[e40e335] | 1 | c **************************************************************
|
---|
| 2 | c
|
---|
| 3 | c
|
---|
| 4 | c This file contains the subroutines: addend, redchg, rplgrp
|
---|
| 5 | c
|
---|
| 6 | c Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
|
---|
| 7 | c Shura Hayryan, Chin-Ku
|
---|
| 8 | c Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
|
---|
| 9 | c Jan H. Meinke, Sandipan Mohanty
|
---|
| 10 | c
|
---|
| 11 | c $Id: addend.f 334 2007-08-07 09:23:59Z meinke $
|
---|
| 12 | c **************************************************************
|
---|
| 13 | subroutine addend(nml,grpn,grpc)
|
---|
| 14 |
|
---|
| 15 | c ..............................................................
|
---|
| 16 | c PURPOSE: modify terminal residues to complete bonding scheme
|
---|
| 17 | c with residue 'grpn' at N- and residue 'grpc' at C-terminus
|
---|
| 18 | c ! need initial co-ordinates for residues to modify
|
---|
| 19 | c ! for N-terminus: may add only simple groups
|
---|
| 20 | c
|
---|
| 21 | c CALLS: rplgrp,tolost,redchg
|
---|
| 22 | c ..............................................................
|
---|
| 23 |
|
---|
| 24 | include 'INCL.H'
|
---|
| 25 |
|
---|
| 26 | character grpn*4,grpc*4
|
---|
| 27 |
|
---|
| 28 | character res*4,rpat*4,sbrs*4,grn*4,grc*4
|
---|
| 29 |
|
---|
| 30 |
|
---|
| 31 | grn = grpn
|
---|
| 32 | call tolost(grn)
|
---|
| 33 | grc = grpc
|
---|
| 34 | call tolost(grc)
|
---|
| 35 |
|
---|
| 36 | if (grn(:3).eq.'ace'.or.grc(:3).eq.'ace'
|
---|
| 37 | #.or.grn(:3).eq.'nme'.or.grc(:3).eq.'nme') then
|
---|
| 38 |
|
---|
| 39 | write(*,'(2a)') ' addend> N-Acetyl (ace) or N-Methylamide (nme)'
|
---|
| 40 | # ,' should be put in SEQUENCE file, not added as end groups'
|
---|
| 41 |
|
---|
| 42 | stop
|
---|
| 43 | endif
|
---|
| 44 |
|
---|
| 45 | c __________________________________________ N-terminus
|
---|
| 46 | ifirs=irsml1(nml)
|
---|
| 47 | rpat='n '
|
---|
| 48 | res=seq(ifirs)
|
---|
| 49 | call tolost(res)
|
---|
| 50 | if (res(:3).ne.'ace') then
|
---|
| 51 | if (grn(:3).eq.'nh2') then
|
---|
| 52 | if (res(:3).eq.'hyp'.and..not.flex) then
|
---|
| 53 | if(sh2) then
|
---|
| 54 | sbrs='nh2+'
|
---|
| 55 | else
|
---|
| 56 | write (*,'(2a)') ' addend> ',
|
---|
| 57 | # ' No N-terminal Hyp possible with ECEPP/3 dataset'
|
---|
| 58 | stop
|
---|
| 59 | endif
|
---|
| 60 |
|
---|
| 61 | elseif (res(:3).eq.'pro') then
|
---|
| 62 | sbrs='nh1 '
|
---|
| 63 | elseif (res(:3).eq.'gly'.and..not.flex) then
|
---|
| 64 | if (sh2) then
|
---|
| 65 | sbrs='nh2 '
|
---|
| 66 | else
|
---|
| 67 | sbrs='nh2g'
|
---|
| 68 | endif
|
---|
| 69 | else
|
---|
| 70 | sbrs='nh2 '
|
---|
| 71 | endif
|
---|
| 72 |
|
---|
| 73 | elseif (grn.eq.'nh3+') then
|
---|
| 74 | if (res(:3).eq.'pro'.and..not.flex) then
|
---|
| 75 | sbrs='nh2+'
|
---|
| 76 | elseif (res(:3).eq.'gly'.and..not.flex) then
|
---|
| 77 | sbrs='nh3g'
|
---|
| 78 | else
|
---|
| 79 | sbrs='nh3+'
|
---|
| 80 | endif
|
---|
| 81 |
|
---|
| 82 | else
|
---|
| 83 |
|
---|
| 84 | write(*,'(2a)') ' addend> Can add only ',
|
---|
| 85 | * 'nh2 or nh3+ to N-terminus'
|
---|
| 86 | stop
|
---|
| 87 |
|
---|
| 88 | endif
|
---|
| 89 |
|
---|
| 90 | call rplgrp(nml,ifirs,rpat,sbrs)
|
---|
| 91 | if (flex) call redchg(nml,ifirs,rpat,sbrs) ! Flex dataset
|
---|
| 92 |
|
---|
| 93 | else ! ace
|
---|
| 94 |
|
---|
| 95 | write(*,'(2a)') ' addend> Acetyl group',
|
---|
| 96 | # ' at N-terminus not modified'
|
---|
| 97 | endif
|
---|
| 98 |
|
---|
| 99 | c __________________________________________ C-terminus
|
---|
| 100 | ilars=irsml2(nml)
|
---|
| 101 | rpat='c '
