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)
20 integer rescode,iterter(maxres)
30 read (ipdbin,'(a80)',end=10) card
31 if (card(:5).eq.'HELIX') then
34 read(card(22:25),*) hfrag(1,nhfrag)
35 read(card(34:37),*) hfrag(2,nhfrag)
37 if (card(:5).eq.'SHEET') then
40 read(card(24:26),*) bfrag(1,nbfrag)
41 read(card(35:37),*) bfrag(2,nbfrag)
42 crc----------------------------------------
43 crc to be corrected !!!
44 bfrag(3,nbfrag)=bfrag(1,nbfrag)
45 bfrag(4,nbfrag)=bfrag(2,nbfrag)
46 crc----------------------------------------
48 if (card(:3).eq.'END') then
50 else if (card(:3).eq.'TER') then
53 itype(ires_old-1)=ntyp1
58 write (iout,*) "Chain ended",ires,ishift,ires_old
61 dc(j,ires)=sccor(j,iii)
64 call sccenter(ires,iii,sccor)
67 C Fish out the ATOM cards.
68 if (index(card(1:4),'ATOM').gt.0) then
69 read (card(14:16),'(a3)') atom
70 if (atom.eq.'CA' .or. atom.eq.'CH3') then
71 C Calculate the CM of the preceding residue.
75 dc(j,ires+nres)=sccor(j,iii)
78 call sccenter(ires,iii,sccor)
82 c write (iout,'(a80)') card
83 read (card(24:26),*) ires
84 read (card(18:20),'(a3)') res
87 if (res.ne.'GLY' .and. res.ne. 'ACE') then
91 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
93 else if (ibeg.eq.2) then
95 ishift=-ires_old+ires-1
96 c write (iout,*) "New chain started",ires,ishift
100 c write (2,*) "ires",ires," ishift",ishift
101 if (res.eq.'ACE') then
104 itype(ires)=rescode(ires,res,0)
106 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
107 if(me.eq.king.or..not.out1file)
108 & write (iout,'(2i3,2x,a,3f8.3)')
109 & ires,itype(ires),res,(c(j,ires),j=1,3)
112 sccor(j,iii)=c(j,ires)
114 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
115 & atom.ne.'N ' .and. atom.ne.'C ') then
117 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
121 10 if(me.eq.king.or..not.out1file)
122 & write (iout,'(a,i5)') ' Nres: ',ires
123 C Calculate dummy residue coordinates inside the "chain" of a multichain
127 write (iout,*) i,itype(i),itype(i+1)
128 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
129 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
130 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
131 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
132 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
134 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
135 print *,i,'tu dochodze'
136 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
144 c(j,i)=c(j,i-1)-1.9d0*e2(j)
148 dcj=(c(j,i-2)-c(j,i-3))/2.0
149 if (dcj.eq.0) dcj=1.23591524223
154 else !itype(i+1).eq.ntyp1
156 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
157 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
164 c(j,i)=c(j,i+1)-1.9d0*e2(j)
168 dcj=(c(j,i+3)-c(j,i+2))/2.0
169 if (dcj.eq.0) dcj=1.23591524223
174 endif !itype(i+1).eq.ntyp1
175 endif !itype.eq.ntyp1
177 C Calculate the CM of the last side chain.
180 dc(j,ires)=sccor(j,iii)
183 call sccenter(ires,iii,sccor)
187 if (itype(nres).ne.10) then
191 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
192 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
199 c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
203 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
204 if (dcj.eq.0) dcj=1.23591524223
205 c(j,nres)=c(j,nres-1)+dcj
206 c(j,2*nres)=c(j,nres)
217 c(j,2*nres)=c(j,nres)
219 if (itype(1).eq.ntyp1) then
223 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
224 call refsys(2,3,4,e1,e2,e3,fail)
231 c(j,1)=c(j,2)-1.9d0*e2(j)
235 dcj=(c(j,4)-c(j,3))/2.0
241 C Calculate internal coordinates.
242 if(me.eq.king.or..not.out1file)then
244 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
245 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
246 & (c(j,nres+ires),j=1,3)
249 call int_from_cart(.true.,.false.)
250 call sc_loc_geom(.true.)
