1 subroutine readpdb(lprn,iprot,efree_temp,*)
2 C Read the PDB file and convert the peptide geometry into virtual-chain
6 include 'DIMENSIONS.ZSCOPT'
7 include 'COMMON.CONTROL'
10 include 'COMMON.CHAIN'
11 include 'COMMON.INTERACT'
12 include 'COMMON.IOUNITS'
14 include 'COMMON.NAMES'
16 integer i,j,iprot,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
19 double precision e1(3),e2(3),e3(3)
20 double precision dcj,efree_temp
21 character*3 seq,atom,res
23 double precision sccor(3,20)
29 c write (2,*) "UNRES_PDB",unres_pdb
34 read (ipdbin,'(a80)',end=10) card
35 c write (iout,'(a)') card
36 if (card(:3).eq.'END') goto 10
37 c if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
39 if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
40 C Fish out the ATOM cards.
41 if (index(card(1:4),'ATOM').gt.0) then
42 read (card(14:16),'(a3)') atom
43 c if (atom.eq.'CA' .or. atom.eq.'CH3') then
44 read (card(23:26),*) ires
45 read (card(18:20),'(a3)') res
46 c write (iout,*) "ires",ires,ires-ishift+ishift1,
47 c & " ires_old",ires_old
48 c write (iout,*) "ishift",ishift," ishift1",ishift1
49 c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
50 if (ires-ishift+ishift1.ne.ires_old) then
51 C Calculate the CM of the preceding residue.
52 c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
54 c write (iout,*) "Calculating sidechain center iii",iii
57 dc(j,ires)=sccor(j,iii)
60 call sccenter(ires,iii,sccor)
65 if (res.eq.'Cl-' .or. res.eq.'Na+') then
68 else if (ibeg.eq.1) then
69 c write (iout,*) "BEG ires",ires
71 if (res.ne.'GLY' .and. res.ne. 'ACE') then
75 ires=ires-ishift+ishift1
77 c write (iout,*) "ishift",ishift," ires",ires,
78 c & " ires_old",ires_old
81 ishift=ishift-(ires-ishift+ishift1-ires_old-1)
82 ires=ires-ishift+ishift1
85 if (res.eq.'ACE' .or. res.eq.'NHE') then
88 itype(ires)=rescode(ires,res,0)
91 ires=ires-ishift+ishift1
93 c write (iout,*) "ires_old",ires_old," ires",ires
94 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
97 c write (2,*) "ires",ires," res ",res," ity",ity
98 if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
99 & res.eq.'NHE'.and.atom(:2).eq.'HN') then
100 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
102 write (iout,'(2i3,2x,a,3f8.3)')
103 & ires,itype(ires),res,(c(j,ires),j=1,3)
107 sccor(j,iii)=c(j,ires)
109 c write (*,*) card(23:27),ires,itype(ires)
110 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
111 & atom.ne.'N ' .and. atom.ne.'C ' .and.
112 & atom.ne.'OXT') then
114 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
118 10 write (iout,'(a,i5)') ' Number of residues found: ',ires
119 if (ires.eq.0) return1
120 C Calculate the CM of the last side chain.
124 dc(j,ires)=sccor(j,iii)
127 call sccenter(ires,iii,sccor)
133 if (itype(nres).ne.10) then
137 dcj=c(j,nres-2)-c(j,nres-3)
138 c(j,nres)=c(j,nres-1)+dcj
139 c(j,2*nres)=c(j,nres)
149 c(j,2*nres)=c(j,nres)
151 if (itype(1).eq.21) then
152 nsup(iprot)=nsup(iprot)-1
155 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
156 call refsys(2,3,4,e1,e2,e3,fail)
163 c(j,1)=c(j,2)-3.8d0*e2(j)
173 C Copy the coordinates to reference coordinates
176 c cref(j,i,iprot)=c(j,i)
179 C Calculate internal coordinates.
182 & "Cartesian coordinates of the reference structure"
183 write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
184 & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
186 write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
187 & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
188 & (c(j,ires+nres),j=1,3)
191 call int_from_cart(.true.,lprn)
193 c phi_ref(i,iprot)=phi(i)
194 c theta_ref(i,iprot)=theta(i)
195 c alph_ref(i,iprot)=alph(i)
196 c omeg_ref(i,iprot)=omeg(i)
201 c---------------------------------------------------------------------------
202 subroutine int_from_cart(lside,lprn)
205 include 'DIMENSIONS.ZSCOPT'
206 include 'COMMON.LOCAL'
208 include 'COMMON.CHAIN'
209 include 'COMMON.INTERACT'
210 include 'COMMON.IOUNITS'
212 include 'COMMON.NAMES'
214 double precision dist,alpha,beta,di
215 character*3 seq,atom,res
217 double precision sccor(3,20)
222 & 'Internal coordinates of the reference structure.'
224 write (iout,'(8a)') 'Residue',' dvb',' Theta',
225 & ' Phi',' Dsc_id',' Dsc',' Alpha',
228 write (iout,'(4a)') 'Residue',' dvb',' Theta',
234 if (iti.ne.21 .and. itype(i+1).ne.21 .and.
235 & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
236 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
239 vbld(i+1)=dist(i,i+1)
240 vbld_inv(i+1)=1.0d0/vbld(i+1)
241 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
242 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
244 dc(j,i)=c(j,i+1)-c(j,i)
245 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
251 c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
256 if (itype(i).ne.10) then
257 vbld_inv(i+nres)=1.0d0/di
259 dc(j,i+nres)=c(j,i+nres)-c(j,i)
260 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
263 vbld_inv(i+nres)=0.0d0
266 dc_norm(j,i+nres)=0.0d0
270 alph(i)=alpha(nres+i,i,maxres2)
271 omeg(i)=beta(nres+i,i,maxres2,i+1)
274 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
275 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,
276 & rad2deg*alph(i),rad2deg*omeg(i)
283 write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
284 & rad2deg*theta(i),rad2deg*phi(i)
289 c---------------------------------------------------------------------------
290 subroutine sccenter(ires,nscat,sccor)
293 include 'DIMENSIONS.ZSCOPT'
294 include 'COMMON.CHAIN'
295 integer ires,nscat,i,j
296 double precision sccmj
297 double precision sccor(3,20)
301 sccmj=sccmj+sccor(j,i)
303 dc(j,ires)=sccmj/nscat