2(i).gt.maxx2) maxx2=x2(i)
255 if (y2(i).gt.maxy2) maxy2=y2(i)
256 if (z2(i).gt.maxz2) maxz2=z2(i)
258 c write(*,300) minx, maxx, miny, maxy, minz, maxz
260 c write(*,*) nazwaa1(i)
261 if (nazwaa2(i).eq.' CA ') then
265 ile_reszt_mol2 = ile_reszt_mol2 + 1
268 if (atoma2(i).eq.'TER ') goto 111
269 if (atoma2(i).eq.'END ') goto 111
270 c if (i.eq.1) write(3,'(a6)') "REMARK"
271 c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
272 c & numerr2(i),x2(i),y2(i),z2(i)
273 c write(*,*) i, x(i),y(i),z(i)
284 xcm2 = xcm2 / (ile_reszt_mol2*1.0)
285 ycm2 = ycm2 / (ile_reszt_mol2*1.0)
286 zcm2 = zcm2 / (ile_reszt_mol2*1.0)
292 c write(*,*) x2(i),y2(i),z2(i)
296 c write(*,*) xt2(i,1), xt2(i,2), xt2(i,3)
303 if (nazwaa2(i).eq.' CA ') then
309 xcm2 = xcm2 / (ile_reszt_mol2*1.0)
310 ycm2 = ycm2 / (ile_reszt_mol2*1.0)
311 zcm2 = zcm2 / (ile_reszt_mol2*1.0)
317 c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
318 c & numerr2(i),x2(i)-xcm2,y2(i)-ycm2,z2(i)-zcm2
320 dist2cmt = dsqrt(((xcm2-x2(i))**2)+
324 c write(*,*) dist2cmt, dist2cm, i, cm2
325 if (dist2cm.gt.dist2cmt) then
335 dist2cmt = dsqrt(((x2(j)-x2(i))**2)+
336 & ((y2(j)-y2(i))**2)+
337 & ((z2(j)-z2(i))**2))
338 if (dist2acm.lt.dist2cmt) then
353 r1e=nazwar1(ile_reszt_mol1)
354 r2e=nazwar2(ile_reszt_mol2)
356 if (r1s.eq."GLY") then
358 write(*,*) "Chain 1 is starting from Gly ", r1s, glys1
361 if (r2s.eq."GLY") then
363 write(*,*) "Chain 2 is starting from Gly ", r2s, glys2
366 if (r1e.eq."GLY") then
368 write(*,*) "Chain 1 is ending at Gly ", r1e, glye1
372 if (r2e.eq."GLY") then
374 write(*,*) "Chain 2 is ending from Gly ", r2e, glye2
380 if(glys1.eq.1) ilee=ilee-1
381 if(glys2.eq.1) ilee=ilee-1
382 if(glye1.eq.1) ilee=ilee-1
383 if(glye2.eq.1) ilee=ilee-1
384 write(*,*) "How many dummy atoms:", ilee
388 write(*,*) "Molecule 2 calculated"
389 write(*,*) "Number of atoms:", ilosc_atomow1, ilosc_atomow2
391 write(*,*) "Min and max coordinates in the systems"
392 write(*,300) minx1, maxx1, miny1, maxy1, minz1, maxz1
393 write(*,300) minx2, maxx2, miny2, maxy2, minz2, maxz2
395 write(*,*) "Distances in axes x, y, z"
396 write(*,301) distx1, disty1, distz1
397 write(*,301) distx2, disty2, distz2
399 boxx = (distx1 + distx2)*1.5 + 20.0
400 boxy = (disty1 + disty2)*1.5 + 20.0
401 boxz = (distz1 + distz2)*1.5 + 20.0
403 c write(*,*) "Boxsize [x, y, z]"
404 c write(*,301) boxx, boxy, boxz
406 write(*,*) "Maximum distances:"
407 write(*,*) dist1acm, dist2acm
409 write(*,*) "Boxsize (suggested)"
410 write(*,*) (dist1acm+dist2acm)*1.2+20
411 open(61,file='boxsize.txt')
412 write(61,302) ((dist1acm+dist2acm)*1.2+20)
415 write(*,*) "Center of masses:"
416 write(*,301) xcm1, ycm1, zcm1
417 write(*,301) xcm2, ycm2, zcm2
419 write(*,*) "Center of masses atoms:"
420 write(*,800) atoma1(cm1),numera1(cm1),nazwaa1(cm1),nazwar1(cm1),
421 & " ",numerr1(cm1),x1(cm1),y1(cm1),z1(cm1)
422 write(*,800) atoma2(cm2),numera2(cm2),nazwaa2(cm2),nazwar2(cm2),
423 & " ",numerr2(cm2),x2(cm2),y2(cm2),z2(cm2)
426 write(*,*) "Number of amino-acid residues in two proteins:"
427 write(*,*) ile_reszt_mol1, ile_reszt_mol2
430 c ---------------------------------------------------------------------
432 c ---------------------------------------------------------------------
434 korekta1 = numerr1(1)
435 write(*,*) "Original number of the first residue in
436 & the first protein:"
437 write(*,*) numerr1(1)
439 write(*,*) "Correction of the first residue in the first protein:"
443 c wymiar=(distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2)
447 c write(*,*) "Minimum required distance between centers of mass:"
450 boxx = (6.5+distx1 + dist2acm)/2.0
451 boxy = (6.5+disty1 + dist2acm)/2.0
452 boxz = (6.5+distz1 + dist2acm)/2.0
453 write(*,*) "Rotation space (+/-):", boxx, boxy, boxz
469 write (plik3, "(A6,I1,a4)") "model0", ii1, ".pdb"
471 write (plik3, "(A5,I2,a4)") "model", ii1, ".pdb"
474 write(*,*) "Conformation will be saved to file:", plik3
476 c plik3a = plik3//ilosc
481 write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),"A",
482 & (numerr1(i)-korekta1+1),
486 c write(3,304) "ENDMDL"
