! write (iout,100)
! do i=1,nres
-! write (iout,110) restyp(itype(i)),i,c(1,i),c(2,i),&
+! write (iout,110) restyp(itype(i,1)),i,c(1,i),c(2,i),&
! c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
! enddo
! 100 format (//' alpha-carbon coordinates ',&
real(kind=8) :: v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,si,&
dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,&
- res1
+ res1,epsijlip,epspeptube,epssctube,sigmapeptube, &
+ sigmasctube
integer :: ichir1,ichir2
! real(kind=8),dimension(maxterm,-maxtor:maxtor,-maxtor:maxtor,2) :: v1_el,v2_el !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
!el allocate(v1_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
allocate(isc(ntyp+1)) !(ntyp+1)
allocate(restok(ntyp+1)) !(ntyp+1)
allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
-
+ allocate(long_r_sidechain(ntyp))
+ allocate(short_r_sidechain(ntyp))
dsc(:)=0.0d0
dsc_inv(:)=0.0d0
endif
enddo
#else
- read (ibond,*) junk,vbldpDUM,vbldp0,akp,rjunk,mp,ip,pstok
+ read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp,ip,pstok
do i=1,ntyp
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),&
j=1,nbondterm(i)),msc(i),isc(i),restok(i)
'inertia','Pstok'
write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp,ip,pstok
do i=1,ntyp
- write (iout,'(a10,i3,6f10.5)') restyp(i),nbondterm(i),&
+ write (iout,'(a10,i3,6f10.5)') restyp(i,1),nbondterm(i),&
vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i),isc(i),restok(i)
do j=2,nbondterm(i)
write (iout,'(13x,3f10.5)') &
theta0(:)=0.0D0
sig0(:)=0.0D0
sigc0(:)=0.0D0
+ allocate(liptranene(ntyp))
+!C reading lipid parameters
+ write (iout,*) "iliptranpar",iliptranpar
+ call flush(iout)
+ read(iliptranpar,*) pepliptran
+ print *,pepliptran
+ do i=1,ntyp
+ read(iliptranpar,*) liptranene(i)
+ print *,liptranene(i)
+ enddo
+ close(iliptranpar)
#ifdef CRYST_THETA
!
' ATHETA0 ',' A1 ',' A2 ',&
' B1 ',' B2 '
do i=1,ntyp
- write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,&
+ write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,&
a0thet(i),(athet(j,i,1,1),j=1,2),(bthet(j,i,1,1),j=1,2)
enddo
write (iout,'(/a/9x,5a/79(1h-))') &
' ALPH0 ',' ALPH1 ',' ALPH2 ',&
' ALPH3 ',' SIGMA0C '
do i=1,ntyp
- write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,&
+ write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,&
(polthet(j,i),j=0,3),sigc0(i)
enddo
write (iout,'(/a/9x,5a/79(1h-))') &
' THETA0 ',' SIGMA0 ',' G1 ',&
' G2 ',' G3 '
do i=1,ntyp
- write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,theta0(i),&
+ write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,theta0(i),&
sig0(i),(gthet(j,i),j=1,3)
enddo
else
' theta0 ',' a1*10^2 ',' a2*10^2 ',&
' b1*10^1 ',' b2*10^1 '
do i=1,ntyp
- write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),&
+ write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),&
a0thet(i),(100*athet(j,i,1,1),j=1,2),&
(10*bthet(j,i,1,1),j=1,2)
enddo
' alpha0 ',' alph1 ',' alph2 ',&
' alhp3 ',' sigma0c '
do i=1,ntyp
- write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i),&
+ write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i,1),&
(polthet(j,i),j=0,3),sigc0(i)
enddo
write (iout,'(/a/9x,5a/79(1h-))') &
' theta0 ',' sigma0*10^2 ',' G1*10^-1',&
' G2 ',' G3*10^1 '
do i=1,ntyp
- write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),theta0(i),&
+ write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),theta0(i),&
100*sig0(i),gthet(1,i)*0.1D0,gthet(2,i),gthet(3,i)*10.0D0
enddo
endif
