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 character*3 seq,atom,res
20 read (ipdbin,'(a80)',end=10) card
21 if (card(:3).eq.'END') then
23 else if (card(:3).eq.'TER') then
26 itype(ires_old-1)=ntyp1
29 c write (iout,*) "Chain ended",ires,ishift,ires_old
30 call sccenter(ires,iii,sccor)
32 C Fish out the ATOM cards.
33 if (index(card(1:4),'ATOM').gt.0) then
34 read (card(14:16),'(a3)') atom
35 if (atom.eq.'CA' .or. atom.eq.'CH3') then
36 C Calculate the CM of the preceding residue.
38 call sccenter(ires,iii,sccor)
41 c write (iout,'(a80)') card
42 read (card(24:26),*) ires
43 read (card(18:20),'(a3)') res
46 if (res.ne.'GLY' .and. res.ne. 'ACE') then
50 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
52 else if (ibeg.eq.2) then
54 ishift=-ires_old+ires-1
55 c write (iout,*) "New chain started",ires,ishift
59 c write (2,*) "ires",ires," ishift",ishift
60 if (res.eq.'ACE') then
63 itype(ires)=rescode(ires,res,0)
65 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
66 write (iout,'(2i3,2x,a,3f8.3)')
67 & ires,itype(ires),res,(c(j,ires),j=1,3)
70 sccor(j,iii)=c(j,ires)
72 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
73 & atom.ne.'N ' .and. atom.ne.'C ') then
75 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
79 10 write (iout,'(a,i5)') ' Nres: ',ires
80 C Calculate dummy residue coordinates inside the "chain" of a multichain
84 c write (iout,*) i,itype(i)
85 if (itype(i).eq.ntyp1) then
86 if (itype(i+1).eq.ntyp1) then
88 c write (iout,*) "dummy",i,itype(i)
90 C c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
91 c c(j,i)=(c(j,i-1)+c(j,i+1))/2
95 dcj=(c(j,i-2)-c(j,i-3))/2.0
100 else !itype(i+1).eq.ntyp1
102 dcj=(c(j,i+3)-c(j,i+2))/2.0
107 endif !itype(i+1).eq.ntyp1
108 endif !itype.eq.ntyp1
110 C Calculate the CM of the last side chain.
111 call sccenter(ires,iii,sccor)
114 if (itype(nres).ne.10) then
118 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
119 c(j,nres)=c(j,nres-1)+dcj
120 c(j,2*nres)=c(j,nres)
130 c(j,2*nres)=c(j,nres)
132 if (itype(1).eq.ntyp1) then
136 dcj=(c(j,4)-c(j,3))/2.0
141 C Calculate internal coordinates.
143 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
144 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
145 & (c(j,nres+ires),j=1,3)
147 call int_from_cart(.true.,.false.)
150 dc(j,i)=c(j,i+1)-c(j,i)
151 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
156 dc(j,i+nres)=c(j,i+nres)-c(j,i)
157 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
159 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
163 C Copy the coordinates to reference coordinates
175 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
177 if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
180 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
186 cref(j,i+nres,cou)=c(j,i+nres)
188 chain_rep(j,lll,kkk)=c(j,i)
189 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
194 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
195 chain_rep(j,chain_length+nres,symetr)
196 &=chain_rep(j,chain_length+nres,1)
199 if (symetr.gt.1) then
206 c write(iout,*) "tabperm", (tabperm(i,kkk),kkk=1,4)
212 c write (iout,*) i,icha
213 do lll=1,chain_length
215 if (cou.le.nres) then
217 kupa=mod(lll,chain_length)
218 iprzes=(kkk-1)*chain_length+lll
219 if (kupa.eq.0) kupa=chain_length
220 c write (iout,*) "kupa", kupa
221 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
222 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
230 C-koniec robienia kopidm
232 write (iout,*) "nowa struktura", nperm
234 write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
236 &cref(3,i,kkk),cref(1,nres+i,kkk),
237 &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
239 100 format (//' alpha-carbon coordinates ',
240 & ' centroid coordinates'/
241 1 ' ', 6X,'X',11X,'Y',11X,'Z',
242 & 10X,'X',11X,'Y',11X,'Z')
243 110 format (a,'(',i3,')',6f12.5)
250 c---------------------------------------------------------------------------
251 subroutine int_from_cart(lside,lprn)
252 implicit real*8 (a-h,o-z)
254 include 'COMMON.LOCAL'
256 include 'COMMON.CHAIN'
257 include 'COMMON.INTERACT'
258 include 'COMMON.IOUNITS'
260 include 'COMMON.NAMES'
261 character*3 seq,atom,res
263 dimension sccor(3,20)
268 & 'Internal coordinates calculated from crystal structure.'
270 write (iout,'(8a)') ' Res ',' dvb',' Theta',
271 & ' Phi',' Dsc_id',' Dsc',' Alpha',
274 write (iout,'(4a)') ' Res ',' dvb',' Theta',
281 c write (iout,*) i,dist(i,i-1)
282 if (dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0) then
283 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
286 theta(i+1)=alpha(i-1,i,i+1)
287 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
292 c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
297 alph(i)=alpha(nres+i,i,maxres2)
298 omeg(i)=beta(nres+i,i,maxres2,i+1)
301 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
302 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,rad2deg*alph(i),
308 write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
309 & rad2deg*theta(i),rad2deg*phi(i)
314 c---------------------------------------------------------------------------
315 subroutine sccenter(ires,nscat,sccor)
316 implicit real*8 (a-h,o-z)
318 include 'COMMON.CHAIN'
319 dimension sccor(3,20)
323 sccmj=sccmj+sccor(j,i)
325 dc(j,ires)=sccmj/nscat