2 C Read the PDB file and convert the peptide geometry into virtual-chain
4 implicit real*8 (a-h,o-z)
9 include 'COMMON.INTERACT'
10 include 'COMMON.IOUNITS'
12 include 'COMMON.NAMES'
13 include 'COMMON.CONTROL'
14 include 'COMMON.DISTFIT'
15 include 'COMMON.SETUP'
16 character*3 seq,atom,res
19 double precision e1(3),e2(3),e3(3)
27 read (ipdbin,'(a80)',end=10) card
28 if (card(:5).eq.'HELIX') then
31 read(card(22:25),*) hfrag(1,nhfrag)
32 read(card(34:37),*) hfrag(2,nhfrag)
34 if (card(:5).eq.'SHEET') then
37 read(card(24:26),*) bfrag(1,nbfrag)
38 read(card(35:37),*) bfrag(2,nbfrag)
39 crc----------------------------------------
40 crc to be corrected !!!
41 bfrag(3,nbfrag)=bfrag(1,nbfrag)
42 bfrag(4,nbfrag)=bfrag(2,nbfrag)
43 crc----------------------------------------
45 if (card(:3).eq.'END') then
47 else if (card(:3).eq.'TER') then
52 c write (iout,*) "Chain ended",ires,ishift,ires_old
55 dc(j,ires)=sccor(j,iii)
58 call sccenter(ires,iii,sccor)
61 C Fish out the ATOM cards.
62 if (index(card(1:4),'ATOM').gt.0) then
63 read (card(14:16),'(a3)') atom
64 if (atom.eq.'CA' .or. atom.eq.'CH3') then
65 C Calculate the CM of the preceding residue.
69 dc(j,ires+nres)=sccor(j,iii)
72 call sccenter(ires,iii,sccor)
76 c write (iout,'(a80)') card
77 read (card(24:26),*) ires
78 read (card(18:20),'(a3)') res
81 if (res.ne.'GLY' .and. res.ne. 'ACE') then
85 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
87 else if (ibeg.eq.2) then
89 ishift=-ires_old+ires-1
90 c write (iout,*) "New chain started",ires,ishift
94 c write (2,*) "ires",ires," ishift",ishift
95 if (res.eq.'ACE') then
98 itype(ires)=rescode(ires,res,0)
100 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
101 if(me.eq.king.or..not.out1file)
102 & write (iout,'(2i3,2x,a,3f8.3)')
103 & ires,itype(ires),res,(c(j,ires),j=1,3)
106 sccor(j,iii)=c(j,ires)
108 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
109 & atom.ne.'N ' .and. atom.ne.'C ') then
111 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
115 10 if(me.eq.king.or..not.out1file)
116 & write (iout,'(a,i5)') ' Nres: ',ires
117 C Calculate dummy residue coordinates inside the "chain" of a multichain
121 c write (iout,*) i,itype(i)
122 if (itype(i).eq.ntyp1) then
123 c write (iout,*) "dummy",i,itype(i)
125 c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
126 c c(j,i)=(c(j,i-1)+c(j,i+1))/2
131 C Calculate the CM of the last side chain.
134 dc(j,ires)=sccor(j,iii)
137 call sccenter(ires,iii,sccor)
141 if (itype(nres).ne.10) then
145 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
146 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
153 c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
157 dcj=c(j,nres-2)-c(j,nres-3)
158 c(j,nres)=c(j,nres-1)+dcj
159 c(j,2*nres)=c(j,nres)
170 c(j,2*nres)=c(j,nres)
172 if (itype(1).eq.ntyp1) then
176 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
177 call refsys(2,3,4,e1,e2,e3,fail)
184 c(j,1)=c(j,2)-3.8d0*e2(j)
194 C Calculate internal coordinates.
195 if(me.eq.king.or..not.out1file)then
197 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
198 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
199 & (c(j,nres+ires),j=1,3)
202 call int_from_cart(.true.,.false.)
203 call sc_loc_geom(.true.)
