2 C Read the PDB file and convert the peptide geometry into virtual-chain
4 implicit real*8 (a-h,o-z)
10 include 'COMMON.INTERACT'
11 include 'COMMON.IOUNITS'
13 include 'COMMON.NAMES'
14 include 'COMMON.CONTROL'
15 c include 'COMMON.DISTFIT'
16 include 'COMMON.SETUP'
17 integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
19 logical lprn /.false./,fail
20 double precision e1(3),e2(3),e3(3)
21 double precision dcj,efree_temp
25 double precision sccor(3,20)
31 c write (2,*) "UNRES_PDB",unres_pdb
39 read (ipdbin,'(a80)',end=10) card
40 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 crc----------------------------------------
53 crc to be corrected !!!
54 bfrag(3,nbfrag)=bfrag(1,nbfrag)
55 bfrag(4,nbfrag)=bfrag(2,nbfrag)
56 crc----------------------------------------
58 if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
60 if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
61 C Fish out the ATOM cards.
62 if (index(card(1:4),'ATOM').gt.0) then
63 read (card(12:16),*) atom
64 c write (iout,*) "! ",atom," !",ires
65 c if (atom.eq.'CA' .or. atom.eq.'CH3') then
66 read (card(23:26),*) ires
67 read (card(18:20),'(a3)') res
68 c write (iout,*) "ires",ires,ires-ishift+ishift1,
69 c & " ires_old",ires_old
70 c write (iout,*) "ishift",ishift," ishift1",ishift1
71 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
72 if (ires-ishift+ishift1.ne.ires_old) then
73 C Calculate the CM of the preceding residue.
74 c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
76 c write (iout,*) "Calculating sidechain center iii",iii
79 c dc(j,ires)=sccor(j,iii)
82 call sccenter(ires_old,iii,sccor)
87 if (res.eq.'Cl-' .or. res.eq.'Na+') then
90 else if (ibeg.eq.1) then
91 c write (iout,*) "BEG ires",ires
93 if (res.ne.'GLY' .and. res.ne. 'ACE') then
97 ires=ires-ishift+ishift1
99 c write (iout,*) "ishift",ishift," ires",ires,
100 c & " ires_old",ires_old
103 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
104 ires=ires-ishift+ishift1
107 if (res.eq.'ACE' .or. res.eq.'NHE') then
110 itype(ires)=rescode(ires,res,0)
113 ires=ires-ishift+ishift1
115 c write (iout,*) "ires_old",ires_old," ires",ires
116 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
119 c write (2,*) "ires",ires," res ",res," ity",ity
120 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
121 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
122 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
123 c write (iout,*) "backbone ",atom
125 write (iout,'(2i3,2x,a,3f8.3)')
126 & ires,itype(ires),res,(c(j,ires),j=1,3)
130 sccor(j,iii)=c(j,ires)
132 if (ishift.ne.0) then
133 ires_ca=ires+ishift-ishift1
137 c write (*,*) card(23:27),ires,itype(ires)
138 else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
139 & atom.ne.'N' .and. atom.ne.'C' .and.
140 & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
141 & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
142 c write (iout,*) "sidechain ",atom
144 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
150 write (iout,'(a,i5)') ' Number of residues found: ',ires
152 if (ires.eq.0) return
153 C Calculate the CM of the last side chain.
155 c if (unres_pdb) then
157 c dc(j,ires)=sccor(j,iii)
160 call sccenter(ires,iii,sccor)
166 if (itype(nres).ne.10) then
170 dcj=c(j,nres-2)-c(j,nres-3)
171 c(j,nres)=c(j,nres-1)+dcj
172 c(j,2*nres)=c(j,nres)
182 c(j,2*nres)=c(j,nres)
184 if (itype(1).eq.21) then
187 c if (unres_pdb) then
188 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
189 c call refsys(2,3,4,e1,e2,e3,fail)
196 c c(j,1)=c(j,2)-3.8d0*e2(j)
206 C Copy the coordinates to reference coordinates
212 C Calculate internal coordinates.
215 & "Cartesian coordinates of the reference structure"
216 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
217 & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
219 write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
220 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
221 & (c(j,ires+nres),j=1,3)
224 C Calculate internal coordinates.
225 if(me.eq.king.or..not.out1file)then
227 & "Backbone and SC coordinates as read from the PDB"
229 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
230 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
231 & (c(j,nres+ires),j=1,3)
234 call int_from_cart1(.false.)
235 call int_from_cart(.true.,.false.)
236 call sc_loc_geom(.false.)
