2 C Read the PDB file and convert the peptide geometry into virtual-chain
9 include 'COMMON.INTERACT'
10 include 'COMMON.IOUNITS'
12 include 'COMMON.NAMES'
13 include 'COMMON.CONTROL'
15 include 'COMMON.SETUP'
16 include 'COMMON.SBRIDGE'
17 character*3 seq,atom,res
19 double precision sccor(3,50)
20 double precision e1(3),e2(3),e3(3)
21 integer rescode,iterter(maxres),cou
23 integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg,ifree
24 double precision dcj!,efree_temp
38 read (ipdbin,'(a80)',end=10) card
39 c write (iout,'(a)') card
41 if (card(:5).eq.'HELIX') then
44 read(card(22:25),*) hfrag(1,nhfrag)
45 read(card(34:37),*) hfrag(2,nhfrag)
47 if (card(:5).eq.'SHEET') then
50 read(card(24:26),*) bfrag(1,nbfrag)
51 read(card(35:37),*) bfrag(2,nbfrag)
52 !rc----------------------------------------
53 !rc to be corrected !!!
54 bfrag(3,nbfrag)=bfrag(1,nbfrag)
55 bfrag(4,nbfrag)=bfrag(2,nbfrag)
56 !rc----------------------------------------
58 if (card(:3).eq.'END') then
60 else if (card(:3).eq.'TER') then
63 itype(ires_old-1)=ntyp1
69 write (iout,*) "Chain ended",ires,ishift,ires_old,ibeg
72 dc(j,ires)=sccor(j,iii)
75 call sccenter(ires,iii,sccor)
81 c if (index(card,"FREE ENERGY").gt.0) then
82 c ifree=index(card,"FREE ENERGY")+12
83 c read(card(ifree:),*,err=1115,end=1115) efree_temp
86 ! Fish out the ATOM cards.
87 if (index(card(1:4),'ATOM').gt.0) then
89 read (card(12:16),*) atom
90 c write (2,'(a)') card
91 c write (iout,*) "ibeg",ibeg
92 c write (iout,*) "! ",atom," !",ires
93 ! if (atom.eq.'CA' .or. atom.eq.'CH3') then
94 read (card(23:26),*) ires
95 read (card(18:20),'(a3)') res
96 c write (iout,*) "ires",ires,ires-ishift+ishift1,
97 c & " ires_old",ires_old
98 c write (iout,*) "ishift",ishift," ishift1",ishift1
99 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
100 if (ires-ishift+ishift1.ne.ires_old) then
101 ! Calculate the CM of the preceding residue.
102 ! if (ibeg.eq.0) call sccenter(ires,iii,sccor)
104 c write (iout,*) "Calculating sidechain center iii",iii
105 c write (iout,*) "ires",ires
107 c write (iout,'(i5,3f10.5)') ires,(sccor(j,iii),j=1,3)
109 dc(j,ires_old)=sccor(j,iii)
112 call sccenter(ires_old,iii,sccor)
118 c write (iout,*) "ibeg",ibeg
119 if (res.eq.'Cl-' .or. res.eq.'Na+') then
122 else if (ibeg.eq.1) then
123 c write (iout,*) "BEG ires",ires
125 if (res.ne.'GLY' .and. res.ne. 'ACE') then
129 ires=ires-ishift+ishift1
131 ! write (iout,*) "ishift",ishift," ires",ires,&
132 ! " ires_old",ires_old
134 else if (ibeg.eq.2) then
136 ishift=-ires_old+ires-1 !!!!!
137 c ishift1=ishift1-1 !!!!!
138 c write (iout,*) "New chain started",ires,ires_old,ishift,
140 ires=ires-ishift+ishift1
141 write (iout,*) "New chain started ires",ires
146 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
147 ires=ires-ishift+ishift1
150 if (res.eq.'ACE' .or. res.eq.'NHE') then
153 itype(ires)=rescode(ires,res,0)
156 ires=ires-ishift+ishift1
158 c write (iout,*) "ires_old",ires_old," ires",ires
159 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
162 c write (2,*) "ires",ires," res ",res!," ity"!,ity
163 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
164 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
165 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
166 c write (iout,*) "backbone ",atom
167 c write (iout,*) ires,res,(c(j,ires),j=1,3)
169 write (iout,'(i6,i3,2x,a,3f8.3)')
170 & ires,itype(ires),res,(c(j,ires),j=1,3)
174 sccor(j,iii)=c(j,ires)
176 c write (2,*) card(23:27),ires,itype(ires),iii
177 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
178 & atom.ne.'N' .and. atom.ne.'C' .and.