nlobi=nlob(i)
if (nlobi.gt.0) then
if (LaTeX) then
- write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i),&
+ write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i,1),&
' # of gaussian lobes:',nlobi,' dsc:',dsc(i)
write (iout,'(1h&,a,3(2h&&,f8.3,2h&&))') &
'log h',(bsc(j,i),j=1,nlobi)
do i=-ntyp,-1
itortyp(i)=-itortyp(-i)
enddo
-! itortyp(ntyp1)=ntortyp
-! itortyp(-ntyp1)=-ntortyp
+ itortyp(ntyp1)=ntortyp
+ itortyp(-ntyp1)=-ntortyp
do iblock=1,2
write (iout,*) 'ntortyp',ntortyp
do i=0,ntortyp-1
allocate(eps_scp(ntyp,2),rscp(ntyp,2)) !(ntyp,2)
allocate(sigma0(ntyp),rr0(ntyp),sigii(ntyp)) !(ntyp)
allocate(chip(ntyp1),alp(ntyp1)) !(ntyp)
-
+ allocate(epslip(ntyp,ntyp))
augm(:,:)=0.0D0
chip(:)=0.0D0
alp(:)=0.0D0
call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,a)') 'residue','sigma'
- write (iout,'(a3,6x,f10.5)') (restyp(i),sigma0(i),i=1,ntyp)
+ write (iout,'(a3,6x,f10.5)') (restyp(i,1),sigma0(i),i=1,ntyp)
endif
! goto 50
!----------------------- LJK potential --------------------------------
call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,2a)') 'residue',' sigma ',' r0 '
- write (iout,'(a3,6x,2f10.5)') (restyp(i),sigma0(i),rr0(i),&
+ write (iout,'(a3,6x,2f10.5)') (restyp(i,1),sigma0(i),rr0(i),&
i=1,ntyp)
endif
! goto 50
read (isidep,*,end=117,err=117)(sigii(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(chip(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(alp(i),i=1,ntyp)
+ do i=1,ntyp
+ read (isidep,*,end=117,err=117)(epslip(i,j),j=i,ntyp)
+ enddo
+
! For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,4a)') 'residue',' sigma ','s||/s_|_^2',&
' chip ',' alph '
- write (iout,'(a3,6x,4f10.5)') (restyp(i),sigma0(i),sigii(i),&
+ write (iout,'(a3,6x,4f10.5)') (restyp(i,1),sigma0(i),sigii(i),&
chip(i),alp(i),i=1,ntyp)
endif
! goto 50
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,5a)') 'residue',' sigma ',' r0 ',&
's||/s_|_^2',' chip ',' alph '
- write (iout,'(a3,6x,5f10.5)') (restyp(i),sigma0(i),rr0(i),&
+ write (iout,'(a3,6x,5f10.5)') (restyp(i,1),sigma0(i),rr0(i),&
sigii(i),chip(i),alp(i),i=1,ntyp)
endif
case default
! Calculate the "working" parameters of SC interactions.
!el from module energy - COMMON.INTERACT-------
- allocate(aa(ntyp1,ntyp1),bb(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ allocate(aa_aq(ntyp1,ntyp1),bb_aq(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ allocate(aa_lip(ntyp1,ntyp1),bb_lip(ntyp1,ntyp1)) !(ntyp,ntyp)
allocate(sigma(0:ntyp1,0:ntyp1),r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
- aa(:,:)=0.0D0
- bb(:,:)=0.0D0
+ allocate(acavtub(ntyp1),bcavtub(ntyp1),ccavtub(ntyp1),&
+ dcavtub(ntyp1))
+ allocate(sc_aa_tube_par(ntyp1),sc_bb_tube_par(ntyp1),&
+ tubetranene(ntyp1))
+ aa_aq(:,:)=0.0D0
+ bb_aq(:,:)=0.0D0
+ aa_lip(:,:)=0.0D0
+ bb_lip(:,:)=0.0D0
chi(:,:)=0.0D0
sigma(:,:)=0.0D0
r0(:,:)=0.0D0
-
+ acavtub(:)=0.0d0
+ bcavtub(:)=0.0d0
+ ccavtub(:)=0.0d0
+ dcavtub(:)=0.0d0
+ sc_aa_tube_par(:)=0.0d0
+ sc_bb_tube_par(:)=0.0d0
+
!--------------------------------
do i=2,ntyp
do j=1,i-1
eps(i,j)=eps(j,i)
+ epslip(i,j)=epslip(j,i)
enddo
enddo
do i=1,ntyp
epsij=eps(i,j)
sigeps=dsign(1.0D0,epsij)
epsij=dabs(epsij)
- aa(i,j)=epsij*rrij*rrij
- bb(i,j)=-sigeps*epsij*rrij
- aa(j,i)=aa(i,j)
- bb(j,i)=bb(i,j)
+ aa_aq(i,j)=epsij*rrij*rrij
+ bb_aq(i,j)=-sigeps*epsij*rrij
+ aa_aq(j,i)=aa_aq(i,j)
+ bb_aq(j,i)=bb_aq(i,j)
+ epsijlip=epslip(i,j)
+ sigeps=dsign(1.0D0,epsijlip)
+ epsijlip=dabs(epsijlip)
+ aa_lip(i,j)=epsijlip*rrij*rrij