|
---|
| 102 | res=seq(ilars)
|
---|
| 103 | call tolost(res)
|
---|
| 104 |
|
---|
| 105 | if (res(:3).ne.'nme') then
|
---|
| 106 |
|
---|
| 107 | if (grc.eq.'cooh') then
|
---|
| 108 |
|
---|
| 109 | if (res(:3).eq.'gly'.and..not.sh2) then
|
---|
| 110 | sbrs='gooh'
|
---|
| 111 | else
|
---|
| 112 | sbrs='cooh'
|
---|
| 113 | endif
|
---|
| 114 |
|
---|
| 115 | elseif (grc.eq.'coo-') then
|
---|
| 116 |
|
---|
| 117 | if (res(:3).eq.'gly'.and..not.sh2) then
|
---|
| 118 | sbrs='goo-'
|
---|
| 119 | else
|
---|
| 120 | sbrs='coo-'
|
---|
| 121 | endif
|
---|
| 122 |
|
---|
| 123 | else
|
---|
| 124 |
|
---|
| 125 | write(*,'(2a)') ' addend> Can add only ',
|
---|
| 126 | # 'cooh or coo- to C-terminus'
|
---|
| 127 | stop
|
---|
| 128 |
|
---|
| 129 | endif
|
---|
| 130 |
|
---|
| 131 | call rplgrp(nml,ilars,rpat,sbrs)
|
---|
| 132 | if (flex) call redchg(nml,ilars,rpat,sbrs) ! Flex dataset
|
---|
| 133 |
|
---|
| 134 | else ! N'-methylamide
|
---|
| 135 |
|
---|
| 136 | write(*,'(2a)') ' addend> N-Methylamide',
|
---|
| 137 | # ' at C-terminus not modified'
|
---|
| 138 |
|
---|
| 139 | endif
|
---|
| 140 |
|
---|
| 141 | c ----------------------------- net charge of molecule
|
---|
| 142 | cg = 0.d0
|
---|
| 143 | do i=iatrs1(irsml1(nml)),iatrs2(irsml2(nml))
|
---|
| 144 | cg = cg + cgat(i)
|
---|
| 145 | enddo
|
---|
| 146 | if (abs(cg).gt.1.d-5) write(*,'(a,i2,a,f7.3,/)')
|
---|
| 147 | # ' addend> Net charge of molecule #'
|
---|
| 148 | # ,nml,': ',cg
|
---|
| 149 |
|
---|
| 150 | return
|
---|
| 151 | end
|
---|
| 152 | c ****************************************
|
---|
| 153 | subroutine rplgrp(nml,nrs,rpat,sbrs)
|
---|
| 154 |
|
---|
| 155 | c ...............................................................
|
---|
| 156 | c PURPOSE: replace atom(s) rooted at atom 'rpat' in residue
|
---|
| 157 | c 'nrs' of molecule 'nml' by atom(s) rooted at
|
---|
| 158 | c 'rpat' of residue 'sbrs' (same name of root
|
---|
| 159 | c atom 'rpat' maintains bonding geometry for
|
---|
| 160 | c preceeding atoms in 'nrs')
|
---|
| 161 | c
|
---|
| 162 | c is NOT performed if 'rpat' is within mainchain,
|
---|
| 163 | c except it is first/last mainchain atom of 'nml'
|
---|
| 164 | c
|
---|
| 165 | c CALLS: dihedr,iopfil,iendst,eyring,fndbrn,redres,setsys,valang
|
---|
| 166 | c ...............................................................
|
---|
| 167 |
|
---|
| 168 | include 'INCL.H'
|
---|
| 169 |
|
---|
| 170 | character rpat*4,sbrs*4
|
---|
| 171 | logical ntbb,bb
|
---|
| 172 |
|
---|
| 173 | dimension ibd(mxbd+1),iybd(mxbd+1)
|
---|
| 174 |
|
---|
| 175 |
|
---|
| 176 | ifirs=irsml1(nml)
|
---|
| 177 | ilars=irsml2(nml)
|
---|
| 178 |
|
---|
| 179 | nxt=ixatrs(nrs)
|
---|
| 180 | nfi=iatrs1(nrs)
|
---|
| 181 | nla=iatrs2(nrs)
|
---|
| 182 | c __________________________ indices of atoms to be replaced
|
---|
| 183 | do i=nfi,nla
|
---|
| 184 | if (rpat.eq.nmat(i)) then
|
---|
| 185 | nfirp=i
|
---|
| 186 | goto 1
|
---|
| 187 | endif
|
---|
| 188 | enddo
|
---|
| 189 | write (*,'(4a,i4,a,i4)') ' rplgrp> cannot find atom >',rpat,
|
---|
| 190 | #'< to be replaced in residue ',seq(nrs),nrs,' of molecule ',nml
|
---|
| 191 | stop
|
---|
| 192 |
|
---|
| 193 | 1 call fndbrn(nml,nrs,nfirp,nlarp,irng1,irng2,bb)
|
---|
| 194 | if (irng1.gt.0) goto 10
|
---|
| 195 | ntbb=.false.
|
---|
| 196 |
|
---|
| 197 | if (bb) then ! ..... backbone
|
---|
| 198 |
|
---|
| 199 | if (nfirp.eq.nxt.and.nrs.eq.ilars) goto 2 ! last mainchain atom
|
---|
| 200 |
|
---|
| 201 | if (nfirp.eq.nfi.and.nrs.eq.ifirs) then ! 1st MAINCHAIN ATOM !
|
---|
| 202 |
|
---|
| 203 | ntbb=.true.