179 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
180 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
181 ! write (iout,*) "sidechain ",atom
183 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
184 c write (2,*) "iii",iii
188 10 if(me.eq.king.or..not.out1file)
189 & write (iout,'(a,i5)') ' Nres: ',ires
190 c write (iout,*) "iii",iii
191 C Calculate dummy residue coordinates inside the "chain" of a multichain
194 c write (iout,*) "dc"
196 c write (iout,'(i5,3f10.5)') i,(dc(j,i),j=1,3)
199 c write (iout,*) i,itype(i),itype(i+1),ntyp1,iterter(i)
200 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
201 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
202 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
203 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
204 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
206 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
207 c print *,i,'tu dochodze'
208 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
216 c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
220 dcj=(c(j,i-2)-c(j,i-3))/2.0
221 if (dcj.eq.0) dcj=1.23591524223
227 else !itype(i+1).eq.ntyp1
229 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
230 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
237 c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
241 dcj=(c(j,i+3)-c(j,i+2))/2.0
242 if (dcj.eq.0) dcj=1.23591524223
248 endif !itype(i+1).eq.ntyp1
249 endif !itype.eq.ntyp1
251 write (iout,*) "After loop in readpbd"
252 C Calculate the CM of the last side chain.
253 if (.not. sccalc) then
256 dc(j,ires)=sccor(j,iii)
259 c write (iout,*) "Calling sccenter iii",iii
260 call sccenter(ires,iii,sccor)
265 if (itype(nres).ne.10) then
269 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
270 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
277 c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
281 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
282 if (dcj.eq.0) dcj=1.23591524223
283 c(j,nres)=c(j,nres-1)+dcj
284 c(j,2*nres)=c(j,nres)
295 c(j,2*nres)=c(j,nres)
297 if (itype(1).eq.ntyp1) then
301 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
302 call refsys(2,3,4,e1,e2,e3,fail)
309 c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
313 dcj=(c(j,4)-c(j,3))/2.0
319 C Calculate internal coordinates.
320 if(me.eq.king.or..not.out1file)then
322 & "Cartesian coordinates of the reference structure"
323 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
324 & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
326 write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
327 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
328 & (c(j,ires+nres),j=1,3)
334 zero=zero.or.itype(ires).eq.0
337 write (iout,'(2a)') "Gaps in PDB coordinates detected;",
338 & " look for ZERO in the control output above."
339 write (iout,'(2a)') "Repair the PDB file using MODELLER",
340 & " or other softwared and resubmit."
344 c write(iout,*)"before int_from_cart nres",nres
345 call int_from_cart(.true.,.false.)
353 dc(j,i)=c(j,i+1)-c(j,i)
354 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
356 c write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3),
361 dc(j,i+nres)=c(j,i+nres)-c(j,i)
362 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
364 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
367 call sc_loc_geom(.false.)
368 call int_from_cart1(.false.)
370 C Copy the coordinates to reference coordinates
374 cref(j,i+nres)=c(j,i+nres)
377 100 format (//' alpha-carbon coordinates ',
378 & ' centroid coordinates'/
379 1 ' ', 7X,'X',11X,'Y',11X,'Z',
380 & 10X,'X',11X,'Y',11X,'Z')
381 110 format (a,'(',i4,')',6f12.5)
385 bfrag(i,j)=bfrag(i,j)-ishift
391 hfrag(i,j)=hfrag(i,j)-ishift
396 c---------------------------------------------------------------------------
397 subroutine readpdb_template(k)
398 C Read the PDB file for read_constr_homology with read2sigma
399 C and convert the peptide geometry into virtual-chain geometry.
402 include 'COMMON.LOCAL'
404 include 'COMMON.CHAIN'
405 include 'COMMON.INTERACT'
406 include 'COMMON.IOUNITS'
408 include 'COMMON.NAMES'
409 include 'COMMON.CONTROL'
410 include 'COMMON.FRAG'
411 include 'COMMON.SETUP'
412 integer i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
414 logical lprn /.false./,fail
415 double precision e1(3),e2(3),e3(3)
416 double precision dcj,efree_temp
420 double precision sccor(3,50)
421 integer rescode,iterter(maxres)
429 c write (2,*) "UNRES_PDB",unres_pdb
437 read (ipdbin,'(a80)',end=10) card
438 if (card(:3).eq.'END') then
440 else if (card(:3).eq.'TER') then
443 itype(ires_old-1)=ntyp1
444 iterter(ires_old-1)=1
445 itype(ires_old)=ntyp1
448 c write (iout,*) "Chain ended",ires,ishift,ires_old
451 dc(j,ires)=sccor(j,iii)
454 call sccenter(ires,iii,sccor)
