| [bd2278d] | 1 | ! **************************************************************
|
|---|
| 2 | !
|
|---|
| 3 | ! This file contains the subroutines: pdbread,pdbvars,atixpdb,getpar
|
|---|
| 4 | !
|
|---|
| 5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
|
|---|
| [32289cd] | 6 | ! Shura Hayryan, Chin-Ku
|
|---|
| [bd2278d] | 7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
|
|---|
| 8 | ! Jan H. Meinke, Sandipan Mohanty
|
|---|
| 9 | !
|
|---|
| 10 | ! **************************************************************
|
|---|
| [e40e335] | 11 |
|
|---|
| 12 | subroutine pdbread(pdbfil,ier)
|
|---|
| 13 |
|
|---|
| [bd2278d] | 14 | ! ....................................................
|
|---|
| 15 | ! PURPOSE: read protein atom coordinates from 'pdbfil'
|
|---|
| 16 | ! (no Hydrogens, only ATOM records)
|
|---|
| 17 | !
|
|---|
| 18 | ! RETURNS: 0 = no errors / 1 = error
|
|---|
| 19 | !
|
|---|
| 20 | ! CALLS: iopfil,iendst
|
|---|
| 21 | ! ......................................................
|
|---|
| [e40e335] | 22 |
|
|---|
| 23 | include 'INCP.H'
|
|---|
| [32289cd] | 24 |
|
|---|
| 25 | double precision cor
|
|---|
| 26 |
|
|---|
| 27 | integer ier, l, iendst, lunpdb, io, iopfil, iat, i
|
|---|
| [e40e335] | 28 |
|
|---|
| [bd2278d] | 29 | ! -------------------------- input
|
|---|
| [e40e335] | 30 | character*(*) pdbfil
|
|---|
| [bd2278d] | 31 | ! -------------------------- local
|
|---|
| [e40e335] | 32 | dimension cor(3)
|
|---|
| 33 | character atm*4,rsn*3,rsno*3,chn,chno,
|
|---|
| [38d77eb] | 34 | & rsid*5,rsido*5,line*132, logString*255
|
|---|
| [e40e335] | 35 |
|
|---|
| 36 | natp=0
|
|---|
| 37 | nchp=0
|
|---|
| 38 | nrsp=0
|
|---|
| 39 |
|
|---|
| 40 | ier=1
|
|---|
| 41 |
|
|---|
| 42 | chno='&'
|
|---|
| 43 | rsno='#&#'
|
|---|
| 44 | rsido='#&#&#'
|
|---|
| 45 |
|
|---|
| 46 | l=iendst(pdbfil)
|
|---|
| 47 | if (l.gt.0) then
|
|---|
| 48 | lunpdb = 99
|
|---|
| 49 | else
|
|---|
| [38d77eb] | 50 | write (logString, '(a)')
|
|---|
| [bd2278d] | 51 | & ' pdbread> empty file name to read pdb-structure'
|
|---|
| [e40e335] | 52 |
|
|---|
| 53 | return
|
|---|
| 54 | endif
|
|---|
| 55 |
|
|---|
| 56 | io=iopfil(lunpdb,pdbfil,'old','formatted')
|
|---|
| 57 |
|
|---|
| 58 | if (io.le.0) then
|
|---|
| [38d77eb] | 59 | write (logString, '(a,/,a)')
|
|---|
| [bd2278d] | 60 | & ' pdbread> ERROR opening file to read pdb-structure: ',
|
|---|
| 61 | & pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 62 |
|
|---|
| 63 | return
|
|---|
| 64 | endif
|
|---|
| 65 |
|
|---|
| 66 | 1 read (lunpdb,'(a)',end=3,err=2) line
|
|---|
| 67 | l=iendst(line)
|
|---|
| 68 |
|
|---|
| 69 | if (l.lt.54.or.index(line(1:4),'ATOM').le.0) goto 1
