1 subroutine parmread(iparm,*)
3 C Read the parameters of the probability distributions of the virtual-bond
4 C valence angles and the side chains and energy parameters.
6 implicit real*8 (a-h,o-z)
8 include 'DIMENSIONS.ZSCOPT'
9 include 'DIMENSIONS.FREE'
10 include 'COMMON.IOUNITS'
11 include 'COMMON.CHAIN'
12 include 'COMMON.INTERACT'
14 include 'COMMON.LOCAL'
15 include 'COMMON.TORSION'
16 include 'COMMON.FFIELD'
17 include 'COMMON.NAMES'
18 include 'COMMON.SBRIDGE'
19 include 'COMMON.WEIGHTS'
20 include 'COMMON.ENEPS'
21 include 'COMMON.SCCOR'
22 include 'COMMON.SCROT'
25 character*1 onelett(4) /"G","A","P","D"/
26 character*1 toronelet(-2:2) /"p","a","G","A","P"/
28 dimension blower(3,3,maxlob)
29 character*800 controlcard
30 character*256 bondname_t,thetname_t,rotname_t,torname_t,
31 & tordname_t,fouriername_t,elename_t,sidename_t,scpname_t,
37 double precision ip,mp
41 C Set LPRINT=.TRUE. for debugging
42 dwa16=2.0d0**(1.0d0/6.0d0)
45 C Assign virtual-bond length
49 call card_concat(controlcard,.true.)
52 key = wname(i)(:ilen(wname(i)))
53 call reada(controlcard,key(:ilen(key)),ww(i),1.0d0)
56 write (iout,*) "iparm",iparm," myparm",myparm
57 c If reading not own parameters, skip assignment
59 if (iparm.eq.myparm .or. .not.separate_parset) then
62 c Setup weights for UNRES
84 call card_concat(controlcard,.false.)
86 c Return if not own parameters
88 if (iparm.ne.myparm .and. separate_parset) return
90 call reads(controlcard,"BONDPAR",bondname_t,bondname)
91 open (ibond,file=bondname_t,status='old')
93 call reads(controlcard,"THETPAR",thetname_t,thetname)
94 open (ithep,file=thetname_t,status='old')
96 call reads(controlcard,"ROTPAR",rotname_t,rotname)
97 open (irotam,file=rotname_t,status='old')
99 call reads(controlcard,"TORPAR",torname_t,torname)
100 open (itorp,file=torname_t,status='old')
102 call reads(controlcard,"TORDPAR",tordname_t,tordname)
103 open (itordp,file=tordname_t,status='old')
105 call reads(controlcard,"SCCORAR",sccorname_t,sccorname)
106 open (isccor,file=sccorname_t,status='old')
108 call reads(controlcard,"FOURIER",fouriername_t,fouriername)
109 open (ifourier,file=fouriername_t,status='old')
111 call reads(controlcard,"ELEPAR",elename_t,elename)
112 open (ielep,file=elename_t,status='old')
114 call reads(controlcard,"SIDEPAR",sidename_t,sidename)
115 open (isidep,file=sidename_t,status='old')
117 call reads(controlcard,"SCPPAR",scpname_t,scpname)
118 open (iscpp,file=scpname_t,status='old')
120 write (iout,*) "Parameter set:",iparm
121 write (iout,*) "Energy-term weights:"
123 write (iout,'(a16,f10.5)') wname(i),ww(i)
125 write (iout,*) "Sidechain potential file : ",
126 & sidename_t(:ilen(sidename_t))
128 write (iout,*) "SCp potential file : ",
129 & scpname_t(:ilen(scpname_t))
131 write (iout,*) "Electrostatic potential file : ",
132 & elename_t(:ilen(elename_t))
133 write (iout,*) "Cumulant coefficient file : ",
134 & fouriername_t(:ilen(fouriername_t))
135 write (iout,*) "Torsional parameter file : ",
136 & torname_t(:ilen(torname_t))
137 write (iout,*) "Double torsional parameter file : ",
