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
28 c write (iout,*) "Chain ended",ires,ishift,ires_old
29 call sccenter(ires,iii,sccor)
31 C Fish out the ATOM cards.
32 if (index(card(1:4),'ATOM').gt.0) then
33 read (card(14:16),'(a3)') atom
34 if (atom.eq.'CA' .or. atom.eq.'CH3') then
35 C Calculate the CM of the preceding residue.
37 call sccenter(ires,iii,sccor)
40 c write (iout,'(a80)') card
41 read (card(24:26),*) ires
42 read (card(18:20),'(a3)') res
45 if (res.ne.'GLY' .and. res.ne. 'ACE') then
49 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
51 else if (ibeg.eq.2) then
53 ishift=-ires_old+ires-1
54 c write (iout,*) "New chain started",ires,ishift
58 c write (2,*) "ires",ires," ishift",ishift
59 if (res.eq.'ACE') then
62 itype(ires)=rescode(ires,res,0)
64 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
65 write (iout,'(2i3,2x,a,3f8.3)')
66 & ires,itype(ires),res,(c(j,ires),j=1,3)
69 sccor(j,iii)=c(j,ires)
71 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
72 & atom.ne.'N ' .and. atom.ne.'C ') then
74 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
78 10 write (iout,'(a,i5)') ' Nres: ',ires
79 C Calculate dummy residue coordinates inside the "chain" of a multichain
83 c write (iout,*) i,itype(i)
84 if (itype(i).eq.21) then
85 c write (iout,*) "dummy",i,itype(i)
87 c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
88 c c(j,i)=(c(j,i-1)+c(j,i+1))/2
93 C Calculate the CM of the last side chain.
94 call sccenter(ires,iii,sccor)
97 if (itype(nres).ne.10) then
101 dcj=c(j,nres-2)-c(j,nres-3)
102 c(j,nres)=c(j,nres-1)+dcj
103 c(j,2*nres)=c(j,nres)
113 c(j,2*nres)=c(j,nres)
115 if (itype(1).eq.21) then
124 C Calculate internal coordinates.
126 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
127 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
128 & (c(j,nres+ires),j=1,3)
130 call int_from_cart(.true.,.false.)
133 dc(j,i)=c(j,i+1)-c(j,i)
134 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
139 dc(j,i+nres)=c(j,i+nres)-c(j,i)
140 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
142 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
146 C Copy the coordinates to reference coordinates
156 c---------------------------------------------------------------------------
157 subroutine int_from_cart(lside,lprn)
158 implicit real*8 (a-h,o-z)
160 include 'COMMON.LOCAL'
162 include 'COMMON.CHAIN'
163 include 'COMMON.INTERACT'
164 include 'COMMON.IOUNITS'
166 include 'COMMON.NAMES'
167 character*3 seq,atom,res
169 dimension sccor(3,20)
174 & 'Internal coordinates calculated from crystal structure.'
176 write (iout,'(8a)') ' Res ',' dvb',' Theta',
177 & ' Phi',' Dsc_id',' Dsc',' Alpha',
180 write (iout,'(4a)') ' Res ',' dvb',' Theta',
187 c write (iout,*) i,dist(i,i-1)
188 if (dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0) then
189 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
192 theta(i+1)=alpha(i-1,i,i+1)
193 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
198 c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
203 alph(i)=alpha(nres+i,i,maxres2)
204 omeg(i)=beta(nres+i,i,maxres2,i+1)
207 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
208 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,rad2deg*alph(i),
214 write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
215 & rad2deg*theta(i),rad2deg*phi(i)
220 c---------------------------------------------------------------------------
221 subroutine sccenter(ires,nscat,sccor)
222 implicit real*8 (a-h,o-z)
224 include 'COMMON.CHAIN'
225 dimension sccor(3,20)
229 sccmj=sccmj+sccor(j,i)
231 dc(j,ires)=sccmj/nscat