|
---|
| 204 |
|
---|
| 205 | ibd(1)=iowat(nfirp)
|
---|
| 206 | iybd(1)=iyowat(nfirp)
|
---|
| 207 |
|
---|
| 208 | do i=1,mxbd
|
---|
| 209 | ibd(i+1)=ibdat(i,nfirp)
|
---|
| 210 | iybd(i+1)=iybdat(i,nfirp)
|
---|
| 211 | enddo
|
---|
| 212 |
|
---|
| 213 | ibdrg=0 ! __________________ check ring
|
---|
| 214 | iybdrg=1
|
---|
| 215 |
|
---|
| 216 | do i=1,nbdat(nfirp)+1
|
---|
| 217 | if (iowat(ibd(i)).ne.nfirp) then
|
---|
| 218 | if (ibdrg.ne.0) then
|
---|
| 219 | write (*,'(2a,i3)')
|
---|
| 220 | # ' rplgrp> Can handle only simple ring at 1st',
|
---|
| 221 | # ' atom of molecule #',nml
|
---|
| 222 | stop
|
---|
| 223 | endif
|
---|
| 224 | ibdrg=ibd(i)
|
---|
| 225 | iybdrg=iybd(i)
|
---|
| 226 | endif
|
---|
| 227 | enddo
|
---|
| 228 | nxtbb1=nlarp+1 ! _________________ next backbone atoms
|
---|
| 229 | isgbb1=iyowat(nxtbb1)
|
---|
| 230 |
|
---|
| 231 | if (nxtbb1.eq.nxt) then
|
---|
| 232 | if (nrs.lt.ilars) then
|
---|
| 233 | nxtbb2=iatrs1(nrs+1)
|
---|
| 234 | goto 3
|
---|
| 235 | endif
|
---|
| 236 | else
|
---|
| 237 | do i=nxt,nxtbb1+1,-1
|
---|
| 238 | if (iowat(i).eq.nxtbb1) then
|
---|
| 239 | nxtbb2=i
|
---|
| 240 | goto 3
|
---|
| 241 | endif
|
---|
| 242 | enddo
|
---|
| 243 | endif
|
---|
| 244 | goto 11
|
---|
| 245 | else
|
---|
| 246 | write (*,'(4a,i4,a,i4)')
|
---|
| 247 | # ' rplgrp> Cannot replace BACKBONE atom ',rpat,
|
---|
| 248 | # ' of residue ',seq(nrs),nrs,' in molecule #',nml
|
---|
| 249 | stop
|
---|
| 250 | endif
|
---|
| 251 |
|
---|
| 252 | endif ! N-terminus
|
---|
| 253 | c _________________________________ previous atoms
|
---|
| 254 | 2 if (nfirp.eq.nfi.and.nrs.eq.ifirs) goto 11
|
---|
| 255 | nxtbb1=iowat(nfirp)
|
---|
| 256 | if (nxtbb1.eq.nfi.and.nrs.eq.ifirs) goto 11
|
---|
| 257 | nxtbb2=iowat(nxtbb1)
|
---|
| 258 | c _______________________________ get data for substituent atoms
|
---|
| 259 | 3 if (iopfil(lunlib,reslib,'old','formatted').le.izero) then
|
---|
| 260 | write (*,'(a,/,a,i3,2a)')
|
---|
| 261 | # ' rplgrp> ERROR opening library of residues:',
|
---|
| 262 | # ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib))
|
---|
| 263 | stop
|
---|
| 264 | endif
|
---|
| 265 | call redres(sbrs,natsb,nxtsb,nvrsb)
|
---|
| 266 | close (lunlib)
|
---|
| 267 | c __________________________ indices of substituent atoms
|
---|
| 268 | do i=1,natsb
|
---|
| 269 | if (rpat.eq.nmath(i)) then
|
---|
| 270 | nfisb=i
|
---|
| 271 | goto 4
|
---|
| 272 | endif
|
---|
| 273 | enddo
|
---|
| 274 | write (*,'(4a)') ' rplgrp> Cannot find atom >',rpat,
|
---|
| 275 | #'< in substituent residue ',sbrs
|
---|
| 276 | stop
|
---|
| 277 |
|
---|
| 278 | 4 nlasb=nfisb
|
---|
| 279 | do i=1,nbdath(nfisb)
|
---|
| 280 | ib=ibdath(i,nfisb)
|
---|
| 281 | if (iowath(ib).lt.nfisb) goto 10
|
---|
| 282 | do j=ib,natsb
|
---|
| 283 | if (j.gt.ib.and.iowath(j).lt.ib) goto 5
|
---|
| 284 | do k=1,nbdath(j)
|
---|
| 285 | if (ibdath(k,j).lt.nfisb) goto 10
|
---|
| 286 | enddo
|
---|
| 287 | nlasb=j
|
---|
| 288 | enddo ! ... branch atoms
|
---|
| 289 | 5 enddo ! ... branches
|
---|
| 290 | c _________________________________________________ local axes at 'nfirp'
|
---|
| 291 | call setsys(nxtbb1,nfirp,nxtbb2,x1,x2,x3,y1,y2,y3,z1,z2,z3)
|
---|
| 292 |
|
---|
| 293 | xtoat(nfirp)=x1
|
---|
| 294 | ytoat(nfirp)=x2
|
---|
| 295 | ztoat(nfirp)=x3
|
---|