138 & tordname_t(:ilen(tordname_t))
139 write (iout,*) "Backbone-rotamer parameter file : ",
140 & sccorname(:ilen(sccorname))
141 write (iout,*) "Bond & inertia constant file : ",
142 & bondname_t(:ilen(bondname_t))
143 write (iout,*) "Bending parameter file : ",
144 & thetname_t(:ilen(thetname_t))
145 write (iout,*) "Rotamer parameter file : ",
146 & rotname_t(:ilen(rotname_t))
149 c Read the virtual-bond parameters, masses, and moments of inertia
150 c and Stokes' radii of the peptide group and side chains
153 read (ibond,*) vbldp0,akp
156 read (ibond,*) vbldsc0(1,i),aksc(1,i)
157 dsc(i) = vbldsc0(1,i)
161 dsc_inv(i)=1.0D0/dsc(i)
165 read (ibond,*) ijunk,vbldp0,akp,rjunk
167 read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),
169 dsc(i) = vbldsc0(1,i)
173 dsc_inv(i)=1.0D0/dsc(i)
178 write(iout,'(/a/)')"Force constants virtual bonds:"
179 write (iout,'(a10,a3,6a10)') 'Type','N','VBL','K',
181 write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0
183 write (iout,'(a10,i3,6f10.5)') restyp(i),nbondterm(i),
184 & vbldsc0(1,i),aksc(1,i),abond0(1,i)
186 write (iout,'(13x,3f10.5)')
187 & vbldsc0(j,i),aksc(j,i),abond0(j,i)
193 C Read the parameters of the probability distribution/energy expression
194 C of the virtual-bond valence angles theta
197 read (ithep,*) a0thet(i),(athet(j,i,1,1),j=1,2),
198 & (bthet(j,i,1,1),j=1,2)
199 read (ithep,*) (polthet(j,i),j=0,3)
200 read (ithep,*) (gthet(j,i),j=1,3)
201 read (ithep,*) theta0(i),sig0(i),sigc0(i)
205 athet(1,i,1,-1)=athet(1,i,1,1)
206 athet(2,i,1,-1)=athet(2,i,1,1)
207 bthet(1,i,1,-1)=-bthet(1,i,1,1)
208 bthet(2,i,1,-1)=-bthet(2,i,1,1)
209 athet(1,i,-1,1)=-athet(1,i,1,1)
210 athet(2,i,-1,1)=-athet(2,i,1,1)
211 bthet(1,i,-1,1)=bthet(1,i,1,1)
212 bthet(2,i,-1,1)=bthet(2,i,1,1)
216 athet(1,i,-1,-1)=athet(1,-i,1,1)
217 athet(2,i,-1,-1)=-athet(2,-i,1,1)
218 bthet(1,i,-1,-1)=bthet(1,-i,1,1)
219 bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
220 athet(1,i,-1,1)=athet(1,-i,1,1)
221 athet(2,i,-1,1)=-athet(2,-i,1,1)
222 bthet(1,i,-1,1)=-bthet(1,-i,1,1)
223 bthet(2,i,-1,1)=bthet(2,-i,1,1)
224 athet(1,i,1,-1)=-athet(1,-i,1,1)
225 athet(2,i,1,-1)=athet(2,-i,1,1)
226 bthet(1,i,1,-1)=bthet(1,-i,1,1)
227 bthet(2,i,1,-1)=-bthet(2,-i,1,1)
232 polthet(j,i)=polthet(j,-i)
235 gthet(j,i)=gthet(j,-i)
241 c & 'Parameters of the virtual-bond valence angles:'
242 c write (iout,'(/a/9x,5a/79(1h-))') 'Fourier coefficients:',
243 c & ' ATHETA0 ',' A1 ',' A2 ',
246 c write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,
247 c & a0thet(i),(athet(j,i),j=1,2),(bthet(j,i),j=1,2)
249 c write (iout,'(/a/9x,5a/79(1h-))')
250 c & 'Parameters of the expression for sigma(theta_c):',
251 c & ' ALPH0 ',' ALPH1 ',' ALPH2 ',
252 c & ' ALPH3 ',' SIGMA0C '
254 c write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,
255 c & (polthet(j,i),j=0,3),sigc0(i)
257 c write (iout,'(/a/9x,5a/79(1h-))')
258 c & 'Parameters of the second gaussian:',
259 c & ' THETA0 ',' SIGMA0 ',' G1 ',
262 c write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,theta0(i),
263 c & sig0(i),(gthet(j,i),j=1,3)