488 if (peptide.eq.1) then
489 wymiar=((distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2))/4
492 if (peptide.eq.0) then
493 wymiar=((distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2))/8
497 write(*,*) "Initial minimum distance between centers of mass:",
501 c ROTATIONS OF THE SECOND MOLECULE
506 call ranorND(b,nd,ilosc_atomow2,ii1,seed1)
510 call rot_trans(xt2,t,b,xf,ilosc_atomow2)
520 if (conf.gt.1) goto 133
522 seed = ABS((seed1+proba)/(ii1**2))
525 seed11=ABS(seed+ii1-proba)*proba
526 seed12=ABS(seed+ii1-(proba**2))*proba
527 seed13=ABS(seed+ii1-(proba))*proba**2
528 c write(*,*) seed11, seed12, seed13
529 cm2xr = (rand(seed11)*2*boxx)-(boxx)
530 cm2yr = (rand(seed12)*2*boxy)-(boxy)
531 cm2zr = (rand(seed13)*2*boxz)-(boxz)
540 c SPRAWDZANIE CZY NIE JEST ZBYT PODOBNE DO JUZ WYLOSOWANEGO
548 dd=sqrt((cm2xr-cmxx(ir))**2+(cm2yr-cmyy(ir))**2+
549 & (cm2zr-cmzz(ir))**2)
551 c write(*,*) "Center of mass is", dd, "A away from", ir
552 c write(*,*) "Minimum distance required:", wymiar, "A"
554 c write(*,*) ii1, ir, proba3, dd, wymiar
556 if (dd.lt.wymiar) then
558 if (proba3.gt.1.and.peptide.eq.1) wymiar=wymiar*0.99992
559 if (proba3.gt.1.and.peptide.eq.0) wymiar=wymiar*0.99992
560 c write(*,*) proba3, wymiar
570 c SPRAWDZANIE ODLEGLOSCI
573 c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
574 c & numerr2(i),x2(i)-xcm2,y2(i)-ycm2,z2(i)-zcm2
577 dist12 = sqrt(((x2r(i)-x1(j))**2)+
578 & ((y2r(i)-y1(j))**2)+
579 & ((z2r(i)-z1(j))**2))
580 c write(*,*) dist12, cm2xr, cm2yr, cm2zr
581 if (dist12.lt.2.5) then
586 if (dist12.le.3.5) accept=1
587 c if (dist12.le.3.5) accept=1
588 c if (dist12.gt.3.5) proba2=proba2+1
592 c write(*,*) "No overlaps", proba
593 if (accept.eq.0) goto 200
594 c write(*,*) "No overlaps, contact", conf, proba
595 c write(3,305) "MODEL", conf
600 write(*,*) "Conformation", ii1, "Is accepted after",
601 & proba0x+proba0y+proba0z,
602 & proba1, proba2, proba3, proba, "attempts. ",
603 & "Dist between CoM of previous=", wymiar
606 write(*,*)"Extr",ABS(cm2xr+xcm1), ABS(cm2yr+ycm1), ABS(cm2zr+zcm1)
616 korekta2 = numerr2(1)-1
617 c write(*,*) "Original number of the first residue in
618 c & the second protein:"
619 c write(*,*) numerr2(1)
621 c write(*,*)"Correction of the first residue in the second protein:"
622 c write(*,*) korekta2
624 write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),"B",
625 & (numerr2(i)+ile_reszt_mol1-korekta2),
626 & x2r(i),y2r(i),z2r(i)
629 c write(3,304) "ENDMDL"
630 c write(3,305) "MODEL", conf
644 write (plik4, "(A9,I1,a4)") "template0", ii1, ".sco"
646 write (plik4, "(A8,I2,a4)") "template", ii1, ".sco"
652 if (peptide.eq.1) then
653 do ijl=1,(ile_reszt_mol1+ile_reszt_mol2+ilee)
655 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
656 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
657 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
658 if (ijl.ge.(ile_reszt_mol1+2))
659 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
663 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
664 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
665 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
666 if (ijl.ge.(ile_reszt_mol1+1))
667 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
673 if (peptide.eq.0) then
674 do ijl=1,(ile_reszt_mol1+ile_reszt_mol2+ilee)
677 if (glys1.eq.0.and.glye1.eq.0.and.glys2.eq.0) then
678 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
679 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
680 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
681 if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
682 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
683 if (ijl.gt.(ile_reszt_mol1+3).and.
684 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+3))
685 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
686 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+4))
687 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
692 if (glys1.eq.1.and.glye1.eq.0.and.glys2.eq.0) then
693 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
694 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