| 296 | xbaat(nfirp)=z1
|
---|
| 297 | ybaat(nfirp)=z2
|
---|
| 298 | zbaat(nfirp)=z3
|
---|
| 299 |
|
---|
| 300 | c _____________________ add virtual atoms
|
---|
| 301 | if (ntbb) then
|
---|
| 302 |
|
---|
| 303 | ct=cstoat(nxtbb2) ! t.angle_(+2)
|
---|
| 304 | st=sntoat(nxtbb2)
|
---|
| 305 | ca=csbaat(nxtbb1) ! b.angle_(+1)
|
---|
| 306 | sa=snbaat(nxtbb1)
|
---|
| 307 |
|
---|
| 308 | c ------------------- Eyring
|
---|
| 309 | h2=-sa*ct
|
---|
| 310 | h3=-sa*st
|
---|
| 311 | x1=-ca*x1+h2*y1+h3*z1
|
---|
| 312 | x2=-ca*x2+h2*y2+h3*z2
|
---|
| 313 | x3=-ca*x3+h2*y3+h3*z3
|
---|
| 314 | dx=one/sqrt(x1*x1+x2*x2+x3*x3)
|
---|
| 315 | x1=x1*dx
|
---|
| 316 | x2=x2*dx
|
---|
| 317 | x3=x3*dx
|
---|
| 318 |
|
---|
| 319 | xat(izero)=xat(nfirp)+x1
|
---|
| 320 | yat(izero)=yat(nfirp)+x2
|
---|
| 321 | zat(izero)=zat(nfirp)+x3
|
---|
| 322 | z1=-st*y1+ct*z1
|
---|
| 323 | z2=-st*y2+ct*z2
|
---|
| 324 | z3=-st*y3+ct*z3
|
---|
| 325 | dz=one/sqrt(z1*z1+z2*z2+z3*z3)
|
---|
| 326 | z1=z1*dz
|
---|
| 327 | z2=z2*dz
|
---|
| 328 | z3=z3*dz
|
---|
| 329 |
|
---|
| 330 | ct=cstoat(nxtbb1) ! t.angle_(+1)
|
---|
| 331 | st=sntoat(nxtbb1)
|
---|
| 332 |
|
---|
| 333 | c -------------------- Eyring with b.angle = 90 deg.
|
---|
| 334 | xat(-ione)=xat(izero)-ct*(z2*x3-z3*x2)-st*z1
|
---|
| 335 | yat(-ione)=yat(izero)-ct*(z3*x1-z1*x3)-st*z2
|
---|
| 336 | zat(-ione)=zat(izero)-ct*(z1*x2-z2*x1)-st*z3
|
---|
| 337 |
|
---|
| 338 | endif
|
---|
| 339 | c _____________________________________________ Shift atom data
|
---|
| 340 | nrp=nlarp-nfirp
|
---|
| 341 | nsb=nlasb-nfisb
|
---|
| 342 | if (nrp.ne.nsb) then
|
---|
| 343 | nsh=nsb-nrp
|
---|
| 344 | do i=nfi,nfirp-1 ! bonds to atoms after repl. group
|
---|
| 345 | do j=1,mxbd
|
---|
| 346 | ib=ibdat(j,i)
|
---|
| 347 | if (ib.gt.nlarp.and.ib.le.nla) ibdat(j,i)=ib+nsh
|
---|
| 348 | enddo
|
---|
| 349 | enddo
|
---|
| 350 | ilaat=iatrs2(irsml2(ntlml))
|
---|
| 351 | if (nrp.gt.nsb) then ! less atoms
|
---|
| 352 | i1=nlarp+1
|
---|
| 353 | i2=ilaat
|
---|
| 354 | i3=1
|
---|
| 355 | else ! more atoms
|
---|
| 356 | if ((ilaat+nsh).gt.mxat) then
|
---|
| 357 | write (*,'(a,i5)') ' rplgrp> number of atoms > ',mxat
|
---|
| 358 | stop
|
---|
| 359 | endif
|
---|
| 360 |
|
---|
| 361 | i1=ilaat
|
---|
| 362 | i2=nlarp+1
|
---|
| 363 | i3=-1
|
---|
| 364 | endif
|
---|
| 365 |
|
---|
| 366 | do i=i1,i2,i3
|
---|
| 367 | ii=i+nsh
|
---|
| 368 | nbdat(ii)=nbdat(i)
|
---|
| 369 |
|
---|
| 370 | ibd(1)=iowat(i)
|
---|
| 371 | iybd(1)=iyowat(i)
|
---|
| 372 | do j = 1,mxbd
|
---|
| 373 | ibd(j+1)=ibdat(j,i)
|
---|
| 374 | iybd(j+1)=iybdat(j,i)
|
---|
| 375 | enddo
|
---|
| 376 |
|
---|
| 377 | do j=1,mxbd+1
|
---|
| 378 | if (ibd(j).gt.nfirp) ibd(j)=ibd(j)+nsh
|
---|
| 379 | enddo
|
---|
| 380 |
|
---|
| 381 | iowat(ii)=ibd(1)
|
---|
| 382 | iyowat(ii)=iybd(1)
|
---|
| 383 | do j = 1,mxbd
|
---|
| 384 | ibdat(j,ii)=ibd(j+1)
|
---|
| 385 | iybdat(j,ii)=iybd(j+1)
|
---|
| 386 | enddo
|
---|
| 387 |
|
---|
| 388 | ityat(ii)=ityat(i)
|
---|
| 389 | nmat(ii)=nmat(i)
|
---|
| 390 | cgat(ii)=cgat(i)
|
---|
| 391 | blat(ii)=blat(i)
|
---|
| 392 | baat(ii)=baat(i)
|
---|
| 393 | snbaat(ii)=snbaat(i)
|
---|
| 394 | csbaat(ii)=csbaat(i)
|
---|
| 395 | toat(ii)=toat(i)
|
---|
| 396 | sntoat(ii)=sntoat(i)
|
---|
| 397 | cstoat(ii)=cstoat(i)
|
---|
| 398 | xat(ii)=xat(i)
|
---|
