include 'COMMON.SCCOR'
include 'COMMON.SCROT'
include 'COMMON.FREE'
+ include 'COMMON.SHIELD'
+ include 'COMMON.CONTROL'
character*1 t1,t2,t3
character*1 onelett(4) /"G","A","P","D"/
character*1 toronelet(-2:2) /"p","a","G","A","P"/
character*16 key
integer iparm
double precision ip,mp
+ character*6 res1
+C write (iout,*) "KURWA"
C
C Body
C
write (iout,*) "iparm",iparm," myparm",myparm
c If reading not own parameters, skip assignment
+ call reada(controlcard,"D0CM",d0cm,3.78d0)
+ call reada(controlcard,"AKCM",akcm,15.1d0)
+ call reada(controlcard,"AKTH",akth,11.0d0)
+ call reada(controlcard,"AKCT",akct,12.0d0)
+ call reada(controlcard,"V1SS",v1ss,-1.08d0)
+ call reada(controlcard,"V2SS",v2ss,7.61d0)
+ call reada(controlcard,"V3SS",v3ss,13.7d0)
+ call reada(controlcard,"EBR",ebr,-5.50D0)
+ call reada(controlcard,"DTRISS",dtriss,1.0D0)
+ call reada(controlcard,"ATRISS",atriss,0.3D0)
+ call reada(controlcard,"BTRISS",btriss,0.02D0)
+ call reada(controlcard,"CTRISS",ctriss,1.0D0)
+ dyn_ss=(index(controlcard,'DYN_SS').gt.0)
+ write(iout,*) "ATRISS",atriss
+ write(iout,*) "BTRISS",btriss
+ write(iout,*) "CTRISS",ctriss
+ write(iout,*) "DTRISS",dtriss
+
+C do i=1,maxres
+C dyn_ss_mask(i)=.false.
+C enddo
+C ebr=-12.0D0
+c
+c Old arbitrary potential - commented out.
+c
+c dbr= 4.20D0
+c fbr= 3.30D0
+c
+c Constants of the disulfide-bond potential determined based on the RHF/6-31G**
+c energy surface of diethyl disulfide.
+c A. Liwo and U. Kozlowska, 11/24/03
+c
+ D0CM = 3.78d0
+ AKCM = 15.1d0
+ AKTH = 11.0d0
+ AKCT = 12.0d0
+ V1SS =-1.08d0
+ V2SS = 7.61d0
+ V3SS = 13.7d0
+
+ do i=1,maxres-1
+ do j=i+1,maxres
+ dyn_ssbond_ij(i,j)=1.0d300
+ enddo
+ enddo
+ call reada(controlcard,"HT",Ht,0.0D0)
+C if (dyn_ss) then
+C ss_depth=ebr/wsc-0.25*eps(1,1)
+C write(iout,*) HT,wsc,eps(1,1),'KURWA'
+C Ht=Ht/wsc-0.25*eps(1,1)
+
+C akcm=akcm*whpb/wsc
+C akth=akth*whpb/wsc
+C akct=akct*whpb/wsc
+C v1ss=v1ss*whpb/wsc
+C v2ss=v2ss*whpb/wsc
+C v3ss=v3ss*whpb/wsc
+C else
+C ss_depth=ebr/whpb-0.25*eps(1,1)*wsc/whpb
+C endif
if (iparm.eq.myparm .or. .not.separate_parset) then
wvdwpp=ww(16)
wbond=ww(18)
wsccor=ww(19)
-
+ whpb=ww(15)
+ wstrain=ww(15)
+ wliptran=ww(22)
+ wshield=ww(25)
endif
call card_concat(controlcard,.false.)