695 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
696 if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+2))
697 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
698 if (ijl.gt.(ile_reszt_mol1+2).and.
699 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
700 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
701 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
702 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
706 if (glys1.eq.0.and.glye1.eq.1.and.glys2.eq.0) then
707 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
708 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
709 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
710 if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+2))
711 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
712 if (ijl.gt.(ile_reszt_mol1+2).and.
713 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
714 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
715 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
716 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
719 c chain 1 first Gly and chain 1 last Gly
720 if (glys1.eq.1.and.glye1.eq.1.and.glys2.eq.0) then
721 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
722 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
723 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
724 if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+1))
725 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
726 if (ijl.gt.(ile_reszt_mol1+1).and.
727 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
728 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
729 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
730 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
734 if (glys1.eq.0.and.glye1.eq.0.and.glys2.eq.1) then
735 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
736 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
737 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
738 if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+2))
739 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
740 if (ijl.gt.(ile_reszt_mol1+2).and.
741 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
742 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
743 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
744 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
747 c chain 1 first Gly chain 2 first Gly
748 if (glys1.eq.1.and.glye1.eq.0.and.glys2.eq.1) then
749 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
750 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
751 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
752 if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+1))
753 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
754 if (ijl.gt.(ile_reszt_mol1+1).and.
755 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
756 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
757 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
758 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
761 c chain 1 last Gly chain 2 first Gly
762 if (glys1.eq.0.and.glye1.eq.1.and.glys2.eq.1) then
763 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
764 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
765 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
766 c if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
767 c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
768 if (ijl.gt.(ile_reszt_mol1+1).and.
769 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
770 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
771 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
772 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
776 if (glys1.eq.1.and.glye1.eq.1.and.glys2.eq.1) then
777 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
778 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
779 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
780 c if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
781 c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
782 if (ijl.gt.(ile_reszt_mol1).and.