| 399 | yat(ii)=yat(i)
|
---|
| 400 | zat(ii)=zat(i)
|
---|
| 401 | xtoat(ii)=xtoat(i)
|
---|
| 402 | ytoat(ii)=ytoat(i)
|
---|
| 403 | ztoat(ii)=ztoat(i)
|
---|
| 404 | xbaat(ii)=xbaat(i)
|
---|
| 405 | ybaat(ii)=ybaat(i)
|
---|
| 406 | zbaat(ii)=zbaat(i)
|
---|
| 407 |
|
---|
| 408 | enddo
|
---|
| 409 | c ____________________________________________ Shift residue data
|
---|
| 410 | do i=nrs+1,irsml2(ntlml)
|
---|
| 411 | iatrs1(i)=iatrs1(i)+nsh
|
---|
| 412 | iatrs2(i)=iatrs2(i)+nsh
|
---|
| 413 | ixatrs(i)=ixatrs(i)+nsh
|
---|
| 414 | enddo
|
---|
| 415 | iatrs2(nrs)=nla+nsh
|
---|
| 416 | if (nxt.gt.nlarp) ixatrs(nrs)=nxt+nsh
|
---|
| 417 | else
|
---|
| 418 | nsh=0
|
---|
| 419 | endif
|
---|
| 420 | c _________________________________________ Correct data of 'nfirp'
|
---|
| 421 | ish=nfirp-nfisb
|
---|
| 422 | ityat(nfirp)=ityath(nfisb)
|
---|
| 423 |
|
---|
| 424 | if(.not.sh2) cgat(nfirp)=cgath(nfisb) ! NOT for 'ECEPP/2'
|
---|
| 425 |
|
---|
| 426 | nb=nbdath(nfisb) ! _______________ Bonds
|
---|
| 427 |
|
---|
| 428 | do i=1,mxbd
|
---|
| 429 | ib=ibdath(i,nfisb)
|
---|
| 430 | if (ib.ne.0) then
|
---|
| 431 | ibd(i)=ib+ish
|
---|
| 432 | iybd(i)=iybdath(i,nfisb)
|
---|
| 433 | else
|
---|
| 434 | ibd(i)=0
|
---|
| 435 | iybd(i)=1
|
---|
| 436 | endif
|
---|
| 437 |
|
---|
| 438 | enddo
|
---|
| 439 |
|
---|
| 440 | if (ntbb) then
|
---|
| 441 |
|
---|
| 442 | ibd(mxbd+1)=0
|
---|
| 443 | iybd(mxbd+1)=1
|
---|
| 444 |
|
---|
| 445 | ibd(nb+1)=nxtbb1+nsh ! bond to next backbone atom
|
---|
| 446 | iybd(nb+1)=isgbb1
|
---|
| 447 |
|
---|
| 448 | if (ibdrg.ne.0) then
|
---|
| 449 | nb=nb+1
|
---|
| 450 | if (nb.gt.mxbd) then
|
---|
| 451 | write (*,'(6a,/,2a,3(i4,a))')
|
---|
| 452 | # ' rplgrp> Cannot add atoms following ',rpat,
|
---|
| 453 | # ' from group ',sbrs,' to atom ',rpat,
|
---|
| 454 | # ' of residue ',seq(nrs),nrs,' in molecule #',nml,
|
---|
| 455 | # ' because need >',(mxbd+1),' bonds'
|
---|
| 456 | stop
|
---|
| 457 | endif
|
---|
| 458 | ibd(nb+1)=ibdrg+nsh
|
---|
| 459 | iybd(nb+1)=iybdrg
|
---|
| 460 | endif
|
---|
| 461 | iowat(nfirp)=ibd(1)
|
---|
| 462 | iyowat(nfirp)=iybd(1)
|
---|
| 463 | do i=1,mxbd
|
---|
| 464 | ibdat(i,nfirp)=ibd(i+1)
|
---|
| 465 | iybdat(i,nfirp)=iybd(i+1)
|
---|
| 466 | enddo
|
---|
| 467 | else ! not 'ntbb'
|
---|
| 468 |
|
---|
| 469 | do i=1,mxbd
|
---|
| 470 | ibdat(i,nfirp)=ibd(i)
|
---|
| 471 | iybdat(i,nfirp)=iybd(i)
|
---|
| 472 | enddo
|
---|
| 473 |
|
---|
| 474 | endif
|
---|
| 475 | nbdat(nfirp)=nb
|
---|
| 476 | c _________________________________________ Add data for substituent
|
---|
| 477 | ii=nfirp
|
---|
| 478 | do i=nfisb+1,nlasb
|
---|
| 479 | ii=ii+1
|
---|
| 480 | nbdat(ii)=nbdath(i)
|
---|
| 481 |
|
---|
| 482 | iow=iowath(i)+ish
|
---|
| 483 | iowat(ii)=iow
|
---|
| 484 | iyowat(ii)=iyowath(i)
|
---|
| 485 |
|
---|
| 486 | do j=1,mxbd
|
---|
| 487 | ib=ibdath(j,i)
|
---|
| 488 | if (ib.ge.nfisb) then
|
---|
| 489 | ibdat(j,ii)=ib+ish
|
---|
| 490 | else
|
---|
| 491 | ibdat(j,ii)=ib
|
---|
| 492 | endif
|
---|
| 493 | iybdat(j,ii)=iybdath(j,i)
|
---|
| 494 | enddo
|
---|
| 495 |
|
---|
| 496 | ityat(ii)=ityath(i)
|
---|
| 497 | nmat(ii)=nmath(i)
|
---|
| 498 | cgat(ii)=cgath(i)
|
---|
| 499 | blat(ii)=blath(i)
|
---|
| 500 | ba=baath(i)
|
---|
| 501 | baat(ii)=ba
|
---|
| 502 | csbaat(ii)=cos(ba)
|
---|