242 theta_ref(i)=theta(i)
250 dc(j,i)=c(j,i+1)-c(j,i)
251 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
256 dc(j,i+nres)=c(j,i+nres)-c(j,i)
257 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
259 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
264 C Copy the coordinates to reference coordinates
274 bfrag(i,j)=bfrag(i,j)-ishift
280 hfrag(i,j)=hfrag(i,j)-ishift
286 c---------------------------------------------------------------------------
287 subroutine int_from_cart(lside1,lprn)
288 implicit real*8 (a-h,o-z)
293 include 'COMMON.LOCAL'
295 include 'COMMON.CHAIN'
296 include 'COMMON.INTERACT'
297 include 'COMMON.IOUNITS'
299 include 'COMMON.NAMES'
300 include 'COMMON.CONTROL'
301 include 'COMMON.SETUP'
302 character*3 seq,atom,res
305 double precision sccor(3,20)
306 c dimension sccor(3,20)
309 double precision dist,alpha,beta,di
310 if(me.eq.king.or..not.out1file)then
313 & 'Internal coordinates calculated from crystal structure.'
315 write (iout,'(8a)') ' Res ',' dvb',' Theta',
316 & ' Gamma',' Dsc_id',' Dsc',' Alpha',
319 write (iout,'(4a)') ' Res ',' dvb',' Theta',
326 if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
327 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
330 vbld(i+1)=dist(i,i+1)
331 vbld_inv(i+1)=1.0d0/vbld(i+1)
332 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
333 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
335 c if (unres_pdb) then
336 c if (itype(1).eq.21) then
337 c theta(3)=90.0d0*deg2rad
338 c phi(4)=180.0d0*deg2rad
340 c vbld_inv(2)=1.0d0/vbld(2)
342 c if (itype(nres).eq.21) then
343 c theta(nres)=90.0d0*deg2rad
344 c phi(nres)=180.0d0*deg2rad
346 c vbld_inv(nres)=1.0d0/vbld(2)
352 c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
353 & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
357 C 10/03/12 Adam: Correction for zero SC-SC bond length
358 if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
361 if (itype(i).ne.10) then
362 vbld_inv(i+nres)=1.0d0/di
364 vbld_inv(i+nres)=0.0d0
367 alph(i)=alpha(nres+i,i,maxres2)
368 omeg(i)=beta(nres+i,i,maxres2,i+1)
370 if(me.eq.king.or..not.out1file)then
372 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
373 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
374 & rad2deg*alph(i),rad2deg*omeg(i)
380 if(me.eq.king.or..not.out1file)
381 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
382 & rad2deg*theta(i),rad2deg*phi(i)
387 c-------------------------------------------------------------------------------
388 subroutine sc_loc_geom(lprn)
389 implicit real*8 (a-h,o-z)
394 include 'COMMON.LOCAL'
396 include 'COMMON.CHAIN'
397 include 'COMMON.INTERACT'
398 include 'COMMON.IOUNITS'
400 include 'COMMON.NAMES'
401 include 'COMMON.CONTROL'
402 include 'COMMON.SETUP'
403 double precision x_prime(3),y_prime(3),z_prime(3)
407 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
411 if (itype(i).ne.10) then
413 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
417 dc_norm(j,i+nres)=0.0d0
422 costtab(i+1) =dcos(theta(i+1))
423 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
424 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
425 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
426 cosfac2=0.5d0/(1.0d0+costtab(i+1))
427 cosfac=dsqrt(cosfac2)
428 sinfac2=0.5d0/(1.0d0-costtab(i+1))
429 sinfac=dsqrt(sinfac2)
433 C Compute the axes of tghe local cartesian coordinates system; store in
434 c x_prime, y_prime and z_prime
442 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
443 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
445 call vecpr(x_prime,y_prime,z_prime)
447 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
448 C to local coordinate system. Store in xx, yy, zz.
454 xx = xx + x_prime(j)*dc_norm(j,i+nres)
455 yy = yy + y_prime(j)*dc_norm(j,i+nres)
456 zz = zz + z_prime(j)*dc_norm(j,i+nres)
471 if(me.eq.king.or..not.out1file)
472 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
478 c---------------------------------------------------------------------------
479 subroutine sccenter(ires,nscat,sccor)
480 implicit real*8 (a-h,o-z)
482 include 'COMMON.CHAIN'
483 dimension sccor(3,20)
487 sccmj=sccmj+sccor(j,i)
489 dc(j,ires)=sccmj/nscat
493 c---------------------------------------------------------------------------
494 subroutine bond_regular
495 implicit real*8 (a-h,o-z)
498 include 'COMMON.LOCAL'
499 include 'COMMON.CALC'
500 include 'COMMON.INTERACT'
501 include 'COMMON.CHAIN'
504 vbld_inv(i+1)=1.0d0/vbld(i+1)
505 vbld(i+1+nres)=dsc(itype(i+1))
506 vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
507 c print *,vbld(i+1),vbld(i+1+nres)