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
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 if (res.eq.'Cl-' .or. res.eq.'Na+') then
121 else if (ibeg.eq.1) then
122 c write (iout,*) "BEG ires",ires
124 if (res.ne.'GLY' .and. res.ne. 'ACE') then
128 ires=ires-ishift+ishift1
130 ! write (iout,*) "ishift",ishift," ires",ires,&
131 ! " ires_old",ires_old
133 else if (ibeg.eq.2) then
135 ishift=-ires_old+ires-1 !!!!!
136 ishift1=ishift1-1 !!!!!
137 c write (iout,*) "New chain started",ires,ishift,ishift1,"!"
138 ires=ires-ishift+ishift1
142 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
143 ires=ires-ishift+ishift1
146 if (res.eq.'ACE' .or. res.eq.'NHE') then
149 itype(ires)=rescode(ires,res,0)
152 ires=ires-ishift+ishift1
154 c write (iout,*) "ires_old",ires_old," ires",ires
155 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
158 c write (2,*) "ires",ires," res ",res!," ity"!,ity
159 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
160 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
161 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
162 ! write (iout,*) "backbone ",atom
164 write (iout,'(i6,i3,2x,a,3f8.3)')
165 & ires,itype(ires),res,(c(j,ires),j=1,3)
169 sccor(j,iii)=c(j,ires)
171 c write (2,*) card(23:27),ires,itype(ires),iii
172 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
173 & atom.ne.'N' .and. atom.ne.'C' .and.
174 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
175 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
176 ! write (iout,*) "sidechain ",atom
178 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
179 c write (2,*) "iii",iii
183 10 if(me.eq.king.or..not.out1file)
184 & write (iout,'(a,i5)') ' Nres: ',ires
185 c write (iout,*) "iii",iii
186 C Calculate dummy residue coordinates inside the "chain" of a multichain
189 c write (iout,*) "dc"
191 c write (iout,'(i5,3f10.5)') i,(dc(j,i),j=1,3)
194 c write (iout,*) i,itype(i),itype(i+1),ntyp1,iterter(i)
195 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
196 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
197 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
198 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
199 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
201 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
202 c print *,i,'tu dochodze'
203 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
211 c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
215 dcj=(c(j,i-2)-c(j,i-3))/2.0
216 if (dcj.eq.0) dcj=1.23591524223
222 else !itype(i+1).eq.ntyp1
224 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
225 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
232 c(j,i)=c(j,i+1)-1.9d0*e2(j)
236 dcj=(c(j,i+3)-c(j,i+2))/2.0
237 if (dcj.eq.0) dcj=1.23591524223
243 endif !itype(i+1).eq.ntyp1
244 endif !itype.eq.ntyp1
246 write (iout,*) "After loop in readpbd"
247 C Calculate the CM of the last side chain.
248 if (.not. sccalc) then
251 dc(j,ires)=sccor(j,iii)
254 c write (iout,*) "Calling sccenter iii",iii
255 call sccenter(ires,iii,sccor)
260 if (itype(nres).ne.10) then
264 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
265 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
272 c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
276 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
277 if (dcj.eq.0) dcj=1.23591524223
278 c(j,nres)=c(j,nres-1)+dcj
279 c(j,2*nres)=c(j,nres)
290 c(j,2*nres)=c(j,nres)
292 if (itype(1).eq.ntyp1) then
296 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
297 call refsys(2,3,4,e1,e2,e3,fail)
304 c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
308 dcj=(c(j,4)-c(j,3))/2.0
314 C Calculate internal coordinates.
315 if(me.eq.king.or..not.out1file)then
317 & "Cartesian coordinates of the reference structure"
318 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
319 & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
321 write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
322 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
323 & (c(j,ires+nres),j=1,3)
329 zero=zero.or.itype(ires).eq.0
332 write (iout,'(2a)') "Gaps in PDB coordinates detected;",
333 & " look for ZERO in the control output above."
334 write (iout,'(2a)') "Repair the PDB file using MODELLER",
335 & " or other softwared and resubmit."
339 c write(iout,*)"before int_from_cart nres",nres
340 call int_from_cart(.true.,.false.)
348 dc(j,i)=c(j,i+1)-c(j,i)
349 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
351 c write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3),
356 dc(j,i+nres)=c(j,i+nres)-c(j,i)
357 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
359 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
362 call sc_loc_geom(.false.)
363 call int_from_cart1(.false.)
365 C Copy the coordinates to reference coordinates
369 cref(j,i+nres)=c(j,i+nres)
372 100 format (//' alpha-carbon coordinates ',
373 & ' centroid coordinates'/
374 1 ' ', 7X,'X',11X,'Y',11X,'Z',
375 & 10X,'X',11X,'Y',11X,'Z')
376 110 format (a,'(',i4,')',6f12.5)
380 bfrag(i,j)=bfrag(i,j)-ishift
386 hfrag(i,j)=hfrag(i,j)-ishift
391 c---------------------------------------------------------------------------
392 subroutine readpdb_template(k)