| 503 | snbaat(ii)=sin(ba)
|
---|
| 504 | to=toath(i)
|
---|
| 505 | toat(ii)=to
|
---|
| 506 | cstoat(ii)=cos(to)
|
---|
| 507 | sntoat(ii)=sin(to)
|
---|
| 508 | call eyring(ii,iow)
|
---|
| 509 | if (ntbb) then ! reset some internal coordinates
|
---|
| 510 | if (iow.eq.nfirp) then
|
---|
| 511 | ba=valang(izero,nfirp,ii)
|
---|
| 512 | baat(ii)=ba
|
---|
| 513 | csbaat(ii)=cos(ba)
|
---|
| 514 | snbaat(ii)=sin(ba)
|
---|
| 515 | to=dihedr(-ione,izero,nfirp,ii)
|
---|
| 516 | toat(ii)=to
|
---|
| 517 | cstoat(ii)=cos(to)
|
---|
| 518 | sntoat(ii)=sin(to)
|
---|
| 519 | elseif (iowat(iow).eq.nfirp) then
|
---|
| 520 | to=dihedr(izero,nfirp,iow,ii)
|
---|
| 521 | toat(ii)=to
|
---|
| 522 | cstoat(ii)=cos(to)
|
---|
| 523 | sntoat(ii)=sin(to)
|
---|
| 524 | endif
|
---|
| 525 |
|
---|
| 526 | endif ! ntbb
|
---|
| 527 |
|
---|
| 528 | enddo ! substituent atoms
|
---|
| 529 | c ___________________________________________________ Take care of Variables
|
---|
| 530 | c (assume variables of replaced group/substituent to be stored CONSECUTIVELY)
|
---|
| 531 |
|
---|
| 532 | ilavr=ivrml1(ntlml)+nvrml(ntlml)-1
|
---|
| 533 | ifivr=ivrrs1(nrs) ! variables to be replaced (#=ivrrp,last=lvrrp)
|
---|
| 534 | ivrrp=0
|
---|
| 535 | do i=ifivr,ifivr+nvrrs(nrs)-1
|
---|
| 536 | iat=iatvr(i)
|
---|
| 537 | if (nfirp.lt.iat.and.iat.le.nlarp) then
|
---|
| 538 | ivrrp=ivrrp+1
|
---|
| 539 | lvrrp=i
|
---|
| 540 | endif
|
---|
| 541 | enddo
|
---|
| 542 | if (ivrrp.eq.0) then ! No variables to replace
|
---|
| 543 | do i=ifivr,ilavr
|
---|
| 544 | if (iatvr(i).gt.nlarp) then
|
---|
| 545 | lvrrp=i-1
|
---|
| 546 | goto 6
|
---|
| 547 | endif
|
---|
| 548 | enddo
|
---|
| 549 | lvrrp=ilavr
|
---|
| 550 | endif
|
---|
| 551 | 6 ivrsb=0 ! variables from substituent (#=ivrsb)
|
---|
| 552 | do i=1,nvrsb
|
---|
| 553 | iat=iatvrh(i)
|
---|
| 554 | if (nfisb.lt.iat.and.iat.le.nlasb) then
|
---|
| 555 | ity=ityvrh(i)
|
---|
| 556 | if (ntbb.and.iowath(iat).eq.nfisb.and.ity.gt.2) goto 7
|
---|
| 557 | ivrsb=ivrsb+1
|
---|
| 558 | nmvrh(ivrsb)=nmvrh(i)
|
---|
| 559 | ityvrh(ivrsb)=ityvrh(i)
|
---|
| 560 | iclvrh(ivrsb)=iclvrh(i)
|
---|
| 561 | iatvrh(ivrsb)=iat
|
---|
| 562 | endif
|
---|
| 563 | 7 enddo
|
---|
| 564 | if (nsh.ne.0) then ! if # of atoms changed
|
---|
| 565 | do i=lvrrp+1,ilavr
|
---|
| 566 | iatvr(i)=iatvr(i)+nsh
|
---|
| 567 | enddo
|
---|
| 568 | endif
|
---|
| 569 |
|
---|
| 570 | if (ivrrp.ne.ivrsb) then ! shift data for variables
|
---|
| 571 | jsh=ivrsb-ivrrp
|
---|
| 572 | if (ivrrp.gt.ivrsb) then
|
---|
| 573 | i1=lvrrp+1
|
---|
| 574 | i2=ilavr
|
---|
| 575 | i3=1
|
---|
| 576 | else
|
---|
| 577 | if ((ilavr+jsh).gt.mxvr) then
|
---|
| 578 | write (*,'(a,i5)') ' rplgrp> number of variables > ',mxvr
|
---|
| 579 | stop
|
---|
| 580 | endif
|
---|
| 581 | i1=ilavr
|
---|
| 582 | i2=lvrrp+1
|
---|
| 583 | i3=-1
|
---|
| 584 | endif
|
---|
| 585 | do i=i1,i2,i3
|
---|
| 586 | ii=i+jsh
|
---|
| 587 | ityvr(ii)=ityvr(i)
|
---|
| 588 | iclvr(ii)=iclvr(i)
|
---|
| 589 | nmvr(ii)=nmvr(i)
|
---|
| 590 | iatvr(ii)=iatvr(i)
|
---|
| 591 | enddo
|
---|
| 592 |
|
---|
| 593 | do i=nrs+1,irsml2(ntlml)
|
---|
| 594 | ivrrs1(i)=ivrrs1(i)+jsh
|
---|
| 595 | enddo
|
---|
| 596 | nvrrs(nrs)=nvrrs(nrs)+jsh
|
---|
| 597 | nvrml(nml)=nvrml(nml)+jsh
|
---|
| 598 | do i=nml+1,ntlml
|
---|
| 599 | ivrml1(i)=ivrml1(i)+jsh
