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 integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
18 logical lprn /.true./,fail
19 double precision e1(3),e2(3),e3(3)
20 double precision dcj,efree_temp
24 double precision sccor(3,20)
30 c write (2,*) "UNRES_PDB",unres_pdb
38 read (ipdbin,'(a80)',end=10) card
39 c write (iout,'(a)') card
40 if (card(:5).eq.'HELIX') then
43 read(card(22:25),*) hfrag(1,nhfrag)
44 read(card(34:37),*) hfrag(2,nhfrag)
46 if (card(:5).eq.'SHEET') then
49 read(card(24:26),*) bfrag(1,nbfrag)
50 read(card(35:37),*) bfrag(2,nbfrag)
51 crc----------------------------------------
52 crc to be corrected !!!
53 bfrag(3,nbfrag)=bfrag(1,nbfrag)
54 bfrag(4,nbfrag)=bfrag(2,nbfrag)
55 crc----------------------------------------
57 if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
59 if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
60 C Fish out the ATOM cards.
61 if (index(card(1:4),'ATOM').gt.0) then
62 read (card(12:16),*) atom
63 c write (iout,*) "! ",atom," !",ires
64 c if (atom.eq.'CA' .or. atom.eq.'CH3') then
65 read (card(23:26),*) ires
66 read (card(18:20),'(a3)') res
67 c write (iout,*) "ires",ires,ires-ishift+ishift1,
68 c & " ires_old",ires_old
69 c write (iout,*) "ishift",ishift," ishift1",ishift1
70 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
71 if (ires-ishift+ishift1.ne.ires_old) then
72 C Calculate the CM of the preceding residue.
73 c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
75 c write (iout,*) "Calculating sidechain center iii",iii
78 dc(j,ires)=sccor(j,iii)
81 call sccenter(ires_old,iii,sccor)
86 if (res.eq.'Cl-' .or. res.eq.'Na+') then
89 else if (ibeg.eq.1) then
90 c write (iout,*) "BEG ires",ires
92 if (res.ne.'GLY' .and. res.ne. 'ACE') then
96 ires=ires-ishift+ishift1
98 c write (iout,*) "ishift",ishift," ires",ires,
99 c & " ires_old",ires_old
102 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
103 ires=ires-ishift+ishift1
106 if (res.eq.'ACE' .or. res.eq.'NHE') then
109 itype(ires)=rescode(ires,res,0)
112 ires=ires-ishift+ishift1
114 c write (iout,*) "ires_old",ires_old," ires",ires
115 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
118 c write (2,*) "ires",ires," res ",res," ity",ity
119 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
120 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
121 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
122 c write (iout,*) "backbone ",atom
124 write (iout,'(2i3,2x,a,3f8.3)')
125 & ires,itype(ires),res,(c(j,ires),j=1,3)
129 sccor(j,iii)=c(j,ires)
131 if (ishift.ne.0) then
132 ires_ca=ires+ishift-ishift1
136 c write (*,*) card(23:27),ires,itype(ires)
137 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
138 & atom.ne.'N' .and. atom.ne.'C' .and.
139 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
140 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
141 c write (iout,*) "sidechain ",atom
143 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
147 10 write (iout,'(a,i5)') ' Number of residues found: ',ires
148 if (ires.eq.0) return
149 C Calculate the CM of the last side chain.
153 dc(j,ires)=sccor(j,iii)
156 call sccenter(ires,iii,sccor)
162 if (itype(nres).ne.10) then
166 dcj=c(j,nres-2)-c(j,nres-3)
167 c(j,nres)=c(j,nres-1)+dcj
168 c(j,2*nres)=c(j,nres)
178 c(j,2*nres)=c(j,nres)
180 if (itype(1).eq.21) then
184 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
185 call refsys(2,3,4,e1,e2,e3,fail)
192 c(j,1)=c(j,2)-3.8d0*e2(j)
202 C Copy the coordinates to reference coordinates
208 C Calculate internal coordinates.
211 & "Cartesian coordinates of the reference structure"
212 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
213 & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
215 write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
216 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
217 & (c(j,ires+nres),j=1,3)
220 C Calculate internal coordinates.
221 if(me.eq.king.or..not.out1file)then
223 & "Backbone and SC coordinates as read from the PDB"
225 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
226 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
227 & (c(j,nres+ires),j=1,3)
230 call int_from_cart(.true.,.false.)
231 call sc_loc_geom(.false.)