c and Stokes' radii of the peptide group and side chains
c
#ifdef CRYST_BOND
- read (ibond,*) vbldp0,akp
+ read (ibond,*) vbldp0,vbldpdum,akp
do i=1,ntyp
nbondterm(i)=1
read (ibond,*) vbldsc0(1,i),aksc(1,i)
endif
enddo
#else
- read (ibond,*) ijunk,vbldp0,akp,rjunk
+ read (ibond,*) ijunk,vbldp0,vbldpdum,akp,rjunk
do i=1,ntyp
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),
& j=1,nbondterm(i))
enddo
enddo
endif
+ read(iliptranpar,*) pepliptran
+ do i=1,ntyp
+ read(iliptranpar,*) liptranene(i)
+ enddo
+ close(iliptranpar)
#ifdef CRYST_THETA
C
C Read the parameters of the probability distribution/energy expression
C Read the parameters of Utheta determined from ab initio surfaces
C Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
C
-c write (iout,*) "tu dochodze"
+ write (iout,*) "tu dochodze"
read (ithep,*) nthetyp,ntheterm,ntheterm2,
& ntheterm3,nsingle,ndouble
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
do i=-ntyp1,-1
ithetyp(i)=-ithetyp(-i)
enddo
-c write (iout,*) "tu dochodze"
+ write (iout,*) "tu dochodze"
do iblock=1,2
do i=-maxthetyp,maxthetyp
do j=-maxthetyp,maxthetyp
enddo
enddo
enddo
+C write (iout,*) "KURWA1"
do iblock=1,2
do i=0,nthetyp
do j=-nthetyp,nthetyp
do k=-nthetyp,nthetyp
read (ithep,'(6a)') res1
+ write(iout,*) res1,i,j,k
read (ithep,*) aa0thet(i,j,k,iblock)
read (ithep,*)(aathet(l,i,j,k,iblock),l=1,ntheterm)
read (ithep,*)
enddo
enddo
enddo
+C write(iout,*) "KURWA1.1"
C
C For dummy ends assign glycine-type coefficients of theta-only terms; the
C coefficients of theta-and-gamma-dependent terms are zero.
aa0thet(nthetyp+1,i,nthetyp+1,iblock)=0.0d0
enddo
enddo
+C write(iout,*) "KURWA1.5"
C Substitution for D aminoacids from symmetry.
do iblock=1,2
do i=-nthetyp,0
call flush(iout)
endif
#endif
-
+C write(iout,*) 'KURWA2'
#ifdef CRYST_SC
C
C Read the parameters of the probability distribution/energy expression
enddo
#endif
close(irotam)
+C write (iout,*) 'KURWAKURWA'
#ifdef CRYST_TOR
C
C Read torsional parameters in old format
read (isidep,*)(sigii(i),i=1,ntyp)
read (isidep,*)(chip(i),i=1,ntyp)
read (isidep,*)(alp(i),i=1,ntyp)
+ do i=1,ntyp
+ read (isidep,*)(epslip(i,j),j=i,ntyp)
+C write(iout,*) "WARNING!!",i,ntyp
+ write(iout,*) "epslip", i, (epslip(i,j),j=i,ntyp)
+C do j=1,ntyp
+C epslip(i,j)=epslip(i,j)+0.05d0
+C enddo
+ enddo
C For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
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
do i=1,ntyp
do j=i,ntyp
epsij=eps(i,j)
+ epsijlip=epslip(i,j)
if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
rrij=sigma(i,j)
else
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)
+ 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)
if (ipot.gt.2) then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
C
C Define the constants of the disulfide bridge
C
- ebr=-5.50D0
+C ebr=-12.0D0
c
c Old arbitrary potential - commented out.
c
c energy surface of diethyl disulfide.
c A. Liwo and U. Kozlowska, 11/24/03
c
- D0CM = 3.78d0
- AKCM = 15.1d0
- AKTH = 11.0d0
- AKCT = 12.0d0
- V1SS =-1.08d0
- V2SS = 7.61d0
- V3SS = 13.7d0
+C D0CM = 3.78d0
+C AKCM = 15.1d0
+C AKTH = 11.0d0
+C AKCT = 12.0d0
+C V1SS =-1.08d0
+C V2SS = 7.61d0
+C V3SS = 13.7d0
+ write (iout,*) dyn_ss,'dyndyn'
+ if (dyn_ss) then
+ ss_depth=ebr/wsc-0.25*eps(1,1)
+C write(iout,*) akcm,whpb,wsc,'KURWA'
+ Ht=Ht/wsc-0.25*eps(1,1)
- if (lprint) then
+ akcm=akcm*whpb/wsc
+ akth=akth*whpb/wsc
+ akct=akct*whpb/wsc
+ v1ss=v1ss*whpb/wsc
+ v2ss=v2ss*whpb/wsc
+ v3ss=v3ss*whpb/wsc
+ else
+ ss_depth=ebr/whpb-0.25*eps(1,1)*wsc/whpb
+ endif
+
+C if (lprint) then
write (iout,'(/a)') "Disulfide bridge parameters:"
write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
& ' v3ss:',v3ss
- endif
+C endif
+ 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)
+ enddo
+ buff_shield=1.0d0
+ endif
return
end
projects / unres.git / blobdiff