+ bb_lip(i,j)=-sigeps*epsijlip*rrij
+ aa_lip(j,i)=aa_lip(i,j)
+ bb_lip(j,i)=bb_lip(i,j)
+!C write(iout,*) aa_lip
if (ipot.gt.2) then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
endif
if (lprint) then
write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))') &
- restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),&
+ restyp(i,1),restyp(j,1),aa_aq(i,j),bb_aq(i,j),augm(i,j),&
sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
endif
enddo
enddo
+ write(iout,*) "tube param"
+ read(itube,*) epspeptube,sigmapeptube,acavtubpep,bcavtubpep, &
+ ccavtubpep,dcavtubpep,tubetranenepep
+ sigmapeptube=sigmapeptube**6
+ sigeps=dsign(1.0D0,epspeptube)
+ epspeptube=dabs(epspeptube)
+ pep_aa_tube=4.0d0*epspeptube*sigmapeptube**2
+ pep_bb_tube=-sigeps*4.0d0*epspeptube*sigmapeptube
+ write(iout,*) pep_aa_tube,pep_bb_tube,tubetranenepep
+ do i=1,ntyp
+ read(itube,*) epssctube,sigmasctube,acavtub(i),bcavtub(i), &
+ ccavtub(i),dcavtub(i),tubetranene(i)
+ sigmasctube=sigmasctube**6
+ sigeps=dsign(1.0D0,epssctube)
+ epssctube=dabs(epssctube)
+ sc_aa_tube_par(i)=4.0d0*epssctube*sigmasctube**2
+ sc_bb_tube_par(i)=-sigeps*4.0d0*epssctube*sigmasctube
+ write(iout,*) sc_aa_tube_par(i), sc_bb_tube_par(i),tubetranene(i)
+ enddo
allocate(aad(ntyp,2),bad(ntyp,2)) !(ntyp,2)
bad(:,:)=0.0D0
! End current chain
ires_old=ires+2
ishift1=ishift1+1
- itype(ires_old)=ntyp1
- itype(ires_old-1)=ntyp1
+ itype(ires_old,1)=ntyp1
+ itype(ires_old-1,1)=ntyp1
ibeg=2
! write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
enddo
else
call sccenter(ires,iii,sccor)
+! iii=0
endif
iii=0
endif
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires+ishift1-ishift-1)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
- itype(1)=ntyp1
+ itype(1,1)=ntyp1
endif
ires=ires-ishift+ishift1
ires_old=ires
ires_old=ires
endif
if (res.eq.'ACE' .or. res.eq.'NHE') then
- itype(ires)=10
+ itype(ires,1)=10
else
- itype(ires)=rescode(ires,res,0)
+ itype(ires,1)=rescode(ires,res,0,1)
endif
else
ires=ires-ishift+ishift1
! write (iout,*) "backbone ",atom
#ifdef DEBUG
write (iout,'(2i3,2x,a,3f8.3)') &
- ires,itype(ires),res,(c(j,ires),j=1,3)
+ ires,itype(ires,1),res,(c(j,ires),j=1,3)
#endif
iii=iii+1
do j=1,3
sccor(j,iii)=c(j,ires)
enddo
-! write (*,*) card(23:27),ires,itype(ires)
+! write (*,*) card(23:27),ires,itype(ires,1)
else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. &
atom.ne.'N' .and. atom.ne.'C' .and. &
atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. &
! system
nres=ires
do i=2,nres-1
-! write (iout,*) i,itype(i)
-! if (itype(i).eq.ntyp1) then
-! write (iout,*) "dummy",i,itype(i)
+! write (iout,*) i,itype(i,1)
+! if (itype(i,1).eq.ntyp1) then
+! write (iout,*) "dummy",i,itype(i,1)
! do j=1,3
! c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
! c(j,i)=(c(j,i-1)+c(j,i+1))/2
! dc(j,i)=c(j,i)
! enddo
! endif
- if (itype(i).eq.ntyp1) then
- if (itype(i+1).eq.ntyp1) then
+ if (itype(i,1).eq.ntyp1) then
+ if (itype(i+1,1).eq.ntyp1) then
! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
-! first is connected prevous chain (itype(i+1).eq.ntyp1)=true
-! second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+! first is connected prevous chain (itype(i+1,1).eq.ntyp1)=true
+! second dummy atom is conected to next chain itype(i+1,1).eq.ntyp1=false
if (unres_pdb) then
! 2/15/2013 by Adam: corrected insertion of the last dummy residue
! print *,i,'tu dochodze'
c(j,nres+i)=c(j,i)
enddo
endif !unres_pdb
- else !itype(i+1).eq.ntyp1
