include 'COMMON.SBRIDGE'
include 'COMMON.MD'
include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
character*1 t1,t2,t3
character*1 onelett(4) /"G","A","P","D"/
character*1 toronelet(-2:2) /"p","a","G","A","P"/
#else
read (ibond,*) junk,vbldp0,vbldpdum,akp,rjunk,mp,ip,pstok
do i=1,ntyp
+ print *,i
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),
& j=1,nbondterm(i)),msc(i),isc(i),restok(i)
dsc(i) = vbldsc0(1,i)
enddo
endif
C reading lipid parameters
+ write (iout,*) "iliptranpar",iliptranpar
+ call flush(iout)
read(iliptranpar,*) pepliptran
do i=1,ntyp
read(iliptranpar,*) liptranene(i)
C
read (ithep,*,err=111,end=111) nthetyp,ntheterm,ntheterm2,
& ntheterm3,nsingle,ndouble
+ write (iout,*) "ithep",ithep
+ call flush(iout)
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
read (ithep,*,err=111,end=111) (ithetyp(i),i=1,ntyp1)
do i=-ntyp1,-1
C
if (lprint) then
write (iout,'(//a)') 'Parameter of virtual-bond-angle potential'
- do i=1,nthetyp+1
- do j=1,nthetyp+1
- do k=1,nthetyp+1
+ do iblock=1,2
+ do i=0,nthetyp
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
write (iout,'(//4a)')
- & 'Type ',onelett(i),onelett(j),onelett(k)
+ & 'Type ',toronelet(i),toronelet(j),toronelet(k)
write (iout,'(//a,10x,a)') " l","a[l]"
write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k,iblock)
write (iout,'(i2,1pe15.5)')
enddo
enddo
enddo
+ enddo
enddo
call flush(iout)
endif
C
read (itorp,*,end=113,err=113) ntortyp
read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
+ itortyp(ntyp1)=ntortyp
do iblock=1,2
do i=-ntyp,-1
itortyp(i)=-itortyp(-i)
close (itorp)
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
- do i=1,ntortyp
- do j=1,ntortyp
+ do iblock=1,2
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
write (iout,*) 'ityp',i,' jtyp',j
write (iout,*) 'Fourier constants'
do k=1,nterm(i,j,iblock)
enddo
enddo
enddo
+ enddo
endif
C
enddo
endif
#endif
+C read Czybyshev torsional parameters
+ read (itorkcc,*,end=121,err=121) nkcctyp
+ read (itorkcc,*,end=121,err=121) (itortyp_kcc(i),i=1,ntyp)
+ do i=-ntyp,-1
+ itortyp_kcc(i)=-itortyp_kcc(-i)
+ enddo
+ do i=0,nkcctyp
+ do j=0,nkcctyp
+C first we read the cos and sin gamma parameters
+ read (itorkcc,*,end=121,err=121)
+ & nterm_kcc(j,i),nterm_kcc_Tb(j,i)
+C read (itorkcc,*,end=121,err=121) nterm_kcc_Tb(j,i)
+ do k=1,nterm_kcc(j,i)
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v11_chyb(l,k,j,i)
+ enddo
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v21_chyb(l,k,j,i)
+ enddo
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v12_chyb(l,k,j,i)
+ enddo
+ do l=1,nterm_kcc_Tb(j,i)
+ read (itorkcc,*,end=121,err=121) v22_chyb(l,k,j,i)
+ enddo