210 dc(j,i)=c(j,i+1)-c(j,i)
211 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
216 dc(j,i+nres)=c(j,i+nres)-c(j,i)
217 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
219 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
223 C Copy the coordinates to reference coordinates
224 C Splits to single chain if occurs
230 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
232 if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
235 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
241 cref(j,i+nres,cou)=c(j,i+nres)
243 chain_rep(j,lll,kkk)=c(j,i)
244 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
248 write (iout,*) chain_length
249 if (chain_length.eq.0) chain_length=nres
251 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
252 chain_rep(j,chain_length+nres,symetr)
253 &=chain_rep(j,chain_length+nres,1)
256 c write (iout,*) "spraw lancuchy",chain_length,symetr
258 c do kkk=1,chain_length
259 c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
263 C makes copy of chains
264 write (iout,*) "symetr", symetr
266 if (symetr.gt.1) then
273 write(iout,*) (tabperm(i,kkk),kkk=1,4)
279 c write (iout,*) i,icha
280 do lll=1,chain_length
282 if (cou.le.nres) then
284 kupa=mod(lll,chain_length)
285 iprzes=(kkk-1)*chain_length+lll
286 if (kupa.eq.0) kupa=chain_length
287 c write (iout,*) "kupa", kupa
288 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
289 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
296 C-koniec robienia kopii
299 write (iout,*) "nowa struktura", nperm
301 write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
303 &cref(3,i,kkk),cref(1,nres+i,kkk),
304 &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
306 100 format (//' alpha-carbon coordinates ',
307 & ' centroid coordinates'/
308 1 ' ', 6X,'X',11X,'Y',11X,'Z',
309 & 10X,'X',11X,'Y',11X,'Z')
310 110 format (a,'(',i3,')',6f12.5)
316 bfrag(i,j)=bfrag(i,j)-ishift
322 hfrag(i,j)=hfrag(i,j)-ishift
328 c---------------------------------------------------------------------------
329 subroutine int_from_cart(lside,lprn)
330 implicit real*8 (a-h,o-z)
335 include 'COMMON.LOCAL'
337 include 'COMMON.CHAIN'
338 include 'COMMON.INTERACT'
339 include 'COMMON.IOUNITS'
341 include 'COMMON.NAMES'
342 include 'COMMON.CONTROL'
343 include 'COMMON.SETUP'
344 character*3 seq,atom,res
346 dimension sccor(3,20)
350 if(me.eq.king.or..not.out1file)then
354 & 'Internal coordinates calculated from crystal structure.'
356 write (iout,'(8a)') ' Res ',' dvb',' Theta',
357 & ' Phi',' Dsc_id',' Dsc',' Alpha',
360 write (iout,'(4a)') ' Res ',' dvb',' Theta',
369 if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
370 & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
371 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
374 vbld(i+1)=dist(i,i+1)
375 vbld_inv(i+1)=1.0d0/vbld(i+1)
376 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
377 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
379 c if (unres_pdb) then
380 c if (itype(1).eq.21) then
381 c theta(3)=90.0d0*deg2rad
382 c phi(4)=180.0d0*deg2rad
384 c vbld_inv(2)=1.0d0/vbld(2)
386 c if (itype(nres).eq.21) then
387 c theta(nres)=90.0d0*deg2rad
388 c phi(nres)=180.0d0*deg2rad
390 c vbld_inv(nres)=1.0d0/vbld(2)
396 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
397 & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
402 if (itype(i).ne.10) then
403 vbld_inv(i+nres)=1.0d0/di
405 vbld_inv(i+nres)=0.0d0
408 alph(i)=alpha(nres+i,i,maxres2)
409 omeg(i)=beta(nres+i,i,maxres2,i+1)
411 if(me.eq.king.or..not.out1file)then
413 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
414 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
415 & rad2deg*alph(i),rad2deg*omeg(i)
421 if(me.eq.king.or..not.out1file)
422 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
423 & rad2deg*theta(i),rad2deg*phi(i)
428 c-------------------------------------------------------------------------------
429 subroutine sc_loc_geom(lprn)
430 implicit real*8 (a-h,o-z)
435 include 'COMMON.LOCAL'
437 include 'COMMON.CHAIN'
438 include 'COMMON.INTERACT'
439 include 'COMMON.IOUNITS'
441 include 'COMMON.NAMES'
442 include 'COMMON.CONTROL'
443 include 'COMMON.SETUP'
444 double precision x_prime(3),y_prime(3),z_prime(3)
448 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
452 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
454 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
458 dc_norm(j,i+nres)=0.0d0
463 costtab(i+1) =dcos(theta(i+1))
464 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
465 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
466 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
467 cosfac2=0.5d0/(1.0d0+costtab(i+1))
468 cosfac=dsqrt(cosfac2)
469 sinfac2=0.5d0/(1.0d0-costtab(i+1))
470 sinfac=dsqrt(sinfac2)
472 if (it.ne.10 .and. itype(i).ne.ntyp1) then
474 C Compute the axes of tghe local cartesian coordinates system; store in
475 c x_prime, y_prime and z_prime
483 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
484 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
486 call vecpr(x_prime,y_prime,z_prime)
488 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
489 C to local coordinate system. Store in xx, yy, zz.
495 xx = xx + x_prime(j)*dc_norm(j,i+nres)
496 yy = yy + y_prime(j)*dc_norm(j,i+nres)
497 zz = zz + z_prime(j)*dc_norm(j,i+nres)
513 if(me.eq.king.or..not.out1file)
514 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
517 write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
524 c---------------------------------------------------------------------------
525 subroutine sccenter(ires,nscat,sccor)
526 implicit real*8 (a-h,o-z)
528 include 'COMMON.CHAIN'
529 dimension sccor(3,20)
533 sccmj=sccmj+sccor(j,i)
535 dc(j,ires)=sccmj/nscat
539 c---------------------------------------------------------------------------
540 subroutine bond_regular
541 implicit real*8 (a-h,o-z)
544 include 'COMMON.LOCAL'
545 include 'COMMON.CALC'
546 include 'COMMON.INTERACT'
547 include 'COMMON.CHAIN'
550 vbld_inv(i+1)=1.0d0/vbld(i+1)
551 vbld(i+1+nres)=dsc(iabs(itype(i+1)))
552 vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
553 c print *,vbld(i+1),vbld(i+1+nres)