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
11 real*8 rand, r, boxx, boxy, boxz, dist2acm, dist1acm, b(4), t(3)
12 real*8 minx1, miny1, minz1, maxx1, maxy1, maxz1
13 real*8 minx2, miny2, minz2, maxx2, maxy2, maxz2
14 real*8 distx1, disty1, distz1, distx2, disty2, distz2
15 real*8 xcm1, ycm1, zcm1, xcm2, ycm2, zcm2
16 real*8 dist1cm, dist1cmt, dist2cm, dist2cmt
17 real*8 cm2xr, cm2yr, cm2zr,x2r(90000),y2r(90000),z2r(90000),dist12
18 real*8 angle, c, s, x2new, y2new, z2new
19 character*60 plik1, plik2, plik3, plik4, arg4, arg5
21 real*8 x1(90000),y1(90000),z1(90000),x2(90000),y2(90000),z2(90000)
22 real*8 dd, wymiar, cmxx(900), cmyy(900), cmzz(900),xt2(90000,3)
25 character*3 r1s, r2s, r1e, r2e
26 character*5 atoma1(90000), atoma2(90000)
27 character*6 nazwaa1(90000), nazwar1(90000)
28 character*6 nazwaa2(90000), nazwar2(90000)
33 c write(*,*)"Sposob uruchamiania:"
34 c write(*,*)"nazwa_programu nazwa_pliku_inp_pdb1
35 c & nazwa_pliku_inp_pdb2 nazwa_pliku_out"
40 write(*,*)"program input_pdb1 input_pdb2
41 & [0-1] number_of_models seed_number
42 & 0 for protein, 1 for peptide"
51 open(1,file=plik1,status="old")
52 open(2,file=plik2,status="old")
55 write(*,*) "All files read"
57 read(plik3(1:1),'(i1)') peptide
58 read(arg4,'(i2)') no_models
59 read(arg5,'(i19)') seed1
61 if (peptide.ne.0.and.peptide.ne.1) then
62 write(*,*) "Third parameter must be 0 or 1,
63 & where 0 is for a protein-protein docking,
64 & and 1 is for protein-peptide docking."
68 write(*,*) "Option", peptide, "selected
69 & (0 for protein, 1 for peptide)"
74 read(1,'(a54)',end=22) linia
75 if (linia(1:4).eq.'ATOM'.and.linia(17:17).lt.'B') then
76 write(4,'(a54)') linia
78 if (linia(1:3).eq.'TER') then
79 c write(2,'(a54)') linia
86 write(*,*) "Molecule 1 read"
91 read(2,'(a54)',end=23) linia
92 if (linia(1:4).eq.'ATOM'.and.linia(17:17).lt.'B') then
93 write(5,'(a54)') linia
95 if (linia(1:3).eq.'TER') then
96 c write(2,'(a54)') linia
102 write(*,*) "Molecule 2 read"
135 & atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),chain,numerr1(i),
139 c write(*,300) minx, maxx, miny, maxy, minz, maxz
141 if (x1(i).lt.minx1) minx1=x1(i)
142 if (y1(i).lt.miny1) miny1=y1(i)
143 if (z1(i).lt.minz1) minz1=z1(i)
145 if (x1(i).gt.maxx1) maxx1=x1(i)
146 if (y1(i).gt.maxy1) maxy1=y1(i)
147 if (z1(i).gt.maxz1) maxz1=z1(i)
149 c write(*,300) minx, maxx, miny, maxy, minz, maxz
151 c write(*,*) nazwaa1(i)
152 if (nazwaa1(i).eq.' CA ') then
156 ile_reszt_mol1 = ile_reszt_mol1 +1
159 if (atoma1(i).eq.'TER ') goto 111
160 if (atoma1(i).eq.'END ') goto 111
161 if (i.eq.1) write(3,'(a6)') "REMARK"
162 c write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),
163 c & numerr1(i),x1(i),y1(i),z1(i)
165 c write(*,*) i, x(i),y(i),z(i)
175 xcm1 = xcm1 / (ile_reszt_mol1*1.0)
176 ycm1 = ycm1 / (ile_reszt_mol1*1.0)
177 zcm1 = zcm1 / (ile_reszt_mol1*1.0)