|
---|
| 600 | enddo
|
---|
| 601 | endif
|
---|
| 602 | ii=lvrrp-ivrrp ! Add variables for substitutent
|
---|
| 603 | do i=1,ivrsb
|
---|
| 604 | ii=ii+1
|
---|
| 605 | nmvr(ii)=nmvrh(i)
|
---|
| 606 | ityvr(ii)=ityvrh(i)
|
---|
| 607 | iclvr(ii)=iclvrh(i)
|
---|
| 608 | iatvr(ii)=iatvrh(i)+ish
|
---|
| 609 | enddo
|
---|
| 610 |
|
---|
| 611 | return
|
---|
| 612 | c __________________________________________ Errors
|
---|
| 613 | 10 write (*,'(3a,/,2a,i4,a,i4,/,2a)')
|
---|
| 614 | # ' rplgrp> Cannot replace atom(s) following ',rpat,
|
---|
| 615 | # ' from INSIDE a ring',' in residue: ',seq(nrs),nrs,
|
---|
| 616 | # ' in molecule #',nml,' or in substitute: ',sbrs
|
---|
| 617 | stop
|
---|
| 618 | 11 write (*,'(4a,i4,a,i4,/,a)')
|
---|
| 619 | # ' rplgrp> Cannot replace atom(s) following ',rpat,
|
---|
| 620 | # ' of residue ',seq(nrs),nrs,' in molecule #',nml,
|
---|
| 621 | # ' since necessary 2 previous atoms are not available'
|
---|
| 622 | stop
|
---|
| 623 |
|
---|
| 624 | end
|
---|
| 625 | c ****************************************
|
---|
| 626 | subroutine redchg(nml,nrs,rpat,sbrs)
|
---|
| 627 |
|
---|
| 628 | c .........................................................
|
---|
| 629 | c PURPOSE: read and place atomic point charges from residue
|
---|
| 630 | c 'sbrs' to residue 'nrs' of molecule 'nml'
|
---|
| 631 | c from library 'chglib' with LUN=lunchg, if ilib=1
|
---|
| 632 | c 'reslib' with LUN=lunlib, if ilib=2
|
---|
| 633 | c
|
---|
| 634 | c CALLS: iopfil,iendst,tolost
|
---|
| 635 | c ........................................................
|
---|
| 636 |
|
---|
| 637 | include 'INCL.H'
|
---|
| 638 |
|
---|
| 639 | character rpat*4,sbrs*4,atnm*4,res*4,cgty*5,line*100
|
---|
| 640 |
|
---|
| 641 | ifirs=irsml1(nml)
|
---|
| 642 | ilars=irsml2(nml)
|
---|
| 643 | res=seq(nrs)
|
---|
| 644 | call tolost(res)
|
---|
| 645 |
|
---|
| 646 | if (nrs.eq.ifirs.or.nrs.eq.ilars) then
|
---|
| 647 |
|
---|
| 648 | if (rpat.eq.'n '.or.rpat.eq.'c ') then
|
---|
| 649 | if (nrs.eq.ifirs.and.nrs.eq.ilars) goto 10 ! Dont have this yet
|
---|
| 650 |
|
---|
| 651 | if (rpat.eq.'n '.and.nrs.eq.ifirs) then
|
---|
| 652 | if (res(1:3).eq.'pro'.or.res(1:3).eq.'hyp') then
|
---|
| 653 | if (sbrs.eq.'nh1 ') cgty='n'//res
|
---|
| 654 | if (sbrs.eq.'nh2+') cgty='+'//res
|
---|
| 655 | else
|
---|
| 656 | if (sbrs.eq.'nh2 ') cgty='n'//res
|
---|
| 657 | if (sbrs.eq.'nh3+') cgty='+'//res
|
---|
| 658 | endif
|
---|
| 659 | elseif (rpat.eq.'c '.and.nrs.eq.ilars) then
|
---|
| 660 | if (sbrs.eq.'cooh') cgty='c'//res
|
---|
| 661 | if (sbrs.eq.'coo-') cgty='-'//res
|
---|
| 662 | else
|
---|
| 663 | goto 10
|
---|
| 664 | endif
|
---|
| 665 | else
|
---|
| 666 | write (*,*) ' redchg> dont know which end goup is present'
|
---|
| 667 | stop
|
---|
| 668 | endif
|
---|
| 669 | ilib=1
|
---|
| 670 | else
|
---|
| 671 | cgty(1:)=sbrs
|
---|
| 672 | ilib=2
|
---|
| 673 | endif
|
---|
| 674 |
|
---|
| 675 | if (ilib.eq.1) then
|
---|
| 676 |
|
---|
| 677 | if (iopfil(lunchg,chgfil,'old','formatted').le.izero) then
|
---|
| 678 | write (*,'(a,/,a,i3,2a)')
|
---|
| 679 | # ' redchg> ERROR opening library of charges:',
|
---|
| 680 | # ' LUN=',lunchg,' FILE=',chgfil(1:iendst(chgfil))
|
---|
| 681 | stop
|
---|
| 682 | endif
|
---|
| 683 |
|
---|
| 684 | 1 line=' '
|
---|
| 685 | read (lunchg,'(a)',end=3) line
