2 C Read the PDB file and convert the peptide geometry into virtual-chain
4 implicit real*8 (a-h,o-z)
6 include 'DIMENSIONS.ZSCOPT'
10 include 'COMMON.CHAIN'
11 include 'COMMON.INTERACT'
12 include 'COMMON.IOUNITS'
14 include 'COMMON.NAMES'
15 include 'COMMON.CONTROL'
16 c include 'COMMON.DISTFIT'
17 include 'COMMON.SETUP'
18 integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
20 logical lprn /.false./,fail
21 double precision e1(3),e2(3),e3(3)
22 double precision dcj,efree_temp
26 double precision sccor(3,20)
33 c write (2,*) "UNRES_PDB",unres_pdb
41 read (ipdbin,'(a80)',end=10) card
42 c write (iout,'(a)') card
43 if (card(:5).eq.'HELIX') then
46 read(card(22:25),*) hfrag(1,nhfrag)
47 read(card(34:37),*) hfrag(2,nhfrag)
49 if (card(:5).eq.'SHEET') then
52 read(card(24:26),*) bfrag(1,nbfrag)
53 read(card(35:37),*) bfrag(2,nbfrag)
54 crc----------------------------------------
55 crc to be corrected !!!
56 bfrag(3,nbfrag)=bfrag(1,nbfrag)
57 bfrag(4,nbfrag)=bfrag(2,nbfrag)
58 crc----------------------------------------
60 if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
62 if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
63 C Fish out the ATOM cards.
64 if (index(card(1:4),'ATOM').gt.0) then
65 read (card(12:16),*) atom
66 c write (iout,*) "! ",atom," !",ires
67 c if (atom.eq.'CA' .or. atom.eq.'CH3') then
68 read (card(23:26),*) ires
69 read (card(18:20),'(a3)') res
70 c write (iout,*) "ires",ires,ires-ishift+ishift1,
71 c & " ires_old",ires_old
72 c write (iout,*) "ishift",ishift," ishift1",ishift1
73 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
74 if (ires-ishift+ishift1.ne.ires_old) then
75 C Calculate the CM of the preceding residue.
76 c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
78 c write (iout,*) "Calculating sidechain center iii",iii
81 c dc(j,ires)=sccor(j,iii)
84 call sccenter(ires_old,iii,sccor)
89 if (res.eq.'Cl-' .or. res.eq.'Na+') then
92 else if (ibeg.eq.1) then
93 c write (iout,*) "BEG ires",ires
95 if (res.ne.'GLY' .and. res.ne. 'ACE') then
99 ires=ires-ishift+ishift1
101 c write (iout,*) "ishift",ishift," ires",ires,
102 c & " ires_old",ires_old
105 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
106 ires=ires-ishift+ishift1
109 if (res.eq.'ACE' .or. res.eq.'NHE') then
112 itype(ires)=rescode(ires,res,0)
115 ires=ires-ishift+ishift1
117 c write (iout,*) "ires_old",ires_old," ires",ires
118 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
121 c write (2,*) "ires",ires," res ",res," ity",ity
122 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
123 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
124 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
125 c write (iout,*) "backbone ",atom
127 write (iout,'(2i3,2x,a,3f8.3)')
128 & ires,itype(ires),res,(c(j,ires),j=1,3)
132 sccor(j,iii)=c(j,ires)
134 if (ishift.ne.0) then
135 ires_ca=ires+ishift-ishift1
139 c write (*,*) card(23:27),ires,itype(ires)
140 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
141 & atom.ne.'N' .and. atom.ne.'C' .and.
142 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
143 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
144 c write (iout,*) "sidechain ",atom
146 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
152 write (iout,'(a,i5)') ' Number of residues found: ',ires
154 if (ires.eq.0) return
155 C Calculate the CM of the last side chain.
157 c if (unres_pdb) then
159 c dc(j,ires)=sccor(j,iii)
162 call sccenter(ires,iii,sccor)
168 if (itype(nres).ne.10) then
172 dcj=c(j,nres-2)-c(j,nres-3)
173 c(j,nres)=c(j,nres-1)+dcj
174 c(j,2*nres)=c(j,nres)
184 c(j,2*nres)=c(j,nres)
186 if (itype(1).eq.21) then
189 c if (unres_pdb) then
190 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
191 c call refsys(2,3,4,e1,e2,e3,fail)
198 c c(j,1)=c(j,2)-3.8d0*e2(j)
208 C Copy the coordinates to reference coordinates
214 C Calculate internal coordinates.
217 & "Cartesian coordinates of the reference structure"
218 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
219 & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
221 write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
222 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
223 & (c(j,ires+nres),j=1,3)
226 C Calculate internal coordinates.
227 if(me.eq.king.or..not.out1file)then
229 & "Backbone and SC coordinates as read from the PDB"
231 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
232 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
233 & (c(j,nres+ires),j=1,3)
236 call int_from_cart1(.false.)
237 call int_from_cart(.true.,.false.)
238 call sc_loc_geom(.false.)