190 if (nazwaa1(i).eq.' CA ') then
196 xcm1 = xcm1 / (ile_reszt_mol1*1.0)
197 ycm1 = ycm1 / (ile_reszt_mol1*1.0)
198 zcm1 = zcm1 / (ile_reszt_mol1*1.0)
203 c write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),
204 c & numerr1(i),x1(i)-xcm1,y1(i)-ycm1,z1(i)-zcm1
206 dist1cmt = dsqrt(((xcm1-x1(i))**2)+
210 c write(*,*) dist1cmt, dist1cm, i, cm1
211 if (dist1cm.gt.dist1cmt) then
220 dist1cmt = dsqrt(((x1(j)-x1(i))**2)+
221 & ((y1(j)-y1(i))**2)+
222 & ((z1(j)-z1(i))**2))
223 if (dist1acm.lt.dist1cmt) then
231 c write(3,304) "ENDMDL"
233 write(*,*) "Molecule 1 calculated"
244 & atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),chain,numerr2(i),
247 c write(*,300) minx, maxx, miny, maxy, minz, maxz
249 if (x2(i).lt.minx2) minx2=x2(i)
250 if (y2(i).lt.miny2) miny2=y2(i)
251 if (z2(i).lt.minz2) minz2=z2(i)
253 if (x2(i).gt.maxx2) maxx2=x2(i)
254 if (y2(i).gt.maxy2) maxy2=y2(i)
255 if (z2(i).gt.maxz2) maxz2=z2(i)
257 c write(*,300) minx, maxx, miny, maxy, minz, maxz
259 c write(*,*) nazwaa1(i)
260 if (nazwaa2(i).eq.' CA ') then
264 ile_reszt_mol2 = ile_reszt_mol2 + 1
267 if (atoma2(i).eq.'TER ') goto 111
268 if (atoma2(i).eq.'END ') goto 111
269 c if (i.eq.1) write(3,'(a6)') "REMARK"
270 c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
271 c & numerr2(i),x2(i),y2(i),z2(i)
272 c write(*,*) i, x(i),y(i),z(i)
283 xcm2 = xcm2 / (ile_reszt_mol2*1.0)
284 ycm2 = ycm2 / (ile_reszt_mol2*1.0)
285 zcm2 = zcm2 / (ile_reszt_mol2*1.0)
291 c write(*,*) x2(i),y2(i),z2(i)
295 c write(*,*) xt2(i,1), xt2(i,2), xt2(i,3)
302 if (nazwaa2(i).eq.' CA ') then
308 xcm2 = xcm2 / (ile_reszt_mol2*1.0)
309 ycm2 = ycm2 / (ile_reszt_mol2*1.0)
310 zcm2 = zcm2 / (ile_reszt_mol2*1.0)
316 c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
317 c & numerr2(i),x2(i)-xcm2,y2(i)-ycm2,z2(i)-zcm2
319 dist2cmt = dsqrt(((xcm2-x2(i))**2)+
323 c write(*,*) dist2cmt, dist2cm, i, cm2
324 if (dist2cm.gt.dist2cmt) then
334 dist2cmt = dsqrt(((x2(j)-x2(i))**2)+
335 & ((y2(j)-y2(i))**2)+
336 & ((z2(j)-z2(i))**2))
337 if (dist2acm.lt.dist2cmt) then
352 r1e=nazwar1(ile_reszt_mol1)
353 r2e=nazwar2(ile_reszt_mol2)
355 if (r1s.eq."GLY") then
357 write(*,*) "Chain 1 is starting from Gly ", r1s, glys1
360 if (r2s.eq."GLY") then
362 write(*,*) "Chain 2 is starting from Gly ", r2s, glys2
365 if (r1e.eq."GLY") then
367 write(*,*) "Chain 1 is ending at Gly ", r1e, glye1
371 if (r2e.eq."GLY") then
373 write(*,*) "Chain 2 is ending from Gly ", r2e, glye2
379 if(glys1.eq.1) ilee=ilee-1
380 if(glys2.eq.1) ilee=ilee-1
381 if(glye1.eq.1) ilee=ilee-1
382 if(glye2.eq.1) ilee=ilee-1
383 write(*,*) "How many dummy atoms:", ilee
387 write(*,*) "Molecule 2 calculated"
388 write(*,*) "Number of atoms:", ilosc_atomow1, ilosc_atomow2
390 write(*,*) "Min and max coordinates in the systems"
391 write(*,300) minx1, maxx1, miny1, maxy1, minz1, maxz1
392 write(*,300) minx2, maxx2, miny2, maxy2, minz2, maxz2