266 & 'Parameters of the virtual-bond valence angles:'
267 write (iout,'(/a/9x,5a/79(1h-))')
268 & 'Coefficients of expansion',
269 & ' theta0 ',' a1*10^2 ',' a2*10^2 ',
270 & ' b1*10^1 ',' b2*10^1 '
272 write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),
273 & a0thet(i),(100*athet(j,i,1,1),j=1,2),
274 & (10*bthet(j,i,1,1),j=1,2)
276 write (iout,'(/a/9x,5a/79(1h-))')
277 & 'Parameters of the expression for sigma(theta_c):',
278 & ' alpha0 ',' alph1 ',' alph2 ',
279 & ' alhp3 ',' sigma0c '
281 write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i),
282 & (polthet(j,i),j=0,3),sigc0(i)
284 write (iout,'(/a/9x,5a/79(1h-))')
285 & 'Parameters of the second gaussian:',
286 & ' theta0 ',' sigma0*10^2 ',' G1*10^-1',
289 write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),theta0(i),
290 & 100*sig0(i),gthet(1,i)*0.1D0,gthet(2,i),gthet(3,i)*10.0D0
295 C Read the parameters of Utheta determined from ab initio surfaces
296 C Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
298 read (ithep,*) nthetyp,ntheterm,ntheterm2,
299 & ntheterm3,nsingle,ndouble
300 nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
301 read (ithep,*) (ithetyp(i),i=1,ntyp1)
307 aathet(l,i,j,k)=0.0d0
311 bbthet(m,l,i,j,k)=0.0d0
312 ccthet(m,l,i,j,k)=0.0d0
313 ddthet(m,l,i,j,k)=0.0d0
314 eethet(m,l,i,j,k)=0.0d0
320 ffthet(mm,m,l,i,j,k)=0.0d0
321 ggthet(mm,m,l,i,j,k)=0.0d0
331 read (ithep,'(3a)') res1,res2,res3
332 read (ithep,*) aa0thet(i,j,k)
333 read (ithep,*)(aathet(l,i,j,k),l=1,ntheterm)
335 & ((bbthet(lll,ll,i,j,k),lll=1,nsingle),
336 & (ccthet(lll,ll,i,j,k),lll=1,nsingle),
337 & (ddthet(lll,ll,i,j,k),lll=1,nsingle),
338 & (eethet(lll,ll,i,j,k),lll=1,nsingle),ll=1,ntheterm2)
340 & (((ffthet(llll,lll,ll,i,j,k),ffthet(lll,llll,ll,i,j,k),
341 & ggthet(llll,lll,ll,i,j,k),ggthet(lll,llll,ll,i,j,k),
342 & llll=1,lll-1),lll=2,ndouble),ll=1,ntheterm3)
347 C For dummy ends assign glycine-type coefficients of theta-only terms; the
348 C coefficients of theta-and-gamma-dependent terms are zero.
353 aathet(l,i,j,nthetyp+1)=aathet(l,i,j,1)
354 aathet(l,nthetyp+1,i,j)=aathet(l,1,i,j)
356 aa0thet(i,j,nthetyp+1)=aa0thet(i,j,1)
357 aa0thet(nthetyp+1,i,j)=aa0thet(1,i,j)
360 aathet(l,nthetyp+1,i,nthetyp+1)=aathet(l,1,i,1)
362 aa0thet(nthetyp+1,i,nthetyp+1)=aa0thet(1,i,1)
365 C Control printout of the coefficients of virtual-bond-angle potentials
368 write (iout,'(//a)') 'Parameter of virtual-bond-angle potential'
372 write (iout,'(//4a)')
373 & 'Type ',onelett(i),onelett(j),onelett(k)
374 write (iout,'(//a,10x,a)') " l","a[l]"
375 write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k)
376 write (iout,'(i2,1pe15.5)')
377 & (l,aathet(l,i,j,k),l=1,ntheterm)
379 write (iout,'(//2h m,4(9x,a,3h[m,i1,1h]))')
380 & "b",l,"c",l,"d",l,"e",l
382 write (iout,'(i2,4(1pe15.5))') m,
383 & bbthet(m,l,i,j,k),ccthet(m,l,i,j,k),
384 & ddthet(m,l,i,j,k),eethet(m,l,i,j,k)
388 write (iout,'(//3hm,n,4(6x,a,5h[m,n,i1,1h]))')
389 & "f+",l,"f-",l,"g+",l,"g-",l
392 write (iout,'(i1,1x,i1,4(1pe15.5))') n,m,
393 & ffthet(n,m,l,i,j,k),ffthet(m,n,l,i,j,k),
394 & ggthet(n,m,l,i,j,k),ggthet(m,n,l,i,j,k)