|
|---|
| 70 |
|
|---|
| 71 | if ( line(17:17).ne.' ' ) then
|
|---|
| [38d77eb] | 72 | write (logString, '(a,/,a,/,a,/,2a)')
|
|---|
| [bd2278d] | 73 | & ' pdbread> found alternate atom location: ',
|
|---|
| 74 | & ' !',
|
|---|
| 75 | & line(:l),' in file: ',pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 76 |
|
|---|
| 77 | close(lunpdb)
|
|---|
| 78 | return
|
|---|
| 79 | endif
|
|---|
| 80 |
|
|---|
| 81 | atm=line(13:16)
|
|---|
| 82 |
|
|---|
| 83 | if (index(atm(2:2),'H').gt.0) goto 1 ! no H
|
|---|
| 84 |
|
|---|
| 85 | read(line,10,err=2) iat,rsn,chn,rsid,(cor(i),i=1,3)
|
|---|
| 86 |
|
|---|
| 87 | if ((natp+1).gt.MXATP) then
|
|---|
| [38d77eb] | 88 | write (logString, '(a,i5,a,/,a)')
|
|---|
| [bd2278d] | 89 | & ' pdbread> >MXATP (',MXATP,') ATOM lines in PDB file ',
|
|---|
| 90 | & pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 91 |
|
|---|
| 92 | close(lunpdb)
|
|---|
| 93 | return
|
|---|
| 94 | endif
|
|---|
| 95 |
|
|---|
| 96 | if (chn.ne.chno) then ! new chain
|
|---|
| 97 |
|
|---|
| 98 | if ((nchp+1).gt.MXCHP) then
|
|---|
| [38d77eb] | 99 | write (logString, '(a,i3,a,/,a)')
|
|---|
| [bd2278d] | 100 | & ' pdbread> >MXCHP (',MXCHP,') chains in PDB file ',
|
|---|
| 101 | & pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 102 |
|
|---|
| 103 | close(lunpdb)
|
|---|
| 104 | return
|
|---|
| 105 | endif
|
|---|
| 106 |
|
|---|
| 107 | if ((nrsp+1).gt.MXRSP) then
|
|---|
| [38d77eb] | 108 | write (logString, '(a,i3,a,/,a)')
|
|---|
| [bd2278d] | 109 | & ' pdbread> >MXRSP (',MXRSP,') residues in PDB file ',
|
|---|
| 110 | & pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 111 |
|
|---|
| 112 | close(lunpdb)
|
|---|
| 113 | return
|
|---|
| 114 | endif
|
|---|
| 115 |
|
|---|
| 116 | if (nchp.eq.1) then
|
|---|
| 117 | nchrsp(nchp)=nrsp
|
|---|
| 118 | elseif (nchp.gt.1) then
|
|---|
| 119 | nchrsp(nchp)=nrsp-nchrsp(nchp)
|
|---|
| 120 | endif
|
|---|
| 121 |
|
|---|
| 122 | nchp=nchp+1
|
|---|
| 123 | chno=chn
|
|---|
| 124 | chnp(nchp)=chn
|
|---|
| 125 |
|
|---|
| 126 | nchrsp(nchp)=nrsp ! -1 1st res.
|
|---|
| 127 |
|
|---|
| 128 | if (nrsp.ge.1) then
|
|---|
| 129 | nrsatp(nrsp)=natp-irsatp(nrsp)+1
|
|---|
| 130 | endif
|
|---|
| 131 |
|
|---|
| 132 | rsido=rsid
|
|---|
| 133 | rsno=rsn
|
|---|
| 134 |
|
|---|
| 135 | nrsp=nrsp+1
|
|---|
| 136 | irsatp(nrsp)=natp+1
|
|---|
| 137 | rsnmp(nrsp)=rsn
|
|---|
| 138 | rsidp(nrsp)=rsid
|
|---|
| 139 |
|
|---|
| 140 | elseif (rsid.ne.rsido.or.rsn.ne.rsno) then ! new residue
|
|---|
| 141 |
|
|---|
| 142 | if ((nrsp+1).gt.MXRSP) then
|
|---|
| [38d77eb] | 143 | write (logString, '(a,i3,a,/,a)')
|
|---|