257 dc(j,i)=c(j,i+1)-c(j,i)
258 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
263 dc(j,i+nres)=c(j,i+nres)-c(j,i)
264 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
266 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
270 C Copy the coordinates to reference coordinates
271 C Splits to single chain if occurs
277 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
279 if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
282 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
288 cref(j,i+nres,cou)=c(j,i+nres)
290 chain_rep(j,lll,kkk)=c(j,i)
291 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
295 write (iout,*) chain_length
296 if (chain_length.eq.0) chain_length=nres
298 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
299 chain_rep(j,chain_length+nres,symetr)
300 &=chain_rep(j,chain_length+nres,1)
303 c write (iout,*) "spraw lancuchy",chain_length,symetr
305 c do kkk=1,chain_length
306 c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
310 C makes copy of chains
311 write (iout,*) "symetr", symetr
313 if (symetr.gt.1) then
320 write(iout,*) (tabperm(i,kkk),kkk=1,4)
326 c write (iout,*) i,icha
327 do lll=1,chain_length
329 if (cou.le.nres) then
331 kupa=mod(lll,chain_length)
332 iprzes=(kkk-1)*chain_length+lll
333 if (kupa.eq.0) kupa=chain_length
334 c write (iout,*) "kupa", kupa
335 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
336 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
343 C-koniec robienia kopii
346 write (iout,*) "nowa struktura", nperm
348 write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
350 &cref(3,i,kkk),cref(1,nres+i,kkk),
351 &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
353 100 format (//' alpha-carbon coordinates ',
354 & ' centroid coordinates'/
355 1 ' ', 6X,'X',11X,'Y',11X,'Z',
356 & 10X,'X',11X,'Y',11X,'Z')
357 110 format (a,'(',i3,')',6f12.5)
363 bfrag(i,j)=bfrag(i,j)-ishift
369 hfrag(i,j)=hfrag(i,j)-ishift
374 c---------------------------------------------------------------------------
375 subroutine int_from_cart(lside,lprn)
376 implicit real*8 (a-h,o-z)
381 include 'COMMON.LOCAL'
383 include 'COMMON.CHAIN'
384 include 'COMMON.INTERACT'
385 include 'COMMON.IOUNITS'
387 include 'COMMON.NAMES'
388 include 'COMMON.CONTROL'
389 include 'COMMON.SETUP'
390 character*3 seq,atom,res
392 dimension sccor(3,20)
396 if(me.eq.king.or..not.out1file)then
400 & 'Internal coordinates calculated from crystal structure.'
402 write (iout,'(8a)') ' Res ',' dvb',' Theta',
403 & ' Phi',' Dsc_id',' Dsc',' Alpha',
406 write (iout,'(4a)') ' Res ',' dvb',' Theta',
415 if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
416 & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
417 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
420 vbld(i+1)=dist(i,i+1)
421 vbld_inv(i+1)=1.0d0/vbld(i+1)
422 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
423 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
425 c if (unres_pdb) then
426 c if (itype(1).eq.21) then
427 c theta(3)=90.0d0*deg2rad
428 c phi(4)=180.0d0*deg2rad
430 c vbld_inv(2)=1.0d0/vbld(2)
432 c if (itype(nres).eq.21) then
433 c theta(nres)=90.0d0*deg2rad
434 c phi(nres)=180.0d0*deg2rad
436 c vbld_inv(nres)=1.0d0/vbld(2)
442 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
443 & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
448 if (itype(i).ne.10) then
449 vbld_inv(i+nres)=1.0d0/di
451 vbld_inv(i+nres)=0.0d0
454 alph(i)=alpha(nres+i,i,maxres2)
455 omeg(i)=beta(nres+i,i,maxres2,i+1)
457 if(me.eq.king.or..not.out1file)then
459 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
460 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
461 & rad2deg*alph(i),rad2deg*omeg(i)
467 if(me.eq.king.or..not.out1file)
468 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
469 & rad2deg*theta(i),rad2deg*phi(i)
474 c-------------------------------------------------------------------------------
475 subroutine sc_loc_geom(lprn)
476 implicit real*8 (a-h,o-z)
481 include 'COMMON.LOCAL'
483 include 'COMMON.CHAIN'
484 include 'COMMON.INTERACT'
485 include 'COMMON.IOUNITS'
487 include 'COMMON.NAMES'
488 include 'COMMON.CONTROL'
489 include 'COMMON.SETUP'
490 double precision x_prime(3),y_prime(3),z_prime(3)
494 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
498 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
500 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
504 dc_norm(j,i+nres)=0.0d0
509 costtab(i+1) =dcos(theta(i+1))
510 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
511 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
512 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
513 cosfac2=0.5d0/(1.0d0+costtab(i+1))
514 cosfac=dsqrt(cosfac2)
515 sinfac2=0.5d0/(1.0d0-costtab(i+1))
516 sinfac=dsqrt(sinfac2)
518 if (it.ne.10 .and. itype(i).ne.ntyp1) then
520 C Compute the axes of tghe local cartesian coordinates system; store in
521 c x_prime, y_prime and z_prime
529 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
530 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
532 call vecpr(x_prime,y_prime,z_prime)
534 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
535 C to local coordinate system. Store in xx, yy, zz.
541 xx = xx + x_prime(j)*dc_norm(j,i+nres)
542 yy = yy + y_prime(j)*dc_norm(j,i+nres)
543 zz = zz + z_prime(j)*dc_norm(j,i+nres)
559 if(me.eq.king.or..not.out1file)
560 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
563 write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
570 c---------------------------------------------------------------------------
571 subroutine sccenter(ires,nscat,sccor)
572 implicit real*8 (a-h,o-z)
574 include 'COMMON.CHAIN'
575 dimension sccor(3,20)
579 sccmj=sccmj+sccor(j,i)
581 dc(j,ires)=sccmj/nscat
585 c---------------------------------------------------------------------------
586 subroutine bond_regular
587 implicit real*8 (a-h,o-z)
590 include 'COMMON.LOCAL'
591 include 'COMMON.CALC'
592 include 'COMMON.INTERACT'
593 include 'COMMON.CHAIN'
596 vbld_inv(i+1)=1.0d0/vbld(i+1)
597 vbld(i+1+nres)=dsc(iabs(itype(i+1)))
598 vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
599 c print *,vbld(i+1),vbld(i+1+nres)