407 C Read the parameters of the probability distribution/energy expression
408 C of the side chains.
411 cc write (iout,*) "tu dochodze",i
412 read (irotam,'(3x,i3,f8.3)') nlob(i),dsc(i)
416 dsc_inv(i)=1.0D0/dsc(i)
427 read(irotam,*)(censc(k,1,i),k=1,3),((blower(k,l,1),l=1,k),k=1,3)
428 censc(1,1,-i)=censc(1,1,i)
429 censc(2,1,-i)=censc(2,1,i)
430 censc(3,1,-i)=-censc(3,1,i)
432 read (irotam,*) bsc(j,i)
433 read (irotam,*) (censc(k,j,i),k=1,3),
434 & ((blower(k,l,j),l=1,k),k=1,3)
435 censc(1,j,-i)=censc(1,j,i)
436 censc(2,j,-i)=censc(2,j,i)
437 censc(3,j,-i)=-censc(3,j,i)
438 C BSC is amplitude of Gaussian
445 akl=akl+blower(k,m,j)*blower(l,m,j)
449 if (((k.eq.3).and.(l.ne.3))
450 & .or.((l.eq.3).and.(k.ne.3))) then
451 gaussc(k,l,j,-i)=-akl
452 gaussc(l,k,j,-i)=-akl
464 write (iout,'(/a)') 'Parameters of side-chain local geometry'
468 write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i),
469 & ' # of gaussian lobes:',nlobi,' dsc:',dsc(i)
470 c write (iout,'(/a,8x,i1,4(25x,i1))') 'Lobe:',(j,j=1,nlobi)
471 c write (iout,'(a,f10.4,4(16x,f10.4))')
472 c & 'Center ',(bsc(j,i),j=1,nlobi)
473 c write (iout,'(5(2x,3f8.4))') ((censc(k,j,i),k=1,3),j=1,nlobi)
474 write (iout,'(1h&,a,3(2h&&,f8.3,2h&&))')
475 & 'log h',(bsc(j,i),j=1,nlobi)
476 write (iout,'(1h&,a,3(1h&,f8.3,1h&,f8.3,1h&,f8.3,1h&))')
477 & 'x',((censc(k,j,i),k=1,3),j=1,nlobi)
484 c blower(k,l,j)=gaussc(ind,j,i)
489 write (iout,'(2h& ,5(2x,1h&,3(f7.3,1h&)))')
490 & ((gaussc(k,l,j,i),l=1,3),j=1,nlobi)
497 C Read scrot parameters for potentials determined from all-atom AM1 calculations
498 C added by Urszula Kozlowska 07/11/2007
506 read(irotam,*) sc_parmin(j,i)
514 C Read torsional parameters in old format
516 read (itorp,*) ntortyp,nterm_old
517 write (iout,*) 'ntortyp,nterm',ntortyp,nterm_old
518 read (itorp,*) (itortyp(i),i=1,ntyp)
523 read (itorp,*) kk,v1(k,j,i),v2(k,j,i)
529 write (iout,'(/a/)') 'Torsional constants:'
532 write (iout,'(2i3,6f10.5)') i,j,(v1(k,i,j),k=1,nterm_old)
533 write (iout,'(6x,6f10.5)') (v2(k,i,j),k=1,nterm_old)
541 C Read torsional parameters
543 read (itorp,*) ntortyp
544 read (itorp,*) (itortyp(i),i=1,ntyp)
545 write (iout,*) 'ntortyp',ntortyp
548 itortyp(i)=-itortyp(-i)
550 c write (iout,*) 'ntortyp',ntortyp
552 do j=-ntortyp+1,ntortyp-1
553 read (itorp,*) nterm(i,j,iblock),
555 nterm(-i,-j,iblock)=nterm(i,j,iblock)
556 nlor(-i,-j,iblock)=nlor(i,j,iblock)
559 do k=1,nterm(i,j,iblock)
560 read (itorp,*) kk,v1(k,i,j,iblock),
562 v1(k,-i,-j,iblock)=v1(k,i,j,iblock)
563 v2(k,-i,-j,iblock)=-v2(k,i,j,iblock)
564 v0ij=v0ij+si*v1(k,i,j,iblock)
567 do k=1,nlor(i,j,iblock)
568 read (itorp,*) kk,vlor1(k,i,j),
569 & vlor2(k,i,j),vlor3(k,i,j)
570 v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2)
573 v0(-i,-j,iblock)=v0ij
