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
153 else !itype(i+1).eq.ntyp1
155 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
156 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
163 c(j,i)=c(j,i+1)-1.9d0*e2(j)
167 dcj=(c(j,i+3)-c(j,i+2))/2.0
172 endif !itype(i+1).eq.ntyp1
173 endif !itype.eq.ntyp1
175 C Calculate the CM of the last side chain.
178 dc(j,ires)=sccor(j,iii)
181 call sccenter(ires,iii,sccor)
185 if (itype(nres).ne.10) then
189 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
190 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
197 c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
201 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
202 c(j,nres)=c(j,nres-1)+dcj
203 c(j,2*nres)=c(j,nres)
214 c(j,2*nres)=c(j,nres)
216 if (itype(1).eq.ntyp1) then
220 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
221 call refsys(2,3,4,e1,e2,e3,fail)
228 c(j,1)=c(j,2)-1.9d0*e2(j)
232 dcj=(c(j,4)-c(j,3))/2.0
238 C Calculate internal coordinates.
239 if(me.eq.king.or..not.out1file)then
241 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
242 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
243 & (c(j,nres+ires),j=1,3)
246 call int_from_cart(.true.,.false.)
247 call sc_loc_geom(.true.)
254 dc(j,i)=c(j,i+1)-c(j,i)
255 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
260 dc(j,i+nres)=c(j,i+nres)-c(j,i)
261 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
263 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
267 C Copy the coordinates to reference coordinates
268 C Splits to single chain if occurs
274 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
276 if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
279 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
285 cref(j,i+nres,cou)=c(j,i+nres)
287 chain_rep(j,lll,kkk)=c(j,i)
288 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
292 write (iout,*) chain_length
293 if (chain_length.eq.0) chain_length=nres
295 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
296 chain_rep(j,chain_length+nres,symetr)
297 &=chain_rep(j,chain_length+nres,1)
300 c write (iout,*) "spraw lancuchy",chain_length,symetr
302 c do kkk=1,chain_length
303 c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
307 C makes copy of chains
308 write (iout,*) "symetr", symetr
310 if (symetr.gt.1) then
317 write(iout,*) (tabperm(i,kkk),kkk=1,4)
323 c write (iout,*) i,icha
324 do lll=1,chain_length
326 if (cou.le.nres) then
328 kupa=mod(lll,chain_length)
329 iprzes=(kkk-1)*chain_length+lll
330 if (kupa.eq.0) kupa=chain_length
331 c write (iout,*) "kupa", kupa
332 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
333 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
340 C-koniec robienia kopii
343 write (iout,*) "nowa struktura", nperm
345 write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
347 &cref(3,i,kkk),cref(1,nres+i,kkk),
348 &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
350 100 format (//' alpha-carbon coordinates ',
351 & ' centroid coordinates'/
352 1 ' ', 6X,'X',11X,'Y',11X,'Z',
353 & 10X,'X',11X,'Y',11X,'Z')
354 110 format (a,'(',i3,')',6f12.5)
360 bfrag(i,j)=bfrag(i,j)-ishift
366 hfrag(i,j)=hfrag(i,j)-ishift
372 c---------------------------------------------------------------------------
373 subroutine int_from_cart(lside,lprn)
374 implicit real*8 (a-h,o-z)
379 include 'COMMON.LOCAL'
381 include 'COMMON.CHAIN'
382 include 'COMMON.INTERACT'
383 include 'COMMON.IOUNITS'
385 include 'COMMON.NAMES'
386 include 'COMMON.CONTROL'
387 include 'COMMON.SETUP'
388 character*3 seq,atom,res
390 dimension sccor(3,20)
394 if(me.eq.king.or..not.out1file)then
398 & 'Internal coordinates calculated from crystal structure.'
400 write (iout,'(8a)') ' Res ',' dvb',' Theta',
401 & ' Phi',' Dsc_id',' Dsc',' Alpha',
404 write (iout,'(4a)') ' Res ',' dvb',' Theta',
413 if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
414 & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
415 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
418 vbld(i+1)=dist(i,i+1)
419 vbld_inv(i+1)=1.0d0/vbld(i+1)
420 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
421 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
423 c if (unres_pdb) then
424 c if (itype(1).eq.21) then
425 c theta(3)=90.0d0*deg2rad
426 c phi(4)=180.0d0*deg2rad
428 c vbld_inv(2)=1.0d0/vbld(2)
430 c if (itype(nres).eq.21) then
431 c theta(nres)=90.0d0*deg2rad
432 c phi(nres)=180.0d0*deg2rad
434 c vbld_inv(nres)=1.0d0/vbld(2)
440 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
441 & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
446 if (itype(i).ne.10) then
447 vbld_inv(i+nres)=1.0d0/di
449 vbld_inv(i+nres)=0.0d0
452 alph(i)=alpha(nres+i,i,maxres2)
453 omeg(i)=beta(nres+i,i,maxres2,i+1)
455 if(me.eq.king.or..not.out1file)then
457 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
458 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
459 & rad2deg*alph(i),rad2deg*omeg(i)
465 if(me.eq.king.or..not.out1file)
466 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
467 & rad2deg*theta(i),rad2deg*phi(i)
472 c-------------------------------------------------------------------------------
473 subroutine sc_loc_geom(lprn)
474 implicit real*8 (a-h,o-z)
479 include 'COMMON.LOCAL'
481 include 'COMMON.CHAIN'
482 include 'COMMON.INTERACT'
483 include 'COMMON.IOUNITS'
485 include 'COMMON.NAMES'
486 include 'COMMON.CONTROL'
487 include 'COMMON.SETUP'
488 double precision x_prime(3),y_prime(3),z_prime(3)
492 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
496 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
498 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
502 dc_norm(j,i+nres)=0.0d0
507 costtab(i+1) =dcos(theta(i+1))
508 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
509 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
510 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
511 cosfac2=0.5d0/(1.0d0+costtab(i+1))
512 cosfac=dsqrt(cosfac2)
513 sinfac2=0.5d0/(1.0d0-costtab(i+1))
514 sinfac=dsqrt(sinfac2)
516 if (it.ne.10 .and. itype(i).ne.ntyp1) then
518 C Compute the axes of tghe local cartesian coordinates system; store in
519 c x_prime, y_prime and z_prime
527 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
528 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
530 call vecpr(x_prime,y_prime,z_prime)
532 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
533 C to local coordinate system. Store in xx, yy, zz.
539 xx = xx + x_prime(j)*dc_norm(j,i+nres)
540 yy = yy + y_prime(j)*dc_norm(j,i+nres)
541 zz = zz + z_prime(j)*dc_norm(j,i+nres)
557 if(me.eq.king.or..not.out1file)
558 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
561 write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
568 c---------------------------------------------------------------------------
569 subroutine sccenter(ires,nscat,sccor)
570 implicit real*8 (a-h,o-z)
572 include 'COMMON.CHAIN'
573 dimension sccor(3,20)
577 sccmj=sccmj+sccor(j,i)
579 dc(j,ires)=sccmj/nscat
583 c---------------------------------------------------------------------------
584 subroutine bond_regular
585 implicit real*8 (a-h,o-z)
588 include 'COMMON.LOCAL'
589 include 'COMMON.CALC'
590 include 'COMMON.INTERACT'
591 include 'COMMON.CHAIN'
594 vbld_inv(i+1)=1.0d0/vbld(i+1)
595 vbld(i+1+nres)=dsc(iabs(itype(i+1)))
596 vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
597 c print *,vbld(i+1),vbld(i+1+nres)