| [bd2278d] | 144 | & ' pdbread> >MXRSP (',MXRSP,') residues in PDB file ',
|
|---|
| 145 | & pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 146 |
|
|---|
| 147 | close(lunpdb)
|
|---|
| 148 | return
|
|---|
| 149 | endif
|
|---|
| 150 |
|
|---|
| 151 | nrsatp(nrsp)=natp-irsatp(nrsp)+1
|
|---|
| 152 |
|
|---|
| 153 | rsido=rsid
|
|---|
| 154 | rsno=rsn
|
|---|
| 155 |
|
|---|
| 156 | nrsp=nrsp+1
|
|---|
| 157 | irsatp(nrsp)=natp+1
|
|---|
| 158 | rsnmp(nrsp)=rsn
|
|---|
| 159 | rsidp(nrsp)=rsid
|
|---|
| 160 |
|
|---|
| 161 | endif
|
|---|
| 162 |
|
|---|
| 163 | natp=natp+1
|
|---|
| 164 |
|
|---|
| 165 | noatp(natp)=iat
|
|---|
| 166 | atnmp(natp)=atm
|
|---|
| 167 |
|
|---|
| 168 | xatp(natp)=cor(1)
|
|---|
| 169 | yatp(natp)=cor(2)
|
|---|
| 170 | zatp(natp)=cor(3)
|
|---|
| 171 |
|
|---|
| 172 | goto 1
|
|---|
| 173 |
|
|---|
| [38d77eb] | 174 | 2 write (logString, '(a,/,a,/,2a)')
|
|---|
| [bd2278d] | 175 | & ' pdbread> ERROR reading ATOM line ',
|
|---|
| 176 | & line(:l),
|
|---|
| 177 | & ' from file ',pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 178 |
|
|---|
| 179 | close(lunpdb)
|
|---|
| 180 | return
|
|---|
| 181 |
|
|---|
| 182 | 3 close(lunpdb)
|
|---|
| 183 |
|
|---|
| 184 | if (natp.gt.0) then
|
|---|
| 185 |
|
|---|
| 186 | if (nchp.eq.1) then
|
|---|
| 187 | nchrsp(nchp)=nrsp
|
|---|
| 188 | elseif (nchp.gt.1) then
|
|---|
| 189 | nchrsp(nchp)=nrsp-nchrsp(nchp)
|
|---|
| 190 | endif
|
|---|
| 191 |
|
|---|
| 192 | nrsatp(nrsp)=natp-irsatp(nrsp)+1
|
|---|
| 193 | ier=0
|
|---|
| 194 |
|
|---|
| 195 | else
|
|---|
| 196 |
|
|---|
| [38d77eb] | 197 | write (logString, '(a,/,a)')
|
|---|
| [bd2278d] | 198 | & ' pdbread> NO atom coordinates selected from file ',
|
|---|
| 199 | & pdbfil(1:iendst(pdbfil))
|
|---|
| [e40e335] | 200 |
|
|---|
| 201 | endif
|
|---|
| 202 |
|
|---|
| 203 | return
|
|---|
| 204 |
|
|---|
| 205 | 10 format(6x,i5,6x,a3,1x,a1,a5,3x,3d8.3)
|
|---|
| 206 |
|
|---|
| 207 | end
|
|---|
| [bd2278d] | 208 | ! **************************************************************
|
|---|
| [e40e335] | 209 |
|
|---|
| 210 | subroutine pdbvars()
|
|---|
| 211 |
|
|---|
| [bd2278d] | 212 | ! --------------------------------------------------------------------
|
|---|
| 213 | ! PURPOSE: sequence,indices for selected atoms (data in INCP.H)
|
|---|
| 214 | ! & torsions from PDB to be used to build SMMP structure
|
|---|
| 215 | !
|
|---|
| 216 | ! ixatp(i,)
|
|---|
| 217 | ! = indices for SMMP atoms pointing to PDB atoms
|
|---|
| 218 | ! (=0, if atom not selected)
|
|---|
| 219 | !
|
|---|
| 220 | ! --------------------------------- ref. point & axes
|
|---|
| 221 | ! ixrfpt(3,),rfpt(3,),xrfax(3,),yrfax(3,),zrfax(3,)
|
|---|
| 222 | !