394 write(*,*) "Distances in axes x, y, z"
395 write(*,301) distx1, disty1, distz1
396 write(*,301) distx2, disty2, distz2
398 boxx = (distx1 + distx2)*1.5 + 20.0
399 boxy = (disty1 + disty2)*1.5 + 20.0
400 boxz = (distz1 + distz2)*1.5 + 20.0
402 c write(*,*) "Boxsize [x, y, z]"
403 c write(*,301) boxx, boxy, boxz
405 write(*,*) "Maximum distances:"
406 write(*,*) dist1acm, dist2acm
408 write(*,*) "Boxsize (suggested)"
409 write(*,*) (dist1acm+dist2acm)*1.2+20
410 open(61,file='boxsize.txt')
411 write(61,302) ((dist1acm+dist2acm)*1.2+20)
414 write(*,*) "Center of masses:"
415 write(*,301) xcm1, ycm1, zcm1
416 write(*,301) xcm2, ycm2, zcm2
418 write(*,*) "Center of masses atoms:"
419 write(*,800) atoma1(cm1),numera1(cm1),nazwaa1(cm1),nazwar1(cm1),
420 & " ",numerr1(cm1),x1(cm1),y1(cm1),z1(cm1)
421 write(*,800) atoma2(cm2),numera2(cm2),nazwaa2(cm2),nazwar2(cm2),
422 & " ",numerr2(cm2),x2(cm2),y2(cm2),z2(cm2)
425 write(*,*) "Number of amino-acid residues in two proteins:"
426 write(*,*) ile_reszt_mol1, ile_reszt_mol2
429 c ---------------------------------------------------------------------
431 c ---------------------------------------------------------------------
433 korekta1 = numerr1(1)
434 write(*,*) "Original number of the first residue in
435 & the first protein:"
436 write(*,*) numerr1(1)
438 write(*,*) "Correction of the first residue in the first protein:"
442 c wymiar=(distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2)
446 c write(*,*) "Minimum required distance between centers of mass:"
449 boxx = (6.5+distx1 + dist2acm)/2.0
450 boxy = (6.5+disty1 + dist2acm)/2.0
451 boxz = (6.5+distz1 + dist2acm)/2.0
452 write(*,*) "Rotation space (+/-):", boxx, boxy, boxz
468 write (plik3, "(A6,I1,a4)") "model0", ii1, ".pdb"
470 write (plik3, "(A5,I2,a4)") "model", ii1, ".pdb"
473 write(*,*) "Conformation will be saved to file:", plik3
475 c plik3a = plik3//ilosc
480 write(3,800) atoma1(i),numera1(i),nazwaa1(i),nazwar1(i),"A",
481 & (numerr1(i)-korekta1+1),
485 c write(3,304) "ENDMDL"
487 if (peptide.eq.1) then
488 wymiar=((distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2))/4
491 if (peptide.eq.0) then
492 wymiar=((distx1 + distx2)+(disty1 + disty2)+(distz1 + distz2))/8
496 write(*,*) "Initial minimum distance between centers of mass:",
500 c ROTATIONS OF THE SECOND MOLECULE
505 call ranorND(b,nd,ilosc_atomow2,ii1,seed1)
509 call rot_trans(xt2,t,b,xf,ilosc_atomow2)
519 if (conf.gt.1) goto 133
521 seed = ABS((seed1+proba)/(ii1**2))
524 seed11=ABS(seed+ii1-proba)*proba
525 seed12=ABS(seed+ii1-(proba**2))*proba
526 seed13=ABS(seed+ii1-(proba))*proba**2
527 c write(*,*) seed11, seed12, seed13
528 cm2xr = (rand(seed11)*2*boxx)-(boxx)
529 cm2yr = (rand(seed12)*2*boxy)-(boxy)
530 cm2zr = (rand(seed13)*2*boxz)-(boxz)
539 c SPRAWDZANIE CZY NIE JEST ZBYT PODOBNE DO JUZ WYLOSOWANEGO