+ read (itorkcc,*,end=121,err=121) v1_kcc(k,j,i)
+ read (itorkcc,*,end=121,err=121) v2_kcc(k,j,i)
+ enddo
+ enddo
+ enddo
+ if (lprint) then
+c Print valence-torsional parameters
+ write (iout,'(a)')
+ & "Parameters of the valence-torsional potentials"
+ do i=0,nkcctyp
+ do j=0,nkcctyp
+ write (iout,'(3a)') "Type ",toronelet(i),toronelet(j)
+ write (iout,'(2a20,a15)') "v_kcc","v1_chyb","v2_chyb"
+ do k=1,nterm_kcc(j,i)
+ write (iout,'(i5,f15.10,i5,2f15.10)')
+ & k,v1_kcc(k,j,i),1,v11_chyb(1,k,j,i),v21_chyb(1,k,j,i)
+ do l=2,nterm_kcc_Tb(j,i)
+ write (iout,'(20x,i5,2f15.10)')
+ & l,v11_chyb(l,k,j,i),v21_chyb(l,k,j,i)
+ enddo
+ write (iout,'(i5,f15.10,i5,2f15.10)')
+ & k,v2_kcc(k,j,i),1,v12_chyb(1,k,j,i),v22_chyb(1,k,j,i)
+ do l=2,nterm_kcc_Tb(j,i)
+ write (iout,'(20x,i5,2f15.10)')
+ & l,v12_chyb(l,k,j,i),v22_chyb(l,k,j,i)
+ enddo
+ write (iout,'(a)')
+ enddo
+ enddo
+ enddo
+ endif
+C here will be the apropriate recalibrating for D-aminoacid
+C read (ithetkcc,*,end=121,err=121) nkcctyp
+ do i=0,nkcctyp
+ read (ithetkcc,*,end=121,err=121) nbend_kcc_Tb(i)
+ do j=1,nbend_kcc_Tb(i)
+ read (ithetkcc,*,end=121,err=121) v1bend_chyb(j,i)
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)')
+ & "Parameters of the valence-only potentials"
+ do i=0,nkcctyp
+ write (iout,'(2a)') "Type ",toronelet(i)
+ do k=1,nbend_kcc_Tb(i)
+ write(iout,'(i5,f15.10)') k,v1bend_chyb(k,i)
+ enddo
+ enddo
+ endif
C Read of Side-chain backbone correlation parameters
C Modified 11 May 2012 by Adasko
CCC
#else
read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
c write (iout,*) 'ntortyp',ntortyp
+ do i=-ntyp,-1
+ isccortyp(i)=-isccortyp(-i)
+ enddo
maxinter=3
cc maxinter is maximum interaction sites
+C NOW READING FOR LL aminoacid chirality
do l=1,maxinter
do i=1,nsccortyp
do j=1,nsccortyp
read (isccor,*,end=119,err=119)
& nterm_sccor(i,j),nlor_sccor(i,j)
+ nterm_sccor(-i,-j)=nterm_sccor(i,j)
+ v0ijsccor=0.0d0
+ si=-1.0d0
+
+ do k=1,nterm_sccor(i,j)
+ read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j)
+ & ,v2sccor(k,l,i,j)
+ v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
+ si=-si
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+
+ enddo
+ do k=1,nlor_sccor(i,j)
+ read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),
+ & vlor2sccor(k,i,j),vlor3sccor(k,i,j)
+ v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
+ &(1+vlor3sccor(k,i,j)**2)
+ enddo
+ v0sccor(l,i,j)=v0ijsccor
+ v0sccor(l,-i,-j)=v0ijsccor
+ enddo
+ enddo
+ enddo
+C NOW READING FOR LD aminoacid chirality
+ do l=1,maxinter
+ do i=1,nsccortyp
+ do j=-nsccortyp,-1
+ read (isccor,*,end=119,err=119)
+ & nterm_sccor(i,j),nlor_sccor(i,j)
+ nterm_sccor(-i,-j)=nterm_sccor(i,j)
v0ijsccor=0.0d0
si=-1.0d0