238 dc(j,i)=c(j,i+1)-c(j,i)
239 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
244 dc(j,i+nres)=c(j,i+nres)-c(j,i)
245 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
247 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
251 C Copy the coordinates to reference coordinates
261 bfrag(i,j)=bfrag(i,j)-ishift
267 hfrag(i,j)=hfrag(i,j)-ishift
273 c---------------------------------------------------------------------------
274 subroutine int_from_cart(lside,lprn)
275 implicit real*8 (a-h,o-z)
280 include 'COMMON.LOCAL'
282 include 'COMMON.CHAIN'
283 include 'COMMON.INTERACT'
284 include 'COMMON.IOUNITS'
286 include 'COMMON.NAMES'
287 include 'COMMON.CONTROL'
288 include 'COMMON.SETUP'
292 dimension sccor(3,20)
295 if(me.eq.king.or..not.out1file)then
298 & 'Internal coordinates calculated from crystal structure.'
300 write (iout,'(8a)') ' Res ',' dvb',' Theta',
301 & ' Gamma',' Dsc_id',' Dsc',' Alpha',
304 write (iout,'(4a)') ' Res ',' dvb',' Theta',
311 if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
312 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
315 vbld(i+1)=dist(i,i+1)
316 vbld_inv(i+1)=1.0d0/vbld(i+1)
317 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
318 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
320 c if (unres_pdb) then
321 c if (itype(1).eq.21) then
322 c theta(3)=90.0d0*deg2rad
323 c phi(4)=180.0d0*deg2rad
325 c vbld_inv(2)=1.0d0/vbld(2)
327 c if (itype(nres).eq.21) then
328 c theta(nres)=90.0d0*deg2rad
329 c phi(nres)=180.0d0*deg2rad
331 c vbld_inv(nres)=1.0d0/vbld(2)
337 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
338 & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
342 C 10/03/12 Adam: Correction for zero SC-SC bond length
343 if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
346 if (itype(i).ne.10) then
347 vbld_inv(i+nres)=1.0d0/di
349 vbld_inv(i+nres)=0.0d0
352 alph(i)=alpha(nres+i,i,maxres2)
353 omeg(i)=beta(nres+i,i,maxres2,i+1)
355 if(me.eq.king.or..not.out1file)then
357 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
358 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
359 & rad2deg*alph(i),rad2deg*omeg(i)
365 if(me.eq.king.or..not.out1file)
366 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
367 & rad2deg*theta(i),rad2deg*phi(i)
372 c-------------------------------------------------------------------------------
373 subroutine sc_loc_geom(lprn)
374 implicit real*8 (a-h,o-z)
379 include 'COMMON.LOCAL'
381 include 'COMMON.CHAIN'
382 include 'COMMON.INTERACT'
383 include 'COMMON.IOUNITS'
385 include 'COMMON.NAMES'
386 include 'COMMON.CONTROL'
387 include 'COMMON.SETUP'
388 double precision x_prime(3),y_prime(3),z_prime(3)
392 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
396 if (itype(i).ne.10) then
398 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
402 dc_norm(j,i+nres)=0.0d0
407 costtab(i+1) =dcos(theta(i+1))
408 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
409 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
410 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
411 cosfac2=0.5d0/(1.0d0+costtab(i+1))
412 cosfac=dsqrt(cosfac2)
413 sinfac2=0.5d0/(1.0d0-costtab(i+1))
414 sinfac=dsqrt(sinfac2)
418 C Compute the axes of tghe local cartesian coordinates system; store in
419 c x_prime, y_prime and z_prime
427 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
428 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
430 call vecpr(x_prime,y_prime,z_prime)
432 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
433 C to local coordinate system. Store in xx, yy, zz.
439 xx = xx + x_prime(j)*dc_norm(j,i+nres)
440 yy = yy + y_prime(j)*dc_norm(j,i+nres)
441 zz = zz + z_prime(j)*dc_norm(j,i+nres)
456 if(me.eq.king.or..not.out1file)
457 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
463 c---------------------------------------------------------------------------
464 subroutine sccenter(ires,nscat,sccor)
465 implicit real*8 (a-h,o-z)
467 include 'COMMON.CHAIN'
468 dimension sccor(3,20)
472 sccmj=sccmj+sccor(j,i)
474 dc(j,ires)=sccmj/nscat
478 c---------------------------------------------------------------------------
479 subroutine bond_regular
480 implicit real*8 (a-h,o-z)
483 include 'COMMON.LOCAL'
484 include 'COMMON.CALC'
485 include 'COMMON.INTERACT'
486 include 'COMMON.CHAIN'
489 vbld_inv(i+1)=1.0d0/vbld(i+1)
490 vbld(i+1+nres)=dsc(itype(i+1))
491 vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
492 c print *,vbld(i+1),vbld(i+1+nres)