244 theta_ref(i)=theta(i)
252 dc(j,i)=c(j,i+1)-c(j,i)
253 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
258 dc(j,i+nres)=c(j,i+nres)-c(j,i)
259 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
261 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
266 C Copy the coordinates to reference coordinates
276 bfrag(i,j)=bfrag(i,j)-ishift
282 hfrag(i,j)=hfrag(i,j)-ishift
288 c---------------------------------------------------------------------------
289 subroutine int_from_cart(lside,lprn)
290 implicit real*8 (a-h,o-z)
292 include 'DIMENSIONS.ZSCOPT'
296 include 'COMMON.LOCAL'
298 include 'COMMON.CHAIN'
299 include 'COMMON.INTERACT'
300 include 'COMMON.IOUNITS'
302 include 'COMMON.NAMES'
303 include 'COMMON.CONTROL'
304 include 'COMMON.SETUP'
305 character*3 seq,atom,res
308 double precision sccor(3,20)
309 c dimension sccor(3,20)
312 double precision dist,alpha,beta,di
313 if(me.eq.king.or..not.out1file)then
316 & 'Internal coordinates calculated from crystal structure.'
318 write (iout,'(8a)') ' Res ',' dvb',' Theta',
319 & ' Gamma',' Dsc_id',' Dsc',' Alpha',
322 write (iout,'(4a)') ' Res ',' dvb',' Theta',
329 if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
330 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
333 vbld(i+1)=dist(i,i+1)
334 vbld_inv(i+1)=1.0d0/vbld(i+1)
335 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
336 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
338 c if (unres_pdb) then
339 c if (itype(1).eq.21) then
340 c theta(3)=90.0d0*deg2rad
341 c phi(4)=180.0d0*deg2rad
343 c vbld_inv(2)=1.0d0/vbld(2)
345 c if (itype(nres).eq.21) then
346 c theta(nres)=90.0d0*deg2rad
347 c phi(nres)=180.0d0*deg2rad
349 c vbld_inv(nres)=1.0d0/vbld(2)
355 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
356 & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
360 C 10/03/12 Adam: Correction for zero SC-SC bond length
361 if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
364 if (itype(i).ne.10) then
365 vbld_inv(i+nres)=1.0d0/di
367 vbld_inv(i+nres)=0.0d0
370 alph(i)=alpha(nres+i,i,maxres2)
371 omeg(i)=beta(nres+i,i,maxres2,i+1)
373 if(me.eq.king.or..not.out1file)then
375 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
376 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
377 & rad2deg*alph(i),rad2deg*omeg(i)
383 if(me.eq.king.or..not.out1file)
384 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
385 & rad2deg*theta(i),rad2deg*phi(i)
390 c-------------------------------------------------------------------------------
391 subroutine sc_loc_geom(lprn)
392 implicit real*8 (a-h,o-z)
394 include 'DIMENSIONS.ZSCOPT'
398 include 'COMMON.LOCAL'
400 include 'COMMON.CHAIN'
401 include 'COMMON.INTERACT'
402 include 'COMMON.IOUNITS'
404 include 'COMMON.NAMES'
405 include 'COMMON.CONTROL'
406 include 'COMMON.SETUP'
407 double precision x_prime(3),y_prime(3),z_prime(3)
411 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
415 if (itype(i).ne.10) then
417 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
421 dc_norm(j,i+nres)=0.0d0
426 costtab(i+1) =dcos(theta(i+1))
427 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
428 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
429 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
430 cosfac2=0.5d0/(1.0d0+costtab(i+1))
431 cosfac=dsqrt(cosfac2)
432 sinfac2=0.5d0/(1.0d0-costtab(i+1))
433 sinfac=dsqrt(sinfac2)
437 C Compute the axes of tghe local cartesian coordinates system; store in
438 c x_prime, y_prime and z_prime
446 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
447 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
449 call vecpr(x_prime,y_prime,z_prime)
451 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
452 C to local coordinate system. Store in xx, yy, zz.
458 xx = xx + x_prime(j)*dc_norm(j,i+nres)
459 yy = yy + y_prime(j)*dc_norm(j,i+nres)
460 zz = zz + z_prime(j)*dc_norm(j,i+nres)
475 if(me.eq.king.or..not.out1file)
476 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
482 c---------------------------------------------------------------------------
483 subroutine sccenter(ires,nscat,sccor)
484 implicit real*8 (a-h,o-z)
486 include 'COMMON.CHAIN'
487 dimension sccor(3,20)
491 sccmj=sccmj+sccor(j,i)
493 dc(j,ires)=sccmj/nscat
497 c---------------------------------------------------------------------------
498 subroutine bond_regular
499 implicit real*8 (a-h,o-z)
502 include 'COMMON.LOCAL'
503 include 'COMMON.CALC'
504 include 'COMMON.INTERACT'
505 include 'COMMON.CHAIN'
508 vbld_inv(i+1)=1.0d0/vbld(i+1)
509 vbld(i+1+nres)=dsc(itype(i+1))
510 vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
511 c print *,vbld(i+1),vbld(i+1+nres)