579 write (iout,'(/a/)') 'Torsional constants:'
582 write (iout,*) 'ityp',i,' jtyp',j
583 write (iout,*) 'Fourier constants'
584 do k=1,nterm(i,j,iblock)
585 write (iout,'(2(1pe15.5))') v1(k,i,j,iblock),
588 write (iout,*) 'Lorenz constants'
589 do k=1,nlor(i,j,iblock)
590 write (iout,'(3(1pe15.5))')
591 & vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
597 C 6/23/01 Read parameters for double torsionals
601 do j=-ntortyp+1,ntortyp-1
602 do k=-ntortyp+1,ntortyp-1
603 read (itordp,'(3a1)') t1,t2,t3
604 c write (iout,*) "OK onelett",
607 if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j)
608 & .or. t3.ne.toronelet(k)) then
609 write (iout,*) "Error in double torsional parameter file",
612 call MPI_Finalize(Ierror)
614 stop "Error in double torsional parameter file"
616 read (itordp,*) ntermd_1(i,j,k,iblock),
617 & ntermd_2(i,j,k,iblock)
618 ntermd_1(-i,-j,-k,iblock)=ntermd_1(i,j,k,iblock)
619 ntermd_2(-i,-j,-k,iblock)=ntermd_2(i,j,k,iblock)
620 read (itordp,*) (v1c(1,l,i,j,k,iblock),l=1,
621 & ntermd_1(i,j,k,iblock))
622 read (itordp,*) (v1s(1,l,i,j,k,iblock),l=1,
623 & ntermd_1(i,j,k,iblock))
624 read (itordp,*) (v1c(2,l,i,j,k,iblock),l=1,
625 & ntermd_1(i,j,k,iblock))
626 read (itordp,*) (v1s(2,l,i,j,k,iblock),l=1,
627 & ntermd_1(i,j,k,iblock))
628 C Martix of D parameters for one dimesional foureir series
629 do l=1,ntermd_1(i,j,k,iblock)
630 v1c(1,l,-i,-j,-k,iblock)=v1c(1,l,i,j,k,iblock)
631 v1s(1,l,-i,-j,-k,iblock)=-v1s(1,l,i,j,k,iblock)
632 v1c(2,l,-i,-j,-k,iblock)=v1c(2,l,i,j,k,iblock)
633 v1s(2,l,-i,-j,-k,iblock)=-v1s(2,l,i,j,k,iblock)
634 c write(iout,*) "whcodze" ,
635 c & v1s(2,l,-i,-j,-k,iblock),v1s(2,l,i,j,k,iblock)
637 read (itordp,*) ((v2c(l,m,i,j,k,iblock),
638 & v2c(m,l,i,j,k,iblock),v2s(l,m,i,j,k,iblock),
639 & v2s(m,l,i,j,k,iblock),
640 & m=1,l-1),l=1,ntermd_2(i,j,k,iblock))
641 C Martix of D parameters for two dimesional fourier series
642 do l=1,ntermd_2(i,j,k,iblock)
644 v2c(l,m,-i,-j,-k,iblock)=v2c(l,m,i,j,k,iblock)
645 v2c(m,l,-i,-j,-k,iblock)=v2c(m,l,i,j,k,iblock)
646 v2s(l,m,-i,-j,-k,iblock)=-v2s(l,m,i,j,k,iblock)
647 v2s(m,l,-i,-j,-k,iblock)=-v2s(m,l,i,j,k,iblock)
656 write (iout,*) 'Constants for double torsionals'
659 do j=-ntortyp+1,ntortyp-1
660 do k=-ntortyp+1,ntortyp-1
661 write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k,
662 & ' nsingle',ntermd_1(i,j,k,iblock),
663 & ' ndouble',ntermd_2(i,j,k,iblock)
665 write (iout,*) 'Single angles:'
666 do l=1,ntermd_1(i,j,k,iblock)
667 write (iout,'(i5,2f10.5,5x,2f10.5,5x,2f10.5)') l,
668 & v1c(1,l,i,j,k,iblock),v1s(1,l,i,j,k,iblock),
669 & v1c(2,l,i,j,k,iblock),v1s(2,l,i,j,k,iblock),
670 & v1s(1,l,-i,-j,-k,iblock),v1s(2,l,-i,-j,-k,iblock)
673 write (iout,*) 'Pairs of angles:'
674 write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