|
|---|
| 223 | ! CALLS: tolost,getmol,bldmol,addend,atixpdb,setmvs,mklist,
|
|---|
| 224 | ! dihedr,fnd3ba,setsys,getpar,setvar,rmsdopt
|
|---|
| 225 | ! --------------------------------------------------------------------
|
|---|
| [e40e335] | 226 |
|
|---|
| 227 | include 'INCL.H'
|
|---|
| 228 | include 'INCP.H'
|
|---|
| 229 |
|
|---|
| [32289cd] | 230 | double precision dihedr, rm, av1, av2, rmsd, h, x, y, z
|
|---|
| 231 |
|
|---|
| 232 | integer nml, nrs, nc, irb, ire, irs, i, ii, it, i1, i2, i3, i4, j1
|
|---|
| 233 | integer j2, j3, j4, inew, j, ix
|
|---|
| 234 |
|
|---|
| [e40e335] | 235 | character res*3
|
|---|
| 236 | dimension rm(3,3),av1(3),av2(3),h(3)
|
|---|
| 237 |
|
|---|
| 238 |
|
|---|
| 239 | nml=0
|
|---|
| 240 | nrs=0
|
|---|
| 241 |
|
|---|
| 242 | do nc=1,nchp ! PDB chains
|
|---|
| 243 |
|
|---|
| [bd2278d] | 244 | ! =============================== SMMP molecule
|
|---|
| [e40e335] | 245 | nml=nml+1
|
|---|
| 246 | if (nml.gt.mxml) then
|
|---|
| [38d77eb] | 247 | write (logString, '(a,i4,2a)')' pdbvars> NUMBER of chains > '
|
|---|
| [bd2278d] | 248 | & ,mxml,' in ',' ?'
|
|---|
| [e40e335] | 249 | stop
|
|---|
| 250 | endif
|
|---|
| 251 | ntlml=nml
|
|---|
| [bd2278d] | 252 | ! ----------------------------- 'nmml' = ChainID
|
|---|
| [e40e335] | 253 | nmml(nml)=chnp(nc)
|
|---|
| 254 |
|
|---|
| [bd2278d] | 255 | ! ======================================== get sequence
|
|---|
| [e40e335] | 256 |
|
|---|
| 257 | irb=nrs+1
|
|---|
| 258 | ire=nrs+nchrsp(nc)
|
|---|
| [bd2278d] | 259 | ! ----------------------------- # of 1st & last residue
|
|---|
| [e40e335] | 260 | irsml1(nml)=irb
|
|---|
| 261 | irsml2(nml)=ire
|
|---|
| 262 |
|
|---|
| 263 | do irs=irb,ire ! residues of chain 'nc'
|
|---|
| 264 |
|
|---|
| 265 | nrs=nrs+1
|
|---|
| 266 |
|
|---|
| 267 | if (nrs.gt.mxrs) then
|
|---|
| [38d77eb] | 268 | write (logString, '(a,i4,2a)')
|
|---|
| 269 | & ' pdbvars> NUMBER of residues > ', mxrs, ' in ',' ?'
|
|---|
| [e40e335] | 270 | stop
|
|---|
| 271 | endif
|
|---|
| 272 |
|
|---|
| 273 | res=rsnmp(irs)
|
|---|
| 274 | call tolost(res)
|
|---|
| 275 |
|
|---|
| 276 | seq(nrs)=res
|
|---|
| 277 |
|
|---|
| 278 | if (.not.flex.and.irs.eq.irb.and.seq(nrs)(1:3).eq.'pro')
|
|---|
| [bd2278d] | 279 | & seq(nrs)='pron' ! only ECEPP/3
|
|---|
| [e40e335] | 280 |
|
|---|
| 281 | enddo ! residues
|
|---|
| 282 |
|
|---|
| [bd2278d] | 283 | ! ======================== get initial coords. for molecule 'nml'
|
|---|
| 284 | ! with library values for deg. of freedom
|
|---|
| [e40e335] | 285 |
|
|---|
| 286 | call getmol(nml) ! assemble res. data from libraries
|
|---|
| 287 |
|
|---|
| 288 | do i=1,6 ! initialize global parameters
|
|---|
| 289 | gbpr(i,nml)=zero
|
|---|
| 290 | enddo
|
|---|
| 291 |
|
|---|
| 292 | call bldmol(nml) ! co-ordinates
|
|---|
| 293 | call addend(nml,'nh2 ','cooh') ! modify ends
|
|---|
| 294 |
|
|---|
| 295 | call atixpdb(nml) ! get 'ixatp'
|
|---|
| 296 |
|
|---|
| [bd2278d] | 297 | ! -------------------------- 'load' SMMP variable information
|
|---|
| [e40e335] | 298 | call setmvs(nml) ! moving sets
|
|---|
| 299 | call mklist(nml) ! interaction lists
|
|---|
| 300 |
|
|---|
| [bd2278d] | 301 | ! ================================= get variables for 'nml'
|
|---|
| [e40e335] | 302 |
|
|---|
| 303 | ii=ivrml1(nml)
|
|---|
| 304 | do i=ii,ii+nvrml(nml)-1 ! SMMP torsions
|
|---|
| 305 |
|
|---|
| 306 | isrfvr(i) = .false.
