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 read(card(61:66),*) bfac(ires)
167 c write (iout,*) "backbone ",atom
168 c write (iout,*) ires,res,(c(j,ires),j=1,3)
170 write (iout,'(i6,i3,2x,a,3f8.3)')
171 & ires,itype(ires),res,(c(j,ires),j=1,3)
175 sccor(j,iii)=c(j,ires)
177 c write (2,*) card(23:27),ires,itype(ires),iii
178 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
179 & atom.ne.'N' .and. atom.ne.'C' .and.
180 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
181 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
182 ! write (iout,*) "sidechain ",atom
184 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
185 c write (2,*) "iii",iii
189 10 if(me.eq.king.or..not.out1file)
190 & write (iout,'(a,i7)') ' Nres: ',ires
191 c write (iout,*) "iii",iii
192 C Calculate dummy residue coordinates inside the "chain" of a multichain
195 c write (iout,*) "dc"
197 c write (iout,'(i5,3f10.5)') i,(dc(j,i),j=1,3)
200 c write (iout,*) i,itype(i),itype(i+1),ntyp1,iterter(i)
201 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
202 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
203 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
204 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
205 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
207 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
208 c print *,i,'tu dochodze'
209 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
217 c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
221 dcj=(c(j,i-2)-c(j,i-3))/2.0
222 if (dcj.eq.0) dcj=1.23591524223
228 else !itype(i+1).eq.ntyp1
230 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
231 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
238 c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
242 dcj=(c(j,i+3)-c(j,i+2))/2.0
243 if (dcj.eq.0) dcj=1.23591524223
249 endif !itype(i+1).eq.ntyp1
250 endif !itype.eq.ntyp1
252 write (iout,*) "After loop in readpbd"
253 C Calculate the CM of the last side chain.
254 if (.not. sccalc) then
257 dc(j,ires)=sccor(j,iii)
260 c write (iout,*) "Calling sccenter iii",iii
261 call sccenter(ires,iii,sccor)
266 if (itype(nres).ne.10) then
270 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
271 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
278 c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
282 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
283 if (dcj.eq.0) dcj=1.23591524223
284 c(j,nres)=c(j,nres-1)+dcj
285 c(j,2*nres)=c(j,nres)
296 c(j,2*nres)=c(j,nres)
298 if (itype(1).eq.ntyp1) then
302 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
303 call refsys(2,3,4,e1,e2,e3,fail)
310 c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
314 dcj=(c(j,4)-c(j,3))/2.0
320 C Calculate internal coordinates.
321 if(me.eq.king.or..not.out1file)then
323 & "Cartesian coordinates of the reference structure"
324 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
325 & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
327 write (iout,'(a3,1x,i6,3f8.3,5x,3f8.3)')
328 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
329 & (c(j,ires+nres),j=1,3)
335 zero=zero.or.itype(ires).eq.0
338 write (iout,'(2a)') "Gaps in PDB coordinates detected;",
339 & " look for ZERO in the control output above."
340 write (iout,'(2a)') "Repair the PDB file using MODELLER",
341 & " or other softwared and resubmit."
345 c write(iout,*)"before int_from_cart nres",nres
346 call int_from_cart(.true.,.false.)
354 dc(j,i)=c(j,i+1)-c(j,i)
355 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
357 c write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3),
362 dc(j,i+nres)=c(j,i+nres)-c(j,i)
363 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
365 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
368 call sc_loc_geom(.false.)
369 call int_from_cart1(.false.)
371 C Copy the coordinates to reference coordinates
375 cref(j,i+nres)=c(j,i+nres)
378 100 format (//' alpha-carbon coordinates ',
379 & ' centroid coordinates'/
380 1 ' ', 7X,'X',11X,'Y',11X,'Z',
381 & 10X,'X',11X,'Y',11X,'Z')
382 110 format (a,'(',i4,')',6f12.5)
386 bfrag(i,j)=bfrag(i,j)-ishift
392 hfrag(i,j)=hfrag(i,j)-ishift
397 c---------------------------------------------------------------------------
398 subroutine readpdb_template(k)
399 C Read the PDB file for read_constr_homology with read2sigma
400 C and convert the peptide geometry into virtual-chain geometry.
403 include 'COMMON.LOCAL'
405 include 'COMMON.CHAIN'
406 include 'COMMON.INTERACT'
407 include 'COMMON.IOUNITS'
409 include 'COMMON.NAMES'
410 include 'COMMON.CONTROL'
411 include 'COMMON.FRAG'
412 include 'COMMON.SETUP'
413 integer i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
415 logical lprn /.false./,fail
416 double precision e1(3),e2(3),e3(3)
417 double precision dcj,efree_temp
421 double precision sccor(3,50)
422 integer rescode,iterter(maxres)
430 c write (2,*) "UNRES_PDB",unres_pdb
438 read (ipdbin,'(a80)',end=10) card
439 if (card(:3).eq.'END') then
441 else if (card(:3).eq.'TER') then
444 itype(ires_old-1)=ntyp1
445 iterter(ires_old-1)=1
446 itype(ires_old)=ntyp1
449 c write (iout,*) "Chain ended",ires,ishift,ires_old
452 dc(j,ires)=sccor(j,iii)
455 call sccenter(ires,iii,sccor)