675 do l=1,ntermd_2(i,j,k,iblock)
676 write (iout,'(i5,20f10.5)')
677 & l,(v2c(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock))
680 write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
681 do l=1,ntermd_2(i,j,k,iblock)
682 write (iout,'(i5,20f10.5)')
683 & l,(v2s(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock)),
684 & (v2s(l,m,-i,-j,-k,iblock),m=1,ntermd_2(i,j,k,iblock))
694 C 5/21/07 (AL) Read coefficients of the backbone-local sidechain-local
695 C correlation energies.
697 read (isccor,*) nterm_sccor
703 & kk,v1sccor(k,i,j),v2sccor(k,i,j)
709 write (iout,'(/a/)') 'Torsional constants of SCCORR:'
712 write (iout,*) 'ityp',i,' jtyp',j
714 write (iout,'(2(1pe15.5))') v1sccor(k,i,j),v2sccor(k,i,j)
720 C 9/18/99 (AL) Read coefficients of the Fourier expansion of the local
721 C interaction energy of the Gly, Ala, and Pro prototypes.
723 read (ifourier,*) nloctyp
726 read (ifourier,*) (b(ii,i),ii=1,13)
728 write (iout,*) 'Type',i
729 write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
737 B1tilde(1,i) = b(3,i)
738 B1tilde(2,i) =-b(5,i)
739 B1tilde(1,-i) =-b(3,i)
740 B1tilde(2,-i) =b(5,i)
764 Ctilde(2,1,i)=-b(9,i)
766 Ctilde(1,1,-i)=b(7,i)
767 Ctilde(1,2,-i)=-b(9,i)
768 Ctilde(2,1,-i)=b(9,i)
769 Ctilde(2,2,-i)=b(7,i)
771 c Ctilde(1,1,i)=0.0d0
772 c Ctilde(1,2,i)=0.0d0
773 c Ctilde(2,1,i)=0.0d0
774 c Ctilde(2,2,i)=0.0d0
789 Dtilde(2,1,i)=-b(8,i)
791 Dtilde(1,1,-i)=b(6,i)
792 Dtilde(1,2,-i)=-b(8,i)
793 Dtilde(2,1,-i)=b(8,i)
794 Dtilde(2,2,-i)=b(6,i)
796 c Dtilde(1,1,i)=0.0d0
797 c Dtilde(1,2,i)=0.0d0
798 c Dtilde(2,1,i)=0.0d0
799 c Dtilde(2,2,i)=0.0d0
800 EE(1,1,i)= b(10,i)+b(11,i)
801 EE(2,2,i)=-b(10,i)+b(11,i)
802 EE(2,1,i)= b(12,i)-b(13,i)
803 EE(1,2,i)= b(12,i)+b(13,i)
804 EE(1,1,-i)= b(10,i)+b(11,i)
805 EE(2,2,-i)=-b(10,i)+b(11,i)
806 EE(2,1,-i)=-b(12,i)+b(13,i)
807 EE(1,2,-i)=-b(12,i)-b(13,i)
813 c ee(2,1,i)=ee(1,2,i)
818 write (iout,*) 'Type',i
820 c write (iout,'(f10.5)') B1(:,i)
821 write(iout,*) B1(1,i),B1(2,i)
823 c write (iout,'(f10.5)') B2(:,i)
824 write(iout,*) B2(1,i),B2(2,i)
827 write (iout,'(2f10.5)') CC(j,1,i),CC(j,2,i)
831 write (iout,'(2f10.5)') DD(j,1,i),DD(j,2,i)
835 write (iout,'(2f10.5)') EE(j,1,i),EE(j,2,i)
840 C Read electrostatic-interaction parameters
843 write (iout,'(/a)') 'Electrostatic interaction constants:'
844 write (iout,'(1x,a,1x,a,10x,a,11x,a,11x,a,11x,a)')
845 & 'IT','JT','APP','BPP','AEL6','AEL3'
847 read (ielep,*) ((epp(i,j),j=1,2),i=1,2)
848 read (ielep,*) ((rpp(i,j),j=1,2),i=1,2)
849 read (ielep,*) ((elpp6(i,j),j=1,2),i=1,2)
850 read (ielep,*) ((elpp3(i,j),j=1,2),i=1,2)
855 app (i,j)=epp(i,j)*rri*rri
856 bpp (i,j)=-2.0D0*epp(i,j)*rri
857 ael6(i,j)=elpp6(i,j)*4.2D0**6
858 ael3(i,j)=elpp3(i,j)*4.2D0**3
