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 include 'COMMON.SBRIDGE'
17 character*3 seq,atom,res
20 double precision e1(3),e2(3),e3(3)
21 integer rescode,iterter(maxres),cou
32 read (ipdbin,'(a80)',end=10) card
33 if (card(:5).eq.'HELIX') then
36 read(card(22:25),*) hfrag(1,nhfrag)
37 read(card(34:37),*) hfrag(2,nhfrag)
39 if (card(:5).eq.'SHEET') then
42 read(card(24:26),*) bfrag(1,nbfrag)
43 read(card(35:37),*) bfrag(2,nbfrag)
44 crc----------------------------------------
45 crc to be corrected !!!
46 bfrag(3,nbfrag)=bfrag(1,nbfrag)
47 bfrag(4,nbfrag)=bfrag(2,nbfrag)
48 crc----------------------------------------
50 if (card(:3).eq.'END') then
52 else if (card(:3).eq.'TER') then
55 itype(ires_old-1)=ntyp1
60 write (iout,*) "Chain ended",ires,ishift,ires_old
63 dc(j,ires)=sccor(j,iii)
66 call sccenter(ires,iii,sccor)
69 C Fish out the ATOM cards.
70 if (index(card(1:4),'ATOM').gt.0) then
71 read (card(14:16),'(a3)') atom
72 if (atom.eq.'CA' .or. atom.eq.'CH3') then
73 C Calculate the CM of the preceding residue.
77 dc(j,ires+nres)=sccor(j,iii)
80 call sccenter(ires,iii,sccor)
84 c write (iout,'(a80)') card
85 read (card(23:26),*) ires
86 read (card(18:20),'(a3)') res
89 if (res.ne.'GLY' .and. res.ne. 'ACE') then
93 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
95 else if (ibeg.eq.2) then
97 ishift=-ires_old+ires-1
98 c write (iout,*) "New chain started",ires,ishift
102 c write (2,*) "ires",ires," ishift",ishift
103 if (res.eq.'ACE') then
106 itype(ires)=rescode(ires,res,0)
108 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
109 read(card(61:66),*) bfac(ires)
110 if(me.eq.king.or..not.out1file)
111 & write (iout,'(2i3,2x,a,3f8.3)')
112 & ires,itype(ires),res,(c(j,ires),j=1,3)
115 sccor(j,iii)=c(j,ires)
117 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
118 & atom.ne.'N ' .and. atom.ne.'C ') then
120 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
124 10 if(me.eq.king.or..not.out1file)
125 & write (iout,'(a,i5)') ' Nres: ',ires
126 C Calculate dummy residue coordinates inside the "chain" of a multichain
130 write (iout,*) i,itype(i),itype(i+1)
131 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
132 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
133 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
134 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
135 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
137 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
138 print *,i,'tu dochodze'
139 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
147 c(j,i)=c(j,i-1)-1.9d0*e2(j)
151 dcj=(c(j,i-2)-c(j,i-3))/2.0
152 if (dcj.eq.0) dcj=1.23591524223
157 else !itype(i+1).eq.ntyp1
159 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
160 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
167 c(j,i)=c(j,i+1)-1.9d0*e2(j)
171 dcj=(c(j,i+3)-c(j,i+2))/2.0
172 if (dcj.eq.0) dcj=1.23591524223
177 endif !itype(i+1).eq.ntyp1
178 endif !itype.eq.ntyp1
180 C Calculate the CM of the last side chain.
183 dc(j,ires)=sccor(j,iii)
186 call sccenter(ires,iii,sccor)
190 if (itype(nres).ne.10) then
194 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
195 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
202 c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
206 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
207 if (dcj.eq.0) dcj=1.23591524223
208 c(j,nres)=c(j,nres-1)+dcj
209 c(j,2*nres)=c(j,nres)
220 c(j,2*nres)=c(j,nres)
222 if (itype(1).eq.ntyp1) then
226 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
227 call refsys(2,3,4,e1,e2,e3,fail)
234 c(j,1)=c(j,2)-1.9d0*e2(j)
238 dcj=(c(j,4)-c(j,3))/2.0
244 C Calculate internal coordinates.
245 if(me.eq.king.or..not.out1file)then
247 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
248 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
249 & (c(j,nres+ires),j=1,3)
252 C print *,"before int_from_cart"
253 call int_from_cart(.true.,.false.)
254 call sc_loc_geom(.true.)