|
---|
| 686 | l=iendst(line)
|
---|
| 687 |
|
---|
| 688 | if (l.ge.10.and.line(1:1).eq.'#'.and.line(2:6).eq.cgty) then
|
---|
| 689 | read (line(7:10),'(i4)') nchg
|
---|
| 690 | if (nchg.le.mxath) then
|
---|
| 691 | read (lunchg,'(10(2x,a4,1x))') (nmath(i),i=1,nchg)
|
---|
| 692 | read (lunchg,'(10(f6.4,1x))') (cgath(i),i=1,nchg)
|
---|
| 693 | close(lunchg)
|
---|
| 694 | do i=iatrs1(nrs),iatrs2(nrs)
|
---|
| 695 | atnm=nmat(i)
|
---|
| 696 | do j=1,nchg
|
---|
| 697 | if (nmath(j).eq.atnm) then
|
---|
| 698 | cgat(i)=cgath(j)
|
---|
| 699 | goto 2
|
---|
| 700 | endif
|
---|
| 701 | enddo
|
---|
| 702 | write (*,'(6a)') ' redchg> Cannot find atom: ',atnm,
|
---|
| 703 | # ' for entry: ',cgty,' in library: ',
|
---|
| 704 | # chgfil(1:iendst(chgfil))
|
---|
| 705 | stop
|
---|
| 706 | 2 enddo
|
---|
| 707 | return
|
---|
| 708 | else
|
---|
| 709 | write (*,'(4a)')
|
---|
| 710 | # ' redchg> must increase MXATH to read data for entry: ',
|
---|
| 711 | # cgty,' in library: ',chgfil(1:iendst(chgfil))
|
---|
| 712 | close(lunchg)
|
---|
| 713 | stop
|
---|
| 714 | endif
|
---|
| 715 | endif
|
---|
| 716 | goto 1
|
---|
| 717 | 3 write (*,'(4a)')
|
---|
| 718 | # ' redchg> Cannot find entry: ',cgty,' in library: ',
|
---|
| 719 | # chgfil(1:iendst(chgfil))
|
---|
| 720 | close(lunchg)
|
---|
| 721 | stop
|
---|
| 722 |
|
---|
| 723 | elseif (ilib.eq.2) then
|
---|
| 724 |
|
---|
| 725 | if (iopfil(lunlib,reslib,'old','formatted').le.izero) then
|
---|
| 726 | write (*,'(a,/,a,i3,2a)')
|
---|
| 727 | # ' redchg> ERROR opening library of residues:',
|
---|
| 728 | # ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib))
|
---|
| 729 | stop
|
---|
| 730 | endif
|
---|
| 731 |
|
---|
| 732 | 4 line=' '
|
---|
| 733 | read (lunlib,'(a)',end=6) line
|
---|
| 734 | l=iendst(line)
|
---|
| 735 |
|
---|
| 736 | if (l.ge.9.and.line(1:1).eq.'#'.and.line(2:5).eq.cgty(1:4)) then
|
---|
| 737 | read (line(6:9),'(i4)') nchg
|
---|
| 738 | if (nchg.le.mxath) then
|
---|
| 739 | read (lunlib,'(a4,42x,d7.4)') (nmath(i),cgath(i),i=1,nchg)
|
---|
| 740 | close(lunlib)
|
---|
| 741 | do i=iatrs1(nrs),iatrs2(nrs)
|
---|
| 742 | atnm=nmat(i)
|
---|
| 743 | do j=1,nchg
|
---|
| 744 | if (nmath(j).eq.atnm) then
|
---|
| 745 | cgat(i)=cgath(j)
|
---|
| 746 | goto 5
|
---|
| 747 | endif
|
---|
| 748 | enddo
|
---|
| 749 | write (*,'(6a)') ' redchg> Cannot find atom: ',atnm,
|
---|
| 750 | # ' for entry: ',cgty,' in library: ',
|
---|
| 751 | # reslib(1:iendst(reslib))
|
---|
| 752 | stop
|
---|
| 753 | 5 enddo
|
---|
| 754 | return
|
---|
| 755 | else
|
---|
| 756 | write (*,'(4a)')
|
---|
| 757 | # ' redchg> must increase MXATH to read data for entry: ',
|
---|
| 758 | # cgty,' in library: ',reslib(1:iendst(reslib))
|
---|
| 759 | close(lunchg)
|
---|
| 760 | stop
|
---|
| 761 | endif
|
---|
| 762 | endif
|
---|
| 763 | goto 4
|
---|
| 764 | 6 write (*,'(4a)')
|
---|
| 765 | # ' redchg> Cannot find entry: ',cgty,' in library: ',
|
---|
| 766 | # reslib(1:iendst(reslib))
|
---|
| 767 | close(lunchg)
|
---|
| 768 | stop
|
---|
| 769 |
|
---|
| 770 | endif
|
---|
| 771 |
|
---|
| 772 | 10 write (*,'(4a)')
|
---|
| 773 | # ' redchg> Do not have charges for N/C-terminal residue ',
|
---|
| 774 | # res,' modified with group :',sbrs
|
---|
| 775 | stop
|
---|
| 776 |
|
---|
| 777 | end
|
---|
| 778 |
|
---|