547 dd=sqrt((cm2xr-cmxx(ir))**2+(cm2yr-cmyy(ir))**2+
548 & (cm2zr-cmzz(ir))**2)
550 c write(*,*) "Center of mass is", dd, "A away from", ir
551 c write(*,*) "Minimum distance required:", wymiar, "A"
553 c write(*,*) ii1, ir, proba3, dd, wymiar
555 if (dd.lt.wymiar) then
557 if (proba3.gt.1.and.peptide.eq.1) wymiar=wymiar*0.99992
558 if (proba3.gt.1.and.peptide.eq.0) wymiar=wymiar*0.99992
559 c write(*,*) proba3, wymiar
569 c SPRAWDZANIE ODLEGLOSCI
572 c write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),
573 c & numerr2(i),x2(i)-xcm2,y2(i)-ycm2,z2(i)-zcm2
576 dist12 = sqrt(((x2r(i)-x1(j))**2)+
577 & ((y2r(i)-y1(j))**2)+
578 & ((z2r(i)-z1(j))**2))
579 c write(*,*) dist12, cm2xr, cm2yr, cm2zr
580 if (dist12.lt.2.5) then
585 if (dist12.le.3.5) accept=1
586 c if (dist12.le.3.5) accept=1
587 c if (dist12.gt.3.5) proba2=proba2+1
591 c write(*,*) "No overlaps", proba
592 if (accept.eq.0) goto 200
593 c write(*,*) "No overlaps, contact", conf, proba
594 c write(3,305) "MODEL", conf
599 write(*,*) "Conformation", ii1, "Is accepted after",
600 & proba0x+proba0y+proba0z,
601 & proba1, proba2, proba3, proba, "attempts. ",
602 & "Dist between CoM of previous=", wymiar
605 write(*,*)"Extr",ABS(cm2xr+xcm1), ABS(cm2yr+ycm1), ABS(cm2zr+zcm1)
615 korekta2 = numerr2(1)-1
616 c write(*,*) "Original number of the first residue in
617 c & the second protein:"
618 c write(*,*) numerr2(1)
620 c write(*,*)"Correction of the first residue in the second protein:"
621 c write(*,*) korekta2
623 write(3,800) atoma2(i),numera2(i),nazwaa2(i),nazwar2(i),"B",
624 & (numerr2(i)+ile_reszt_mol1-korekta2),
625 & x2r(i),y2r(i),z2r(i)
628 c write(3,304) "ENDMDL"
629 c write(3,305) "MODEL", conf
643 write (plik4, "(A9,I1,a4)") "template0", ii1, ".sco"
645 write (plik4, "(A8,I2,a4)") "template", ii1, ".sco"
651 if (peptide.eq.1) then
652 do ijl=1,(ile_reszt_mol1+ile_reszt_mol2+ilee)
654 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
655 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
656 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
657 if (ijl.ge.(ile_reszt_mol1+2))
658 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
662 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
663 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
664 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
665 if (ijl.ge.(ile_reszt_mol1+1))
666 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
672 if (peptide.eq.0) then
673 do ijl=1,(ile_reszt_mol1+ile_reszt_mol2+ilee)
676 if (glys1.eq.0.and.glye1.eq.0.and.glys2.eq.0) then
677 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
678 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
679 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
680 if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
681 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
682 if (ijl.gt.(ile_reszt_mol1+3).and.