|
|---|
| 307 | fxvr(i) = .false.
|
|---|
| 308 | idvr(i) = i
|
|---|
| 309 |
|
|---|
| 310 | it = ityvr(i)
|
|---|
| 311 | i1 = iatvr(i)
|
|---|
| 312 |
|
|---|
| 313 | if (it.eq.3) then ! torsion
|
|---|
| 314 |
|
|---|
| 315 | i2=iowat(i1) ! indices of SMMP atoms
|
|---|
| 316 | i3=iowat(i2)
|
|---|
| 317 | i4=iowat(i3)
|
|---|
| 318 |
|
|---|
| 319 | j1=ixatp(i1) ! inds. for corresp. PDB atoms
|
|---|
| 320 | j2=ixatp(i2)
|
|---|
| 321 | j3=ixatp(i3)
|
|---|
| 322 | j4=ixatp(i4)
|
|---|
| 323 |
|
|---|
| 324 | if (j1.le.0.or.j2.le.0.or.j3.le.0.or.j4.le.0) then
|
|---|
| 325 |
|
|---|
| 326 | vlvr(i) = toat(i1) ! default value from library
|
|---|
| 327 |
|
|---|
| 328 | else ! get value from PDB
|
|---|
| 329 |
|
|---|
| 330 | xat(i1)=xatp(j1)
|
|---|
| 331 | yat(i1)=yatp(j1)
|
|---|
| 332 | zat(i1)=zatp(j1)
|
|---|
| 333 |
|
|---|
| 334 | xat(i2)=xatp(j2)
|
|---|
| 335 | yat(i2)=yatp(j2)
|
|---|
| 336 | zat(i2)=zatp(j2)
|
|---|
| 337 |
|
|---|
| 338 | xat(i3)=xatp(j3)
|
|---|
| 339 | yat(i3)=yatp(j3)
|
|---|
| 340 | zat(i3)=zatp(j3)
|
|---|
| 341 |
|
|---|
| 342 | xat(i4)=xatp(j4)
|
|---|
| 343 | yat(i4)=yatp(j4)
|
|---|
| 344 | zat(i4)=zatp(j4)
|
|---|
| 345 |
|
|---|
| 346 | vlvr(i) = dihedr(i1,i2,i3,i4)
|
|---|
| 347 |
|
|---|
| 348 | isrfvr(i) = .true.
|
|---|
| 349 |
|
|---|
| 350 | endif
|
|---|
| 351 |
|
|---|
| 352 | elseif (it.eq.2) then ! b.angle
|
|---|
| 353 | vlvr(i)=baat(i1)
|
|---|
| 354 | elseif (it.eq.1) then ! b.length
|
|---|
| 355 | vlvr(i)=blat(i1)
|
|---|
| 356 | endif
|
|---|
| 357 |
|
|---|
| 358 | olvlvr(i) = vlvr(i)
|
|---|
| 359 |
|
|---|
| 360 | enddo ! SMMP vars.
|
|---|
| 361 |
|
|---|
| 362 | nvr = ivrml1(ntlml)+nvrml(ntlml)-1
|
|---|
| 363 |
|
|---|
| [bd2278d] | 364 | ! ================================= global parameters for 'nml'
|
|---|
| [e40e335] | 365 |
|
|---|
| [bd2278d] | 366 | ! +++++++++++
|
|---|
| [e40e335] | 367 | inew=0
|
|---|
| 368 |
|
|---|
| 369 | if (inew.eq.1) then
|
|---|
| [bd2278d] | 370 | ! ++++++++++++++++++++++++
|
|---|
| [e40e335] | 371 |
|
|---|
| 372 | call setvar(nml,vlvr)
|
|---|
| 373 |
|
|---|
| 374 | nrs = irsml2(nml)-irsml1(nml)+1
|
|---|
| 375 | call rmsdopt(nml,1,nrs,ixatp,xatp,yatp,zatp,0,rm,av1,av2,rmsd)
|
|---|
| 376 |
|
|---|
| [bd2278d] | 377 | ! ---------------------------- retrieve ref. coords.
