2 C Read the PDB file and convert the peptide geometry into virtual-chain
4 implicit real*8 (a-h,o-z)
6 include 'COMMON.CONTROL'
10 include 'COMMON.INTERACT'
11 include 'COMMON.IOUNITS'
13 include 'COMMON.NAMES'
14 character*3 seq,atom,res
18 c write (iout,*) "PDBREAD: SYMETR",symetr
20 c write (iout,*) "AFTER PERMUT"
24 read (ipdbin,'(a80)',end=10) card
25 c write (iout,'(a)') card
26 if (card(:3).eq.'END') then
28 else if (card(:3).eq.'TER') then
31 itype(ires_old-1)=ntyp1
34 c write (iout,*) "Chain ended",ires,ishift,ires_old
35 call sccenter(ires,iii,sccor)
37 C Fish out the ATOM cards.
38 if (index(card(1:4),'ATOM').gt.0) then
39 read (card(14:16),'(a3)') atom
40 if (atom.eq.'CA' .or. atom.eq.'CH3') then
41 C Calculate the CM of the preceding residue.
43 call sccenter(ires,iii,sccor)
46 c write (iout,'(a80)') card
47 read (card(24:26),*) ires
48 read (card(18:20),'(a3)') res
51 if (res.ne.'GLY' .and. res.ne. 'ACE') then
55 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
57 else if (ibeg.eq.2) then
59 ishift=-ires_old+ires-1
60 c write (iout,*) "New chain started",ires,ishift
64 c write (2,*) "ires",ires," ishift",ishift
65 if (res.eq.'ACE') then
68 itype(ires)=rescode(ires,res,0)
70 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
71 c write (iout,'(2i3,2x,a,3f8.3)')
72 c & ires,itype(ires),res,(c(j,ires),j=1,3)
75 sccor(j,iii)=c(j,ires)
77 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
78 & atom.ne.'N ' .and. atom.ne.'C ') then
80 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
84 10 write (iout,'(a,i5)') ' Nres: ',ires
85 C Calculate dummy residue coordinates inside the "chain" of a multichain
89 c write (iout,*) i,itype(i)
90 if (itype(i).eq.ntyp1) then
91 if (itype(i+1).eq.ntyp1) then
93 c write (iout,*) "dummy",i,itype(i)
95 C c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
96 c c(j,i)=(c(j,i-1)+c(j,i+1))/2
100 dcj=(c(j,i-2)-c(j,i-3))/2.0
105 else !itype(i+1).eq.ntyp1
107 dcj=(c(j,i+3)-c(j,i+2))/2.0
112 endif !itype(i+1).eq.ntyp1
113 endif !itype.eq.ntyp1
115 C Calculate the CM of the last side chain.
116 call sccenter(ires,iii,sccor)
119 if (itype(nres).ne.10) then
123 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
124 c(j,nres)=c(j,nres-1)+dcj
125 c(j,2*nres)=c(j,nres)
135 c(j,2*nres)=c(j,nres)
137 if (itype(1).eq.ntyp1) then
141 dcj=(c(j,4)-c(j,3))/2.0
146 C Calculate internal coordinates.
148 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
149 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
150 & (c(j,nres+ires),j=1,3)
152 call int_from_cart(.true.,.false.)
155 dc(j,i)=c(j,i+1)-c(j,i)
156 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
161 dc(j,i+nres)=c(j,i+nres)-c(j,i)
162 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
164 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
167 c write (iout,*) "AFTER DC"
170 C Copy the coordinates to reference coordinates
173 c cref_pdb(j,i)=c(j,i)
180 c write (iout,*) "nres",nres
183 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
185 if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
188 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
189 c write (iout,*) "chain_length",chain_length
194 c write (iout,*) "i",i," lll",lll
196 cref_pdb(j,i,cou)=c(j,i)
197 cref_pdb(j,i+nres,cou)=c(j,i+nres)
199 chain_rep(j,lll,kkk)=c(j,i)
200 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
204 if (chain_length.eq.0) chain_length=nres
206 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
207 chain_rep(j,chain_length+nres,symetr)
208 &=chain_rep(j,chain_length+nres,1)
211 if (symetr.gt.1) then
218 c write(iout,*) "tabperm", (tabperm(i,kkk),kkk=1,4)
224 c write (iout,*) i,icha
225 do lll=1,chain_length
227 if (cou.le.nres) then
229 kupa=mod(lll,chain_length)
230 iprzes=(kkk-1)*chain_length+lll
231 if (kupa.eq.0) kupa=chain_length
232 c write (iout,*) "kupa", kupa
233 cref_pdb(j,iprzes,i)=chain_rep(j,kupa,icha)
234 cref_pdb(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
242 C-koniec robienia kopidm
244 write (iout,*) "nowa struktura", nperm
246 write (iout,110) restyp(itype(i)),i,cref_pdb(1,i,kkk),
248 &cref_pdb(3,i,kkk),cref_pdb(1,nres+i,kkk),
249 &cref_pdb(2,nres+i,kkk),cref_pdb(3,nres+i,kkk)
251 100 format (//' alpha-carbon coordinates ',
252 & ' centroid coordinates'/
253 1 ' ', 6X,'X',11X,'Y',11X,'Z',
254 & 10X,'X',11X,'Y',11X,'Z')
255 110 format (a,'(',i3,')',6f12.5)
262 c---------------------------------------------------------------------------
263 subroutine int_from_cart(lside,lprn)
264 implicit real*8 (a-h,o-z)
266 include 'COMMON.LOCAL'
268 include 'COMMON.CHAIN'
269 include 'COMMON.INTERACT'
270 include 'COMMON.IOUNITS'
272 include 'COMMON.NAMES'
273 character*3 seq,atom,res
275 dimension sccor(3,20)
280 & 'Internal coordinates calculated from crystal structure.'
282 write (iout,'(8a)') ' Res ',' dvb',' Theta',
283 & ' Phi',' Dsc_id',' Dsc',' Alpha',
286 write (iout,'(4a)') ' Res ',' dvb',' Theta',
293 c write (iout,*) i,dist(i,i-1)
294 if (dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0) then
295 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
298 theta(i+1)=alpha(i-1,i,i+1)
299 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
304 c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
309 alph(i)=alpha(nres+i,i,maxres2)
310 omeg(i)=beta(nres+i,i,maxres2,i+1)
313 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
314 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,rad2deg*alph(i),
320 write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
321 & rad2deg*theta(i),rad2deg*phi(i)
326 c---------------------------------------------------------------------------
327 subroutine sccenter(ires,nscat,sccor)
328 implicit real*8 (a-h,o-z)
330 include 'COMMON.CHAIN'
331 dimension sccor(3,20)
335 sccmj=sccmj+sccor(j,i)
337 dc(j,ires)=sccmj/nscat