+ else !itype(i+1,1).eq.ntyp1
if (unres_pdb) then
! 2/15/2013 by Adam: corrected insertion of the first dummy residue
call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
c(j,nres+i)=c(j,i)
enddo
endif !unres_pdb
- endif !itype(i+1).eq.ntyp1
+ endif !itype(i+1,1).eq.ntyp1
endif !itype.eq.ntyp1
enddo
! nres=ires
nsup=nres
nstart_sup=1
- if (itype(nres).ne.10) then
+ if (itype(nres,1).ne.10) then
nres=nres+1
- itype(nres)=ntyp1
+ itype(nres,1)=ntyp1
if (unres_pdb) then
! 2/15/2013 by Adam: corrected insertion of the last dummy residue
call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
e2(3)=0.0d0
endif
do j=1,3
- c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
c(j,nres+1)=c(j,1)
c(j,2*nres)=c(j,nres)
enddo
- if (itype(1).eq.ntyp1) then
+ if (itype(1,1).eq.ntyp1) then
nsup=nsup-1
nstart_sup=2
if (unres_pdb) then
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ c(j,1)=c(j,2)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,4)-c(j,3)
+ dcj=(c(j,4)-c(j,3))/2.0
c(j,1)=c(j,2)-dcj
c(j,nres+1)=c(j,1)
enddo
"Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
do ires=1,nres
write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') &
- restyp(itype(ires)),ires,(c(j,ires),j=1,3),&
+ restyp(itype(ires,1),1),ires,(c(j,ires),j=1,3),&
(c(j,ires+nres),j=1,3)
enddo
endif
"Backbone and SC coordinates as read from the PDB"
do ires=1,nres
write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') &
- ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),&
+ ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),&
(c(j,nres+ires),j=1,3)
enddo
endif
lll=lll+1
!c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
- if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
+ if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
chain_length=lll-1
kkk=kkk+1
! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
! enddiagnostic
! makes copy of chains
write (iout,*) "symetr", symetr
+ do j=1,3
+ dc(j,0)=c(j,1)
+ enddo
if (symetr.gt.1) then
call permut(symetr)
do kkk=1,nperm
write (iout,*) "nowa struktura", nperm
do i=1,nres
- write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),&
+ write (iout,110) restyp(itype(i,1),1),i,cref(1,i,kkk),&
cref(2,i,kkk),&
cref(3,i,kkk),cref(1,nres+i,kkk),&
cref(2,nres+i,kkk),cref(3,nres+i,kkk)
character(len=640) :: controlcard
real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
-
+ integer i
nglob_csa=0
eglob_csa=1d99
timem=timlim
modecalc=0
call reada(controlcard,"T_BATH",t_bath,300.0d0)
+!C SHIELD keyword sets if the shielding effect of side-chains is used
+!C 0 denots no shielding is used all peptide are equally despite the
+!C solvent accesible area
+!C 1 the newly introduced function
+!C 2 reseved for further possible developement
+ call readi(controlcard,'SHIELD',shield_mode,0)
+!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "shield_mode",shield_mode
!C Varibles set size of box
+ with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
+ protein=index(controlcard,"PROTEIN").gt.0
+ ions=index(controlcard,"IONS").gt.0
+ nucleic=index(controlcard,"NUCLEIC").gt.0
+ write (iout,*) "with_theta_constr ",with_theta_constr
+ AFMlog=(index(controlcard,'AFM'))
+ selfguide=(index(controlcard,'SELFGUIDE'))
+ print *,'AFMlog',AFMlog,selfguide,"KUPA"
+ call readi(controlcard,'GENCONSTR',genconstr,0)
call reada(controlcard,'BOXX',boxxsize,100.0d0)
call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ call readi(controlcard,'TUBEMOD',tubemode,0)
+ write (iout,*) TUBEmode,"TUBEMODE"