683 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+3))
684 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
685 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+4))
686 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
691 if (glys1.eq.1.and.glye1.eq.0.and.glys2.eq.0) then
692 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
693 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
694 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
695 if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+2))
696 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
697 if (ijl.gt.(ile_reszt_mol1+2).and.
698 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
699 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
700 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
701 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
705 if (glys1.eq.0.and.glye1.eq.1.and.glys2.eq.0) then
706 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
707 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
708 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
709 if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+2))
710 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
711 if (ijl.gt.(ile_reszt_mol1+2).and.
712 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
713 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
714 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
715 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
718 c chain 1 first Gly and chain 1 last Gly
719 if (glys1.eq.1.and.glye1.eq.1.and.glys2.eq.0) then
720 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
721 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
722 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
723 if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+1))
724 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
725 if (ijl.gt.(ile_reszt_mol1+1).and.
726 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
727 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
728 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
729 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
733 if (glys1.eq.0.and.glye1.eq.0.and.glys2.eq.1) then
734 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
735 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
736 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
737 if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+2))
738 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
739 if (ijl.gt.(ile_reszt_mol1+2).and.
740 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+2))
741 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
742 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+3))
743 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
746 c chain 1 first Gly chain 2 first Gly
747 if (glys1.eq.1.and.glye1.eq.0.and.glys2.eq.1) then
748 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
749 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
750 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
751 if (ijl.ge.(ile_reszt_mol1+1).and.ijl.le.(ile_reszt_mol1+1))
752 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
753 if (ijl.gt.(ile_reszt_mol1+1).and.
754 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
755 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
756 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
757 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
760 c chain 1 last Gly chain 2 first Gly
761 if (glys1.eq.0.and.glye1.eq.1.and.glys2.eq.1) then
762 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "0"
763 if (ijl.le.ile_reszt_mol1+1.and.ijl.gt.1)
764 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
765 c if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
766 c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
767 if (ijl.gt.(ile_reszt_mol1+1).and.
768 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1+1))
769 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
770 if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+2))
771 & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
775 if (glys1.eq.1.and.glye1.eq.1.and.glys2.eq.1) then
776 if (ijl.eq.1) write(7,*) ijl, "1.0 1.0 1.0 ", "1"
777 if (ijl.le.ile_reszt_mol1.and.ijl.gt.1)
778 & write(7,*) ijl, "1.0 1.0 1.0 ", "1"
779 c if (ijl.ge.(ile_reszt_mol1+2).and.ijl.le.(ile_reszt_mol1+3))
780 c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
781 if (ijl.gt.(ile_reszt_mol1).and.
782 & ijl.le.(ile_reszt_mol2+ile_reszt_mol1))
783 & write(7,*) ijl, "1.0 1.0 1.0 ", "2"
784 c if (ijl.ge.(ile_reszt_mol2+ile_reszt_mol1+1))
785 c & write(7,*) ijl, "1.0 1.0 1.0 ", "0"
796 c koniec petli po ilosci struktur
800 c write(*,*) i, cmxx(i), cmyy(i), cmzz(i)
801 c dd=(cm2xr-cmxx(ir))**2+(cm2yr-cmyy(ir))**2+(cm2zr-cmyy(ir))**2
806 c dd=sqrt((cmxx(i)-cmxx(j))**2+(cmyy(i)-cmyy(j))**2+
807 c & (cmzz(i)-cmzz(j))**2)
816 800 format(a4,2X,i5,1X,a4,1X,a3,1X,a1,i4,4X,3f8.3)