|
|---|
| 378 | ! & transform acc. to opt. rmsd
|
|---|
| [e40e335] | 379 | do i=1,3
|
|---|
| 380 | ii=ixrfpt(i,nml)
|
|---|
| 381 |
|
|---|
| 382 | h(1)=xat(ii)-av1(1)
|
|---|
| 383 | h(2)=yat(ii)-av1(2)
|
|---|
| 384 | h(3)=zat(ii)-av1(3)
|
|---|
| 385 |
|
|---|
| 386 | x=av2(1)
|
|---|
| 387 | y=av2(2)
|
|---|
| 388 | z=av2(3)
|
|---|
| 389 |
|
|---|
| 390 | do j=1,3
|
|---|
| 391 | x = x + rm(j,1) * h(j)
|
|---|
| 392 | y = y + rm(j,2) * h(j)
|
|---|
| 393 | z = z + rm(j,3) * h(j)
|
|---|
| 394 | enddo
|
|---|
| 395 |
|
|---|
| 396 | xat(ii)=x
|
|---|
| 397 | yat(ii)=y
|
|---|
| 398 | zat(ii)=z
|
|---|
| 399 | enddo
|
|---|
| 400 |
|
|---|
| 401 | call getpar(nml)
|
|---|
| 402 | call bldmol(nml) ! finally build SMMP molecule
|
|---|
| 403 |
|
|---|
| [bd2278d] | 404 | ! ++++++++++++++++
|
|---|
| [e40e335] | 405 | else ! old
|
|---|
| [bd2278d] | 406 | ! ++++++++++++++++
|
|---|
| [e40e335] | 407 |
|
|---|
| 408 | call fnd3ba(nml,i1,i2,i3) ! three 1st bb atoms in SMMP (e.g. n,ca,c')
|
|---|
| 409 |
|
|---|
| 410 | ixrfpt(1,nml)=i1
|
|---|
| 411 | ixrfpt(2,nml)=i2
|
|---|
| 412 | ixrfpt(3,nml)=i3
|
|---|
| 413 |
|
|---|
| [bd2278d] | 414 | ! -------------------------------- retrieve ref. coords.
|
|---|
| [e40e335] | 415 | do i=1,3
|
|---|
| 416 | ii=ixrfpt(i,nml)
|
|---|
| 417 | ix=ixatp(ii)
|
|---|
| 418 | if (ix.gt.0) then
|
|---|
| 419 | xat(ii)=xatp(ix)
|
|---|
| 420 | yat(ii)=yatp(ix)
|
|---|
| 421 | zat(ii)=zatp(ix)
|
|---|
| 422 | else
|
|---|
| [38d77eb] | 423 | write (logString, '(3a)') ' pdbvars> missing PDB atom ',
|
|---|
| 424 | & nmat(ii), ' is ref. point for SMMP - cannot proceed !'
|
|---|
| [e40e335] | 425 | endif
|
|---|
| 426 | enddo
|
|---|
| 427 |
|
|---|
| 428 | call getpar(nml)
|
|---|
| 429 | call setvar(nml,vlvr) ! finally build SMMP molecule
|
|---|
| 430 |
|
|---|
| 431 | nrs = irsml2(nml)-irsml1(nml)+1
|
|---|
| 432 | call rmsdopt(nml,1,nrs,ixatp,xatp,yatp,zatp,0,rm,av1,av2,rmsd)
|
|---|
| 433 |
|
|---|
| [bd2278d] | 434 | ! ++++++++++
|
|---|
| [e40e335] | 435 | endif
|
|---|
| [bd2278d] | 436 | ! ++++++++++
|
|---|
| [e40e335] | 437 |
|
|---|
| [38d77eb] | 438 | write (logString, *) ' '
|
|---|
| 439 | write (logString, *) ' Initial RMSD ',rmsd
|
|---|
| [e40e335] | 440 |
|
|---|
| 441 | enddo ! chains(molecules)
|
|---|
| 442 |
|
|---|
| 443 | return
|
|---|
| 444 | end
|
|---|
| [bd2278d] | 445 | ! ***************************
|
|---|
| [e40e335] | 446 | subroutine atixpdb(nml)
|
|---|
| 447 |
|
|---|
| [bd2278d] | 448 | ! --------------------------------------------------------------------
|
|---|
| 449 | ! PURPOSE: get ixatp - pointer of each SMMP atom to corresponding atom
|
|---|
| 450 | ! of reference structure loaded in 'INCP.H'
|
|---|
| 451 | ! (=0 if no corr. atom in ref. str.)