393 C Read the PDB file for read_constr_homology with read2sigma
394 C and convert the peptide geometry into virtual-chain geometry.
397 include 'COMMON.LOCAL'
399 include 'COMMON.CHAIN'
400 include 'COMMON.INTERACT'
401 include 'COMMON.IOUNITS'
403 include 'COMMON.NAMES'
404 include 'COMMON.CONTROL'
405 include 'COMMON.FRAG'
406 include 'COMMON.SETUP'
407 integer i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
409 logical lprn /.false./,fail
410 double precision e1(3),e2(3),e3(3)
411 double precision dcj,efree_temp
415 double precision sccor(3,20)
416 integer rescode,iterter(maxres)
423 c write (2,*) "UNRES_PDB",unres_pdb
431 read (ipdbin,'(a80)',end=10) card
432 if (card(:3).eq.'END') then
434 else if (card(:3).eq.'TER') then
437 itype(ires_old-1)=ntyp1
438 iterter(ires_old-1)=1
439 itype(ires_old)=ntyp1
442 c write (iout,*) "Chain ended",ires,ishift,ires_old
445 dc(j,ires)=sccor(j,iii)
448 call sccenter(ires,iii,sccor)
451 C Fish out the ATOM cards.
452 if (index(card(1:4),'ATOM').gt.0) then
453 read (card(12:16),*) atom
454 c write (iout,*) "! ",atom," !",ires
455 c if (atom.eq.'CA' .or. atom.eq.'CH3') then
456 read (card(23:26),*) ires
457 read (card(18:20),'(a3)') res
458 c write (iout,*) "ires",ires,ires-ishift+ishift1,
459 c & " ires_old",ires_old
460 c write (iout,*) "ishift",ishift," ishift1",ishift1
461 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
462 if (ires-ishift+ishift1.ne.ires_old) then
463 C Calculate the CM of the preceding residue.
467 dc(j,ires_old)=sccor(j,iii)
470 call sccenter(ires_old,iii,sccor)
475 if (res.eq.'Cl-' .or. res.eq.'Na+') then
478 else if (ibeg.eq.1) then
479 c write (iout,*) "BEG ires",ires
481 if (res.ne.'GLY' .and. res.ne. 'ACE') then
485 ires=ires-ishift+ishift1
487 c write (iout,*) "ishift",ishift," ires",ires,
488 c & " ires_old",ires_old
489 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
491 else if (ibeg.eq.2) then
493 ishift=-ires_old+ires-1
495 c write (iout,*) "New chain started",ires,ishift
498 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
499 ires=ires-ishift+ishift1
502 if (res.eq.'ACE' .or. res.eq.'NHE') then
505 itype(ires)=rescode(ires,res,0)
508 ires=ires-ishift+ishift1
510 c write (iout,*) "ires_old",ires_old," ires",ires
511 c if (card(27:27).eq."A" .or. card(27:27).eq."B") then
514 c write (2,*) "ires",ires," res ",res," ity",ity
515 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
516 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
517 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
518 c write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
520 write (iout,'(2i3,2x,a,3f8.3)')
521 & ires,itype(ires),res,(c(j,ires),j=1,3)
525 sccor(j,iii)=c(j,ires)
527 if (ishift.ne.0) then
528 ires_ca=ires+ishift-ishift1
532 c write (*,*) card(23:27),ires,itype(ires)
533 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
534 & atom.ne.'N' .and. atom.ne.'C' .and.
535 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
536 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
537 c write (iout,*) "sidechain ",atom
539 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
543 10 if(me.eq.king.or..not.out1file)
544 & write (iout,'(a,i5)') ' Nres: ',ires
545 C Calculate dummy residue coordinates inside the "chain" of a multichain
549 c write (iout,*) i,itype(i),itype(i+1)
550 if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
551 if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
552 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
553 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
554 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
556 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
557 call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
564 c(j,i)=c(j,i-1)-1.9d0*e2(j)
568 dcj=(c(j,i-2)-c(j,i-3))/2.0
569 if (dcj.eq.0) dcj=1.23591524223
574 else !itype(i+1).eq.ntyp1
576 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
577 call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
584 c(j,i)=c(j,i+1)-1.9d0*e2(j)
588 dcj=(c(j,i+3)-c(j,i+2))/2.0
589 if (dcj.eq.0) dcj=1.23591524223
594 endif !itype(i+1).eq.ntyp1
595 endif !itype.eq.ntyp1
597 C Calculate the CM of the last side chain.
600 dc(j,ires)=sccor(j,iii)
603 call sccenter(ires,iii,sccor)
607 if (itype(nres).ne.10) then
611 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
612 call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
619 c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
623 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
624 if (dcj.eq.0) dcj=1.23591524223
625 c(j,nres)=c(j,nres-1)+dcj
626 c(j,2*nres)=c(j,nres)
637 c(j,2*nres)=c(j,nres)
639 if (itype(1).eq.ntyp1) then
643 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
644 call refsys(2,3,4,e1,e2,e3,fail)
651 c(j,1)=c(j,2)-1.9d0*e2(j)
655 dcj=(c(j,4)-c(j,3))/2.0
661 C Copy the coordinates to reference coordinates
667 C Calculate internal coordinates.
668 if (out_template_coord) then
670 & "Cartesian coordinates of the reference structure"
671 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
672 & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
674 write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
675 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
676 & (c(j,ires+nres),j=1,3)
679 C Calculate internal coordinates.
680 call int_from_cart(.true.,out_template_coord)
681 call sc_loc_geom(.false.)
688 dc(j,i)=c(j,i+1)-c(j,i)
689 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
694 dc(j,i+nres)=c(j,i+nres)-c(j,i)
695 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
697 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
703 cref(j,i+nres)=c(j,i+nres)