825 SUBROUTINE SRAND(ISEED)
827 C This subroutine sets the integer seed to be used with the
828 C companion RAND function to the value of ISEED. A flag is
829 C set to indicate that the sequence of pseudo-random numbers
830 C for the specified seed should start from the beginning.
832 COMMON /SEED/JSEED,IFRST
841 C This function returns a pseudo-random number for each invocation.
842 C It is a FORTRAN 77 adaptation of the "Integer Version 2" minimal
843 C standard number generator whose Pascal code appears in the article:
845 C Park, Steven K. and Miller, Keith W., "Random Number Generators:
846 C Good Ones are Hard to Find", Communications of the ACM,
849 PARAMETER (MPLIER=16807,MODLUS=2147483647,MOBYMP=127773,
852 COMMON /SEED/JSEED,IFRST
853 INTEGER HVLUE, LVLUE, TESTV, NEXTN
856 IF (IFRST .EQ. 0) THEN
861 HVLUE = NEXTN / MOBYMP
862 LVLUE = MOD(NEXTN, MOBYMP)
863 TESTV = MPLIER*LVLUE - MOMDMP*HVLUE
864 IF (TESTV .GT. 0) THEN
867 NEXTN = TESTV + MODLUS
869 RAND = REAL(NEXTN)/REAL(MODLUS)
874 COMMON /SEED/JSEED,IFRST
876 DATA JSEED,IFRST/123456789,0/
880 Subroutine ranorND(b,nd,ilosc_atomow2,ii1,seed1)
882 C generates a random vector on a unit sphere onC an ND-dimensional space.
883 C algorithm 40 page 410.
884 C the algorithm assumes that the formula for bz is valid, i.e
885 C bz=(1.0-2.0*ransq),
886 C and also that, ransq can be computed as as the sum of the independent random
887 C numbers to the second power (expression 3).
888 dimension ran(nd-1), b(nd)
890 c write(*,*) "In Subroutine ranorND(b,nd), nd=", nd
891 c write(*,*) "ilosc_atomow2=", ilosc_atomow2
892 c do j=1,ilosc_atomow2
896 do while (ransq.ge.1)
900 ran(i)=1.0-2.0*rand(0)
901 c write(*,*) i, ran(i)
902 rsq=ran(i)*ran(i)+rsq ! (3)
906 c write(*,*) j, ransq
908 ranh=2.0*sqrt(1.0-ransq)
909 c write(*,*) j, ranh, ransq
912 c write(*,*) ran(i), ranh
914 b(nd)=(1.0-2.0*ransq)
915 c write(*,*) b(1,j), b(2,j), b(3,j), b(4,j)
920 subroutine rot_trans(xt2,t,q,xf,ilosc_atomow2)
921 C x coordinates, t translation vector, q quaternion
922 double precision xt2(90000,3),xf(90000,3)
923 double precision t(3),q(4)
925 write(*,*) "Rotation vector:", q(1), q(2), q(3), q(4)
926 r11= q(1)*q(1)+q(2)*q(2)-q(3)*q(3)-q(4)*q(4)
927 r22= q(1)*q(1)-q(2)*q(2)+q(3)*q(3)-q(4)*q(4)
928 r33= q(1)*q(1)-q(2)*q(2)-q(3)*q(3)+q(4)*q(4)
929 r12= 2*(q(2)*q(3)-q(1)*q(4))
930 r21= 2*(q(2)*q(3)+q(1)*q(4))
931 r13= 2*(q(2)*q(4)+q(1)*q(3))
932 r31= 2*(q(2)*q(4)-q(1)*q(3))
933 r23= 2*(q(3)*q(4)-q(1)*q(2))
934 r32= 2*(q(3)*q(4)+q(1)*q(2))
936 c write(*,*) r11, r22, r33, r12, r21, r13, r31, r23, r32
939 xf(i,1)= r11*xt2(i,1)+r12*xt2(i,2)+r13*xt2(i,3) + t(1)
940 xf(i,2)= r21*xt2(i,1)+r22*xt2(i,2)+r23*xt2(i,3) + t(2)
941 xf(i,3)= r31*xt2(i,1)+r32*xt2(i,2)+r33*xt2(i,3) + t(3)
942 c write(*,*) i, xt2(i,1), xt2(i,2), xt2(i,3)
943 c write(*,*) i, xf(i,1), xf(i,2), xf(i,3)