& ,v2sccor(k,l,i,j)
v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
si=-si
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+
enddo
do k=1,nlor_sccor(i,j)
read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),
v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
&(1+vlor3sccor(k,i,j)**2)
enddo
- v0sccor(i,j,iblock)=v0ijsccor
+ v0sccor(l,i,j)=v0ijsccor
+ v0sccor(l,-i,-j)=v0ijsccor
enddo
enddo
enddo
+C symetry for GLY
+ i=10
+ do l=1,maxinter
+ do j=-nsccortyp,-1
+ do k=1,nterm_sccor(i,j)
+ v1sccor(k,l,10,j)=v1sccor(k,l,10,-j)
+ v2sccor(k,l,10,j)=-v2sccor(k,l,10,-j)
+ v1sccor(k,l,j,10)=v1sccor(k,l,-j,10)
+ v2sccor(k,l,j,10)=-v2sccor(k,l,-j,10)
+ enddo
+ enddo
+ enddo
+
close (isccor)
#endif
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
+ do l=1,maxinter
do i=1,nsccortyp
do j=1,nsccortyp
write (iout,*) 'ityp',i,' jtyp',j
enddo
enddo
enddo
+ enddo
endif
C
write (iout,*) "Coefficients of the cumulants"
endif
read (ifourier,*) nloctyp
-
+#ifdef NEWCORR
+ read (ifourier,*,end=115,err=115) (itype2loc(i),i=1,ntyp)
+ read (ifourier,*,end=115,err=115) (iloctyp(i),i=0,nloctyp-1)
+ itype2loc(ntyp1)=nloctyp
+ iloctyp(nloctyp)=ntyp1
+#else
+ do i=1,ntyp1
+ itype2loc(i)=itortyp(i)
+ enddo
+ iloctyp(0)=10
+ iloctyp(1)=9
+ iloctyp(2)=20
+ iloctyp(3)=ntyp1
+#endif
+ do i=1,ntyp1
+ itype2loc(-i)=-itype2loc(i)
+ enddo
+ do i=1,nloctyp
+ iloctyp(-i)=-iloctyp(i)
+ enddo
+ write (iout,*) "itype2loc",(itype2loc(i),i=1,ntyp1)
+ write (iout,*) "nloctyp",nloctyp,
+ & " iloctyp",(iloctyp(i),i=0,nloctyp)
do i=0,nloctyp-1
read (ifourier,*,end=115,err=115)
read (ifourier,*,end=115,err=115) (b(ii,i),ii=1,13)
write (iout,*) 'Type',i
write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
endif
-c B1(1,i) = b(3)
-c B1(2,i) = b(5)
-c B1(1,-i) = b(3)
-c B1(2,-i) = -b(5)
+ b(3,-i)= b(3,i)
+ b(5,-i)=-b(5,i)
+ b(4,-i)=-b(4,i)
+ b(2,-i)= b(2,i)
+ B1(1,i) = b(3,i)
+ B1(2,i) = b(5,i)
+ B1(1,-i) = b(3,i)
+ B1(2,-i) = -b(5,i)
c b1(1,i)=0.0d0
c b1(2,i)=0.0d0
-c B1tilde(1,i) = b(3)
-c B1tilde(2,i) =-b(5)
-c B1tilde(1,-i) =-b(3)
-c B1tilde(2,-i) =b(5)
+ B1tilde(1,i) = b(3,i)
+ B1tilde(2,i) =-b(5,i)
+ B1tilde(1,-i) =-b(3,i)
+ B1tilde(2,-i) =b(5,i)
c b1tilde(1,i)=0.0d0
c b1tilde(2,i)=0.0d0
-c B2(1,i) = b(2)
-c B2(2,i) = b(4)
-c B2(1,-i) =b(2)
-c B2(2,-i) =-b(4)
+ B2(1,i) = b(2,i)
+ B2(2,i) = b(4,i)
+ B2(1,-i) =b(2,i)
+ B2(2,-i) =-b(4,i)
+cc B1tilde(1,i) = b(3,i)
+cc B1tilde(2,i) =-b(5,i)
+C B1tilde(1,-i) =-b(3,i)
+C B1tilde(2,-i) =b(5,i)
+cc b1tilde(1,i)=0.0d0
+cc b1tilde(2,i)=0.0d0
+cc B2(1,i) = b(2,i)
+cc B2(2,i) = b(4,i)
+C B2(1,-i) =b(2,i)
+C B2(2,-i) =-b(4,i)
c b2(1,i)=0.0d0
c b2(2,i)=0.0d0
c ee(1,2,i)=0.0d0
c ee(2,1,i)=ee(1,2,i)
enddo
-c lprint=.true.