783 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1))
784 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
785 c if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+1))
786 c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
797 c koniec petli po ilosci struktur
801 c write(*,*) i, cmxx(i), cmyy(i), cmzz(i)
802 c dd=(cm2xr-cmxx(ir))**2+(cm2yr-cmyy(ir))**2+(cm2zr-cmyy(ir))**2
807 c dd=sqrt((cmxx(i)-cmxx(j))**2+(cmyy(i)-cmyy(j))**2+
808 c & (cmzz(i)-cmzz(j))**2)
817 800 format(a4,2X,i5,1X,a4,1X,a3,1X,a1,i4,4X,3f8.3)
826 SUBROUTINE SRAND(ISEED)
828 C This subroutine sets the integer seed to be used with the
829 C companion RAND function to the value of ISEED. A flag is
830 C set to indicate that the sequence of pseudo-random numbers
831 C for the specified seed should start from the beginning.
833 COMMON /SEED/JSEED,IFRST
842 C This function returns a pseudo-random number for each invocation.
843 C It is a FORTRAN 77 adaptation of the "Integer Version 2" minimal
844 C standard number generator whose Pascal code appears in the article:
846 C Park, Steven K. and Miller, Keith W., "Random Number Generators:
847 C Good Ones are Hard to Find", Communications of the ACM,
850 PARAMETER (MPLIER=16807,MODLUS=2147483647,MOBYMP=127773,
853 COMMON /SEED/JSEED,IFRST
854 INTEGER HVLUE, LVLUE, TESTV, NEXTN
857 IF (IFRST .EQ. 0) THEN
862 HVLUE = NEXTN / MOBYMP
863 LVLUE = MOD(NEXTN, MOBYMP)
864 TESTV = MPLIER*LVLUE - MOMDMP*HVLUE
865 IF (TESTV .GT. 0) THEN
868 NEXTN = TESTV + MODLUS
870 RAND = REAL(NEXTN)/REAL(MODLUS)
875 COMMON /SEED/JSEED,IFRST
877 DATA JSEED,IFRST/123456789,0/
881 Subroutine ranorND(b,nd,ilosc_atomow2,ii1,seed1)
883 C generates a random vector on a unit sphere onC an ND-dimensional space.
884 C algorithm 40 page 410.
885 C the algorithm assumes that the formula for bz is valid, i.e
886 C bz=(1.0-2.0*ransq),
887 C and also that, ransq can be computed as as the sum of the independent random
888 C numbers to the second power (expression 3).
889 dimension ran(nd-1), b(nd)
891 c write(*,*) "In Subroutine ranorND(b,nd), nd=", nd
892 c write(*,*) "ilosc_atomow2=", ilosc_atomow2
893 c do j=1,ilosc_atomow2
897 do while (ransq.ge.1)
901 ran(i)=1.0-2.0*rand(0)
902 c write(*,*) i, ran(i)
903 rsq=ran(i)*ran(i)+rsq ! (3)
907 c write(*,*) j, ransq
909 ranh=2.0*sqrt(1.0-ransq)
910 c write(*,*) j, ranh, ransq
913 c write(*,*) ran(i), ranh
915 b(nd)=(1.0-2.0*ransq)
916 c write(*,*) b(1,j), b(2,j), b(3,j), b(4,j)
921 subroutine rot_trans(xt2,t,q,xf,ilosc_atomow2)
922 C x coordinates, t translation vector, q quaternion
923 double precision xt2(90000,3),xf(90000,3)
924 double precision t(3),q(4)
926 write(*,*) "Rotation vector:", q(1), q(2), q(3), q(4)
927 r11= q(1)*q(1)+q(2)*q(2)-q(3)*q(3)-q(4)*q(4)
928 r22= q(1)*q(1)-q(2)*q(2)+q(3)*q(3)-q(4)*q(4)
929 r33= q(1)*q(1)-q(2)*q(2)-q(3)*q(3)+q(4)*q(4)
930 r12= 2*(q(2)*q(3)-q(1)*q(4))
931 r21= 2*(q(2)*q(3)+q(1)*q(4))
932 r13= 2*(q(2)*q(4)+q(1)*q(3))
933 r31= 2*(q(2)*q(4)-q(1)*q(3))
934 r23= 2*(q(3)*q(4)-q(1)*q(2))
935 r32= 2*(q(3)*q(4)+q(1)*q(2))
937 c write(*,*) r11, r22, r33, r12, r21, r13, r31, r23, r32
940 xf(i,1)= r11*xt2(i,1)+r12*xt2(i,2)+r13*xt2(i,3) + t(1)
941 xf(i,2)= r21*xt2(i,1)+r22*xt2(i,2)+r23*xt2(i,3) + t(2)
942 xf(i,3)= r31*xt2(i,1)+r32*xt2(i,2)+r33*xt2(i,3) + t(3)
943 c write(*,*) i, xt2(i,1), xt2(i,2), xt2(i,3)
944 c write(*,*) i, xf(i,1), xf(i,2), xf(i,3)