458 C Fish out the ATOM cards.
459 if (index(card(1:4),'ATOM').gt.0) then
460 read (card(12:16),*) atom
461 c write (iout,*) "! ",atom," !",ires
462 c if (atom.eq.'CA' .or. atom.eq.'CH3') then
463 read (card(23:26),*) ires
464 read (card(18:20),'(a3)') res
465 c write (iout,*) "ires",ires,ires-ishift+ishift1,
466 c & " ires_old",ires_old
467 c write (iout,*) "ishift",ishift," ishift1",ishift1
468 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
469 if (ires-ishift+ishift1.ne.ires_old) then
470 C Calculate the CM of the preceding residue.
474 dc(j,ires_old)=sccor(j,iii)
477 call sccenter(ires_old,iii,sccor)
482 if (res.eq.'Cl-' .or. res.eq.'Na+') then
485 else if (ibeg.eq.1) then
486 c write (iout,*) "BEG ires",ires
488 if (res.ne.'GLY' .and. res.ne. 'ACE') then
492 ires=ires-ishift+ishift1
494 c write (iout,*) "ishift",ishift," ires",ires,
495 c & " ires_old",ires_old
496 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
498 else if (ibeg.eq.2) then
500 ishift=-ires_old+ires-1
502 c write (iout,*) "New chain started",ires,ishift
505 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
506 ires=ires-ishift+ishift1
509 if (res.eq.'ACE' .or. res.eq.'NHE') then
512 itype(ires)=rescode(ires,res,0)
515 ires=ires-ishift+ishift1
517 c write (iout,*) "ires_old",ires_old," ires",ires
518 c if (card(27:27).eq."A" .or. card(27:27).eq."B") then
521 c write (2,*) "ires",ires," res ",res," ity",ity
522 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
523 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
524 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
525 c write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
527 write (iout,'(2i3,2x,a,3f8.3)')
528 & ires,itype(ires),res,(c(j,ires),j=1,3)
532 sccor(j,iii)=c(j,ires)
534 if (ishift.ne.0) then
535 ires_ca=ires+ishift-ishift1
539 c write (*,*) card(23:27),ires,itype(ires)
540 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
541 & atom.ne.'N' .and. atom.ne.'C' .and.
542 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
543 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
544 c write (iout,*) "sidechain ",atom
546 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
550 10 if(me.eq.king.or..not.out1file)
551 & write (iout,'(a,i7)') ' Nres: ',ires
552 C Calculate dummy residue coordinates inside the "chain" of a multichain
556 c write (iout,*) i,itype(i),itype(i+1)
557 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
558 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
559 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
560 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
561 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
563 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
564 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
571 c(j,i)=c(j,i-1)-1.9d0*e2(j)
575 dcj=(c(j,i-2)-c(j,i-3))/2.0
576 if (dcj.eq.0) dcj=1.23591524223
581 else !itype(i+1).eq.ntyp1
583 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
584 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
591 c(j,i)=c(j,i+1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
595 dcj=(c(j,i+3)-c(j,i+2))/2.0
596 if (dcj.eq.0) dcj=1.23591524223
601 endif !itype(i+1).eq.ntyp1
602 endif !itype.eq.ntyp1
604 C Calculate the CM of the last side chain.
607 dc(j,ires)=sccor(j,iii)
610 call sccenter(ires,iii,sccor)
614 if (itype(nres).ne.10) then
618 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
619 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
626 c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
630 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
631 if (dcj.eq.0) dcj=1.23591524223
632 c(j,nres)=c(j,nres-1)+dcj
633 c(j,2*nres)=c(j,nres)
644 c(j,2*nres)=c(j,nres)
646 if (itype(1).eq.ntyp1) then
650 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
651 call refsys(2,3,4,e1,e2,e3,fail)
658 c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
662 dcj=(c(j,4)-c(j,3))/2.0
668 C Copy the coordinates to reference coordinates
674 C Calculate internal coordinates.
675 if (out_template_coord) then
677 & "Cartesian coordinates of the reference structure"
678 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
679 & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
681 write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
682 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
683 & (c(j,ires+nres),j=1,3)
688 zero=zero.or.itype(ires).eq.0
691 write (iout,'(2a)') "Gaps in PDB coordinates detected;",
692 & " look for ZERO in the control output above."
693 write (iout,'(2a)') "Repair the PDB file using MODELLER",
694 & " or other softwared and resubmit."
698 C Calculate internal coordinates.
699 call int_from_cart(.true.,out_template_coord)
700 call sc_loc_geom(.false.)
708 dc(j,i)=c(j,i+1)-c(j,i)
709 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
714 dc(j,i+nres)=c(j,i+nres)-c(j,i)
715 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
717 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
723 cref(j,i+nres)=c(j,i+nres)