457 C Fish out the ATOM cards.
458 if (index(card(1:4),'ATOM').gt.0) then
459 read (card(12:16),*) atom
460 c write (iout,*) "! ",atom," !",ires
461 c if (atom.eq.'CA' .or. atom.eq.'CH3') then
462 read (card(23:26),*) ires
463 read (card(18:20),'(a3)') res
464 c write (iout,*) "ires",ires,ires-ishift+ishift1,
465 c & " ires_old",ires_old
466 c write (iout,*) "ishift",ishift," ishift1",ishift1
467 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
468 if (ires-ishift+ishift1.ne.ires_old) then
469 C Calculate the CM of the preceding residue.
473 dc(j,ires_old)=sccor(j,iii)
476 call sccenter(ires_old,iii,sccor)
481 if (res.eq.'Cl-' .or. res.eq.'Na+') then
484 else if (ibeg.eq.1) then
485 c write (iout,*) "BEG ires",ires
487 if (res.ne.'GLY' .and. res.ne. 'ACE') then
491 ires=ires-ishift+ishift1
493 c write (iout,*) "ishift",ishift," ires",ires,
494 c & " ires_old",ires_old
495 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
497 else if (ibeg.eq.2) then
499 ishift=-ires_old+ires-1
501 c write (iout,*) "New chain started",ires,ishift
504 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
505 ires=ires-ishift+ishift1
508 if (res.eq.'ACE' .or. res.eq.'NHE') then
511 itype(ires)=rescode(ires,res,0)
514 ires=ires-ishift+ishift1
516 c write (iout,*) "ires_old",ires_old," ires",ires
517 c if (card(27:27).eq."A" .or. card(27:27).eq."B") then
520 c write (2,*) "ires",ires," res ",res," ity",ity
521 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
522 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
523 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
524 c write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
526 write (iout,'(2i3,2x,a,3f8.3)')
527 & ires,itype(ires),res,(c(j,ires),j=1,3)
531 sccor(j,iii)=c(j,ires)
533 if (ishift.ne.0) then
534 ires_ca=ires+ishift-ishift1
538 c write (*,*) card(23:27),ires,itype(ires)
539 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
540 & atom.ne.'N' .and. atom.ne.'C' .and.
541 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
542 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
543 c write (iout,*) "sidechain ",atom
545 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
549 10 if(me.eq.king.or..not.out1file)
550 & write (iout,'(a,i5)') ' Nres: ',ires
551 C Calculate dummy residue coordinates inside the "chain" of a multichain
555 c write (iout,*) i,itype(i),itype(i+1)
556 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
557 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
558 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
559 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
560 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
562 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
563 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
570 c(j,i)=c(j,i-1)-1.9d0*e2(j)
574 dcj=(c(j,i-2)-c(j,i-3))/2.0
575 if (dcj.eq.0) dcj=1.23591524223
580 else !itype(i+1).eq.ntyp1
582 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
583 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
590 c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
594 dcj=(c(j,i+3)-c(j,i+2))/2.0
595 if (dcj.eq.0) dcj=1.23591524223
600 endif !itype(i+1).eq.ntyp1
601 endif !itype.eq.ntyp1
603 C Calculate the CM of the last side chain.
606 dc(j,ires)=sccor(j,iii)
609 call sccenter(ires,iii,sccor)
613 if (itype(nres).ne.10) then
617 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
618 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
625 c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
629 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
630 if (dcj.eq.0) dcj=1.23591524223
631 c(j,nres)=c(j,nres-1)+dcj
632 c(j,2*nres)=c(j,nres)
643 c(j,2*nres)=c(j,nres)
645 if (itype(1).eq.ntyp1) then
649 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
650 call refsys(2,3,4,e1,e2,e3,fail)
657 c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
661 dcj=(c(j,4)-c(j,3))/2.0
667 C Copy the coordinates to reference coordinates
673 C Calculate internal coordinates.
674 if (out_template_coord) then
676 & "Cartesian coordinates of the reference structure"
677 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
678 & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
680 write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
681 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
682 & (c(j,ires+nres),j=1,3)
687 zero=zero.or.itype(ires).eq.0
690 write (iout,'(2a)') "Gaps in PDB coordinates detected;",
691 & " look for ZERO in the control output above."
692 write (iout,'(2a)') "Repair the PDB file using MODELLER",
693 & " or other softwared and resubmit."
697 C Calculate internal coordinates.
698 call int_from_cart(.true.,out_template_coord)
699 call sc_loc_geom(.false.)
707 dc(j,i)=c(j,i+1)-c(j,i)
708 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
713 dc(j,i+nres)=c(j,i+nres)-c(j,i)
714 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
716 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
722 cref(j,i+nres)=c(j,i+nres)