859 if (lprint) write(iout,'(2i3,4(1pe15.4))')i,j,app(i,j),bpp(i,j),
860 & ael6(i,j),ael3(i,j)
864 C Read side-chain interaction parameters.
866 read (isidep,*) ipot,expon
867 if (ipot.lt.1 .or. ipot.gt.5) then
868 write (iout,'(2a)') 'Error while reading SC interaction',
869 & 'potential file - unknown potential type.'
873 write(iout,'(/3a,2i3)') 'Potential is ',potname(ipot),
874 & ', exponents are ',expon,2*expon
875 goto (10,20,30,30,40) ipot
876 C----------------------- LJ potential ---------------------------------
877 10 read (isidep,*)((eps(i,j),j=i,ntyp),i=1,ntyp),(sigma0(i),i=1,ntyp)
879 write (iout,'(/a/)') 'Parameters of the LJ potential:'
880 write (iout,'(a/)') 'The epsilon array:'
881 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
882 write (iout,'(/a)') 'One-body parameters:'
883 write (iout,'(a,4x,a)') 'residue','sigma'
884 write (iout,'(a3,6x,f10.5)') (restyp(i),sigma0(i),i=1,ntyp)
887 C----------------------- LJK potential --------------------------------
888 20 read (isidep,*)((eps(i,j),j=i,ntyp),i=1,ntyp),
889 & (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp)
891 write (iout,'(/a/)') 'Parameters of the LJK potential:'
892 write (iout,'(a/)') 'The epsilon array:'
893 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
894 write (iout,'(/a)') 'One-body parameters:'
895 write (iout,'(a,4x,2a)') 'residue',' sigma ',' r0 '
896 write (iout,'(a3,6x,2f10.5)') (restyp(i),sigma0(i),rr0(i),
900 C---------------------- GB or BP potential -----------------------------
901 30 read (isidep,*)((eps(i,j),j=i,ntyp),i=1,ntyp),
902 & (sigma0(i),i=1,ntyp),(sigii(i),i=1,ntyp),(chip0(i),i=1,ntyp),
904 C For the GB potential convert sigma'**2 into chi'
907 chip(i)=(chip0(i)-1.0D0)/(chip0(i)+1.0D0)
911 write (iout,'(/a/)') 'Parameters of the BP potential:'
912 write (iout,'(a/)') 'The epsilon array:'
913 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
914 write (iout,'(/a)') 'One-body parameters:'
915 write (iout,'(a,4x,4a)') 'residue',' sigma ','s||/s_|_^2',
917 write (iout,'(a3,6x,4f10.5)') (restyp(i),sigma0(i),sigii(i),
918 & chip(i),alp(i),i=1,ntyp)
921 C--------------------- GBV potential -----------------------------------
922 40 read (isidep,*)((eps(i,j),j=i,ntyp),i=1,ntyp),
923 & (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp),(sigii(i),i=1,ntyp),
924 & (chip(i),i=1,ntyp),(alp(i),i=1,ntyp)
926 write (iout,'(/a/)') 'Parameters of the GBV potential:'
927 write (iout,'(a/)') 'The epsilon array:'
928 call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
929 write (iout,'(/a)') 'One-body parameters:'
930 write (iout,'(a,4x,5a)') 'residue',' sigma ',' r0 ',
931 & 's||/s_|_^2',' chip ',' alph '
932 write (iout,'(a3,6x,5f10.5)') (restyp(i),sigma0(i),rr0(i),
933 & sigii(i),chip(i),alp(i),i=1,ntyp)