|
|---|
| 452 | !
|
|---|
| 453 | ! CALLS: toupst
|
|---|
| 454 | ! --------------------------------------------------------------------
|
|---|
| [e40e335] | 455 |
|
|---|
| 456 | include 'INCL.H'
|
|---|
| 457 | include 'INCP.H'
|
|---|
| 458 |
|
|---|
| [32289cd] | 459 | integer irs, nml, i1, i2, iat, ix, i
|
|---|
| 460 |
|
|---|
| [e40e335] | 461 | character*4 atm
|
|---|
| 462 |
|
|---|
| 463 |
|
|---|
| 464 | atm=' '
|
|---|
| 465 |
|
|---|
| 466 | do irs=irsml1(nml),irsml2(nml) ! SMMP residues
|
|---|
| 467 |
|
|---|
| 468 | i1=irsatp(irs)
|
|---|
| 469 | i2=i1+nrsatp(irs)-1
|
|---|
| 470 |
|
|---|
| 471 | do iat=iatrs1(irs),iatrs2(irs) ! SMMP atoms
|
|---|
| 472 |
|
|---|
| 473 | ix=0
|
|---|
| 474 |
|
|---|
| 475 | if (nmat(iat)(1:1).ne.'h') then ! ignore hydrogens
|
|---|
| 476 |
|
|---|
| 477 | atm(2:4)=nmat(iat)(1:3)
|
|---|
| 478 | call toupst(atm)
|
|---|
| 479 |
|
|---|
| 480 | do i=i1,i2 ! atoms of PDB residue
|
|---|
| 481 | if (index(atnmp(i),atm).gt.0) then
|
|---|
| 482 | ix=i
|
|---|
| 483 | goto 1
|
|---|
| 484 | endif
|
|---|
| 485 | enddo
|
|---|
| [32289cd] | 486 |
|
|---|
| [38d77eb] | 487 | ! write (logString, '(8a)') ' pdbvars> ',atm,' not found in '
|
|---|
| [bd2278d] | 488 | ! # ,chnp(nc),' ',rsidp(irs),' ',rsnmp(irs)
|
|---|
| [e40e335] | 489 |
|
|---|
| 490 | endif
|
|---|
| 491 |
|
|---|
| 492 | 1 ixatp(iat)=ix
|
|---|
| 493 |
|
|---|
| [32289cd] | 494 | enddo ! SMMP atoms of 'irs'
|
|---|
| [e40e335] | 495 | enddo ! residues
|
|---|
| 496 |
|
|---|
| 497 | return
|
|---|
| 498 | end
|
|---|
| [bd2278d] | 499 | ! **************************
|
|---|
| [e40e335] | 500 | subroutine getpar(nml)
|
|---|
| 501 |
|
|---|
| 502 | include 'INCL.H'
|
|---|
| 503 |
|
|---|
| [32289cd] | 504 | double precision tol, h1, h2, h3, x1, x2, x3, d, z1, z2, z3, y1
|
|---|
| 505 | double precision y2, y3, yp1, yp2
|
|---|
| 506 |
|
|---|
| 507 | integer i1, nml, i2, i3, i
|
|---|
| 508 |
|
|---|
| [e40e335] | 509 | parameter (TOL = 1.d-12)
|
|---|
| 510 |
|
|---|
| [bd2278d] | 511 | ! Obtain molecule-fixed system (J,K,L) for 1st 3 bb-atoms,
|
|---|
| 512 | ! -> determine global parameters: shifts dX,dY,dZ
|
|---|
| 513 | ! & angles alpha,beta,gamma [rad], put into 'gbpr'
|
|---|
| [32289cd] | 514 | !
|
|---|
| [bd2278d] | 515 | ! CALLS: none
|
|---|
| 516 | !