+ if (TUBEmode.gt.0) then
+ call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
+ call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
+ call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
+ call reada(controlcard,"RTUBE",tubeR0,0.0d0)
+ call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
+ call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
+ call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
+ buftubebot=bordtubebot+tubebufthick
+ buftubetop=bordtubetop-tubebufthick
+ endif
+
! CUTOFFF ON ELECTROSTATICS
call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
+ write(iout,*) "R_CUT_ELE=",r_cut_ele
+! Lipidic parameters
+ call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
+ call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
+ if (lipthick.gt.0.0d0) then
+ bordliptop=(boxzsize+lipthick)/2.0
+ bordlipbot=bordliptop-lipthick
+ if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0)) &
+ write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
+ buflipbot=bordlipbot+lipbufthick
+ bufliptop=bordliptop-lipbufthick
+ if ((lipbufthick*2.0d0).gt.lipthick) &
+ write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
+ endif !lipthick.gt.0
+ write(iout,*) "bordliptop=",bordliptop
+ write(iout,*) "bordlipbot=",bordlipbot
+ write(iout,*) "bufliptop=",bufliptop
+ write(iout,*) "buflipbot=",buflipbot
+ write (iout,*) "SHIELD MODE",shield_mode
!C-------------------------
minim=(index(controlcard,'MINIMIZE').gt.0)
if(me.eq.king.or..not.out1file) &
write (iout,'(2a)') diagmeth(kdiag),&
' routine used to diagonalize matrices.'
+ if (shield_mode.gt.0) then
+ pi=3.141592d0
+!C VSolvSphere the volume of solving sphere
+!C print *,pi,"pi"
+!C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
+!C there will be no distinction between proline peptide group and normal peptide
+!C group in case of shielding parameters
+ VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+ write (iout,*) VSolvSphere,VSolvSphere_div
+!C long axis of side chain
+ do i=1,ntyp
+ long_r_sidechain(i)=vbldsc0(1,i)
+ short_r_sidechain(i)=sigma0(i)
+ write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
+ sigma0(i)
+ enddo
+ buff_shield=1.0d0
+ endif
return
end subroutine read_control
!-----------------------------------------------------------------------------
" stochastic forces of fully exposed sites"
write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
do i=1,ntyp
- write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),&
+ write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i),&
gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
enddo
endif
! print *,"Processor",myrank," opened file IELEP"
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',action='read')
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old',action='read')
+
! print *,"Processor",myrank," opened file ISIDEP"
! print *,"Processor",myrank," opened parameter files"
#elif (defined G77)
open (ielep,file=elename,status='old')
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old')
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
readonly)
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old',action='read')
+
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
open (irotam_pdb,file=rotname_pdb,status='old',action='read')
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
+ totTafm=totT
! do i=1,2*nres
! AL 4/17/17: Now reading d_t(0,:) too
do i=0,2*nres
projects / unres4.git / blobdiff