937 C-----------------------------------------------------------------------
938 C Calculate the "working" parameters of SC interactions.
946 sigma(i,j)=dsqrt(sigma0(i)**2+sigma0(j)**2)
947 sigma(j,i)=sigma(i,j)
948 rs0(i,j)=dwa16*sigma(i,j)
952 if (lprint) write (iout,'(/a/10x,7a/72(1h-))')
953 & 'Working parameters of the SC interactions:',
954 & ' a ',' b ',' augm ',' sigma ',' r0 ',
959 if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
968 sigeps=dsign(1.0D0,epsij)
970 aa(i,j)=epsij*rrij*rrij
971 bb(i,j)=-sigeps*epsij*rrij
979 ratsig1=sigt2sq/sigt1sq
980 ratsig2=1.0D0/ratsig1
981 chi(i,j)=(sigii1-1.0D0)/(sigii1+ratsig1)
982 if (j.gt.i) chi(j,i)=(sigii2-1.0D0)/(sigii2+ratsig2)
983 rsum_max=dsqrt(sigii1*sigt1sq+sigii2*sigt2sq)
987 c if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
988 sigmaii(i,j)=rsum_max
989 sigmaii(j,i)=rsum_max
991 c sigmaii(i,j)=r0(i,j)
992 c sigmaii(j,i)=r0(i,j)
994 cd write (iout,*) i,j,r0(i,j),sigma(i,j),rsum_max
995 if ((ipot.eq.2 .or. ipot.eq.5) .and. r0(i,j).gt.rsum_max) then
996 r_augm=sigma(i,j)*(rrij-sigma(i,j))/rrij
997 augm(i,j)=epsij*r_augm**(2*expon)
998 c augm(i,j)=0.5D0**(2*expon)*aa(i,j)
1005 write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))')
1006 & restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),
1007 & sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
1012 C Define the SC-p interaction constants
1016 C "Soft" SC-p repulsion (causes helices to be too flat, but facilitates
1018 c aad(i,1)=0.3D0*4.0D0**12
1019 C Following line for constants currently implemented
1020 C "Hard" SC-p repulsion (gives correct turn spacing in helices)
1021 aad(i,1)=1.5D0*4.0D0**12
1022 c aad(i,1)=0.17D0*5.6D0**12
1024 C "Soft" SC-p repulsion
1026 C Following line for constants currently implemented
1027 c aad(i,1)=0.3D0*4.0D0**6
1028 C "Hard" SC-p repulsion
1029 bad(i,1)=3.0D0*4.0D0**6
1030 c bad(i,1)=-2.0D0*0.17D0*5.6D0**6
1039 C 8/9/01 Read the SC-p interaction constants from file
1042 read (iscpp,*) (eps_scp(i,j),rscp(i,j),j=1,2)
1045 aad(i,1)=dabs(eps_scp(i,1))*rscp(i,1)**12
1046 aad(i,2)=dabs(eps_scp(i,2))*rscp(i,2)**12
1047 bad(i,1)=-2*eps_scp(i,1)*rscp(i,1)**6
1048 bad(i,2)=-2*eps_scp(i,2)*rscp(i,2)**6
1052 write (iout,*) "Parameters of SC-p interactions:"
1054 write (iout,'(4f8.3,4e12.4)') eps_scp(i,1),rscp(i,1),
1055 & eps_scp(i,2),rscp(i,2),aad(i,1),bad(i,1),aad(i,2),bad(i,2)
1060 C Define the constants of the disulfide bridge
1064 c Old arbitrary potential - commented out.
1069 c Constants of the disulfide-bond potential determined based on the RHF/6-31G**
1070 c energy surface of diethyl disulfide.
1071 c A. Liwo and U. Kozlowska, 11/24/03
1082 write (iout,'(/a)') "Disulfide bridge parameters:"
1083 write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
1084 write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
1085 write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
1086 write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,