|
|---|
| [e40e335] | 517 |
|
|---|
| 518 | i1=ixrfpt(1,nml) ! from 'INCL.H'
|
|---|
| 519 | i2=ixrfpt(2,nml)
|
|---|
| 520 | i3=ixrfpt(3,nml)
|
|---|
| [bd2278d] | 521 | ! -------------------------------------- Shifts
|
|---|
| [e40e335] | 522 | gbpr(1,nml) = xat(i1)
|
|---|
| 523 | gbpr(2,nml) = yat(i1)
|
|---|
| 524 | gbpr(3,nml) = zat(i1)
|
|---|
| 525 |
|
|---|
| 526 | do i = 4,6
|
|---|
| 527 | gbpr(i,nml) = 0.d0
|
|---|
| 528 | enddo
|
|---|
| [bd2278d] | 529 | ! --------------------------------- J
|
|---|
| [e40e335] | 530 | h1=xat(i2)
|
|---|
| 531 | h2=yat(i2)
|
|---|
| 532 | h3=zat(i2)
|
|---|
| 533 |
|
|---|
| 534 | x1=h1-xat(i1)
|
|---|
| 535 | x2=h2-yat(i1)
|
|---|
| 536 | x3=h3-zat(i1)
|
|---|
| 537 |
|
|---|
| 538 | d=sqrt(x1*x1+x2*x2+x3*x3)
|
|---|
| 539 |
|
|---|
| 540 | x1=x1/d
|
|---|
| 541 | x2=x2/d
|
|---|
| 542 | x3=x3/d
|
|---|
| [bd2278d] | 543 | ! --------------------------------- L
|
|---|
| [e40e335] | 544 | h1=xat(i3)-h1
|
|---|
| 545 | h2=yat(i3)-h2
|
|---|
| 546 | h3=zat(i3)-h3
|
|---|
| 547 |
|
|---|
| 548 | z1=x2*h3-x3*h2
|
|---|
| 549 | z2=x3*h1-x1*h3
|
|---|
| 550 | z3=x1*h2-x2*h1
|
|---|
| 551 |
|
|---|
| 552 | d=sqrt(z1*z1+z2*z2+z3*z3)
|
|---|
| 553 |
|
|---|
| 554 | z1=z1/d
|
|---|
| 555 | z2=z2/d
|
|---|
| 556 | z3=z3/d
|
|---|
| 557 |
|
|---|
| [bd2278d] | 558 | ! ---------------------------------- K
|
|---|
| [e40e335] | 559 | y1=z2*x3-z3*x2
|
|---|
| 560 | y2=z3*x1-z1*x3
|
|---|
| 561 | y3=z1*x2-z2*x1
|
|---|
| [32289cd] | 562 |
|
|---|
| [e40e335] | 563 | if ( ( 1.d0 - abs(y3) ) .gt. TOL ) then ! ============ |beta| < PI/2
|
|---|
| 564 |
|
|---|
| [bd2278d] | 565 | ! ----------------------------------------------- Y'
|
|---|
| [e40e335] | 566 | d = sqrt( y1 * y1 + y2 * y2 )
|
|---|
| 567 | yp1= y1 / d
|
|---|
| 568 | yp2= y2 / d
|
|---|
| 569 |
|
|---|
| 570 | gbpr(4,nml)= atan2( -yp1, yp2 ) ! alpha
|
|---|
| 571 | gbpr(5,nml)= atan2( y3, ( y1*yp1+y2*yp2 ) ) ! beta
|
|---|
| 572 | gbpr(6,nml)= atan2( ( z1*yp2-z2*yp1 ),( x1*yp2-x2*yp1 ) ) ! gamma
|
|---|
| 573 |
|
|---|
| 574 | else ! ======================= |beta| = PI/2
|
|---|
| 575 |
|
|---|
| 576 | gbpr(4,nml) = atan2( x2, x1 ) ! alpha+gamma
|
|---|
| 577 |
|
|---|
| 578 | if ( abs(y3) .lt. 1.d0 ) then ! beta
|
|---|
| 579 | gbpr(5,nml) = asin(y3)
|
|---|
| 580 | else if ( y3 .gt. 0.d0 ) then
|
|---|
| 581 | gbpr(5,nml) = pi*.5d0
|
|---|
| 582 | else
|
|---|
| 583 | gbpr(5,nml) = -pi*.5d0
|
|---|
| 584 | endif
|
|---|
| 585 |
|
|---|
| 586 | gbpr(6,nml) = 0.0
|
|---|
| 587 |
|
|---|
| 588 | endif
|
|---|
| 589 |
|
|---|
| 590 | return
|
|---|
| 591 | end
|
|---|
| 592 |
|
|---|