261 dc(j,i)=c(j,i+1)-c(j,i)
262 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
267 dc(j,i+nres)=c(j,i+nres)-c(j,i)
268 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
270 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
274 C Copy the coordinates to reference coordinates
275 C Splits to single chain if occurs
281 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
283 if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
286 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
292 cref(j,i+nres,cou)=c(j,i+nres)
294 chain_rep(j,lll,kkk)=c(j,i)
295 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
299 write (iout,*) chain_length
300 if (chain_length.eq.0) chain_length=nres
302 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
303 chain_rep(j,chain_length+nres,symetr)
304 &=chain_rep(j,chain_length+nres,1)
307 c write (iout,*) "spraw lancuchy",chain_length,symetr
309 c do kkk=1,chain_length
310 c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
314 C makes copy of chains
316 write (iout,*) "symetr", symetr
318 if (symetr.gt.1) then
325 write(iout,*) (tabperm(i,kkk),kkk=1,4)
331 c write (iout,*) i,icha
332 do lll=1,chain_length
334 if (cou.le.nres) then
336 kupa=mod(lll,chain_length)
337 iprzes=(kkk-1)*chain_length+lll
338 if (kupa.eq.0) kupa=chain_length
339 c write (iout,*) "kupa", kupa
340 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
341 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
348 C-koniec robienia kopii
351 write (iout,*) "nowa struktura", nperm
353 write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
355 &cref(3,i,kkk),cref(1,nres+i,kkk),
356 &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
358 100 format (//' alpha-carbon coordinates ',
359 & ' centroid coordinates'/
360 1 ' ', 6X,'X',11X,'Y',11X,'Z',
361 & 10X,'X',11X,'Y',11X,'Z')
362 110 format (a,'(',i3,')',6f12.5)
368 bfrag(i,j)=bfrag(i,j)-ishift
374 hfrag(i,j)=hfrag(i,j)-ishift
379 c---------------------------------------------------------------------------
380 subroutine int_from_cart(lside,lprn)
381 implicit real*8 (a-h,o-z)
386 include 'COMMON.LOCAL'
388 include 'COMMON.CHAIN'
389 include 'COMMON.INTERACT'
390 include 'COMMON.IOUNITS'
392 include 'COMMON.NAMES'
393 include 'COMMON.CONTROL'
394 include 'COMMON.SETUP'
395 character*3 seq,atom,res
397 dimension sccor(3,20)
401 if(me.eq.king.or..not.out1file)then
405 & 'Internal coordinates calculated from crystal structure.'
407 write (iout,'(8a)') ' Res ',' dvb',' Theta',
408 & ' Phi',' Dsc_id',' Dsc',' Alpha',
411 write (iout,'(4a)') ' Res ',' dvb',' Theta',
420 if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
421 & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
422 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
425 vbld(i+1)=dist(i,i+1)
426 vbld_inv(i+1)=1.0d0/vbld(i+1)
427 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
428 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
430 c if (unres_pdb) then
431 c if (itype(1).eq.21) then
432 c theta(3)=90.0d0*deg2rad
433 c phi(4)=180.0d0*deg2rad
435 c vbld_inv(2)=1.0d0/vbld(2)
437 c if (itype(nres).eq.21) then
438 c theta(nres)=90.0d0*deg2rad
439 c phi(nres)=180.0d0*deg2rad
441 c vbld_inv(nres)=1.0d0/vbld(2)
448 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
449 & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
454 if (itype(i).ne.10) then
455 vbld_inv(i+nres)=1.0d0/di
457 vbld_inv(i+nres)=0.0d0
460 alph(i)=alpha(nres+i,i,maxres2)
461 omeg(i)=beta(nres+i,i,maxres2,i+1)
463 if(me.eq.king.or..not.out1file)then
465 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
466 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
467 & rad2deg*alph(i),rad2deg*omeg(i)
473 if(me.eq.king.or..not.out1file)
474 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
475 & rad2deg*theta(i),rad2deg*phi(i)
480 c-------------------------------------------------------------------------------
481 subroutine sc_loc_geom(lprn)
482 implicit real*8 (a-h,o-z)
487 include 'COMMON.LOCAL'
489 include 'COMMON.CHAIN'
490 include 'COMMON.INTERACT'
491 include 'COMMON.IOUNITS'
493 include 'COMMON.NAMES'
494 include 'COMMON.CONTROL'
495 include 'COMMON.SETUP'
496 double precision x_prime(3),y_prime(3),z_prime(3)
500 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
504 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
506 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
510 dc_norm(j,i+nres)=0.0d0
515 costtab(i+1) =dcos(theta(i+1))
516 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
517 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
518 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
519 cosfac2=0.5d0/(1.0d0+costtab(i+1))
520 cosfac=dsqrt(cosfac2)
521 sinfac2=0.5d0/(1.0d0-costtab(i+1))
522 sinfac=dsqrt(sinfac2)
524 if (it.ne.10 .and. itype(i).ne.ntyp1) then
526 C Compute the axes of tghe local cartesian coordinates system; store in
527 c x_prime, y_prime and z_prime
535 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
536 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
538 call vecpr(x_prime,y_prime,z_prime)
540 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
541 C to local coordinate system. Store in xx, yy, zz.
547 xx = xx + x_prime(j)*dc_norm(j,i+nres)
548 yy = yy + y_prime(j)*dc_norm(j,i+nres)
549 zz = zz + z_prime(j)*dc_norm(j,i+nres)
565 if(me.eq.king.or..not.out1file)
566 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
569 write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
576 c---------------------------------------------------------------------------
577 subroutine sccenter(ires,nscat,sccor)
578 implicit real*8 (a-h,o-z)
580 include 'COMMON.CHAIN'
581 dimension sccor(3,20)
585 sccmj=sccmj+sccor(j,i)
587 dc(j,ires)=sccmj/nscat
591 c---------------------------------------------------------------------------
592 subroutine bond_regular
593 implicit real*8 (a-h,o-z)
596 include 'COMMON.LOCAL'
597 include 'COMMON.CALC'
598 include 'COMMON.INTERACT'
599 include 'COMMON.CHAIN'
602 vbld_inv(i+1)=1.0d0/vbld(i+1)
603 vbld(i+1+nres)=dsc(iabs(itype(i+1)))
604 vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
605 c print *,vbld(i+1),vbld(i+1+nres)