+ lprint=.true.
if (lprint) then
do i=1,nloctyp
write (iout,*) 'Type',i
enddo
enddo
endif
-c lprint=.false.
+ lprint=.false.
C
C Read electrostatic-interaction parameters
& ', exponents are ',expon,2*expon
goto (10,20,30,30,40) ipot
C----------------------- LJ potential ---------------------------------
- 10 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ 10 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),
& (sigma0(i),i=1,ntyp)
if (lprint) then
write (iout,'(/a/)') 'Parameters of the LJ potential:'
endif
goto 50
C----------------------- LJK potential --------------------------------
- 20 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ 20 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),
& (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp)
if (lprint) then
write (iout,'(/a/)') 'Parameters of the LJK potential:'
goto 50
C---------------------- GB or BP potential -----------------------------
30 do i=1,ntyp
- read (isidep,*,end=116,err=116)(eps(i,j),j=i,ntyp)
+ read (isidep,*,end=117,err=117)(eps(i,j),j=i,ntyp)
enddo
read (isidep,*,end=116,err=116)(sigma0(i),i=1,ntyp)
read (isidep,*,end=116,err=116)(sigii(i),i=1,ntyp)
C now we start reading lipid
do i=1,ntyp
read (isidep,*,end=1161,err=1161)(epslip(i,j),j=i,ntyp)
+ write(iout,*) "epslip", i, (epslip(i,j),j=i,ntyp)
+
C print *,"WARNING!!"
C do j=1,ntyp
C epslip(i,j)=epslip(i,j)+0.05d0
C enddo
enddo
+ write(iout,*) epslip(1,1),"OK?"
C For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
endif
goto 50
C--------------------- GBV potential -----------------------------------
- 40 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ 40 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),
& (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp),(sigii(i),i=1,ntyp),
& (chip(i),i=1,ntyp),(alp(i),i=1,ntyp)
if (lprint) then
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
+
#ifdef OLDSCP
C
C Define the SC-p interaction constants (hard-coded; old style)
C
C Define the constants of the disulfide bridge
C
- ebr=-5.50D0
+C ebr=-12.00D0
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
c akcm=0.0d0
c akth=0.0d0
c akct=0.0d0
c v2ss=0.0d0
c v3ss=0.0d0
- if(me.eq.king) 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 if(me.eq.king) then
+C write (iout,'(/a)') "Disulfide bridge parameters:"
+C write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
+C write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
+C write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
+C write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
+C & ' v3ss:',v3ss
+C endif
+C set the variables used for shielding effect
+C write (iout,*) "SHIELD MODE",shield_mode
+C if (shield_mode.gt.0) then
+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
+C VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+C VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+C write (iout,*) VSolvSphere,VSolvSphere_div
+C long axis of side chain
+C do i=1,ntyp
+C long_r_sidechain(i)=vbldsc0(1,i)
+C short_r_sidechain(i)=sigma0(i)
+C enddo
+C lets set the buffor value
+C buff_shield=1.0d0
+C endif
return
111 write (iout,*) "Error reading bending energy parameters."
goto 999
118 write (iout,*) "Error reading SCp interaction parameters."
goto 999
119 write (iout,*) "Error reading SCCOR parameters"
+ go to 999
+ 121 write (iout,*) "Error in Czybyshev parameters"
999 continue
#ifdef MPI
call MPI_Finalize(Ierror)
#else
call getenv(var,val)
#endif
-
+C set the variables used for shielding effect
+C if (shield_mode.gt.0) then
+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
+C VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+C VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+C long axis of side chain
+C do i=1,ntyp
+C long_r_sidechain(i)=vbldsc0(1,i)
+C short_r_sidechain(i)=sigma0(i)
+C enddo
+C lets set the buffor value
+C buff_shield=1.0d0
+C endif
return
end
projects / unres.git / blobdiff