character(len=1) :: toronelet(-2:2) = (/"p","a","G","A","P"/)
logical :: lprint,LaTeX
real(kind=8),dimension(3,3,maxlob) :: blower !(3,3,maxlob)
- real(kind=8),dimension(13) :: b
+ real(kind=8),dimension(13) :: buse
character(len=3) :: lancuch !,ucase
!el local variables
integer :: m,n,l,i,j,k,iblock,lll,llll,ll,nlobi,mm
#endif
if (lprint) then
+ l=3
write (iout,'(/a/)') 'Torsional constants:'
do i=1,nsccortyp
do j=1,nsccortyp
do i=0,nloctyp-1
read (ifourier,*,end=115,err=115)
- read (ifourier,*,end=115,err=115) (b(ii),ii=1,13)
+ read (ifourier,*,end=115,err=115) (buse(ii),ii=1,13)
if (lprint) then
write (iout,*) 'Type',i
- write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii),ii=1,13)
+ write (iout,'(a,i2,a,f10.5)') ('buse(',ii,')=',buse(ii),ii=1,13)
endif
- B1(1,i) = b(3)
- B1(2,i) = b(5)
- B1(1,-i) = b(3)
- B1(2,-i) = -b(5)
-! b1(1,i)=0.0d0
-! b1(2,i)=0.0d0
- B1tilde(1,i) = b(3)
- B1tilde(2,i) =-b(5)
- B1tilde(1,-i) =-b(3)
- B1tilde(2,-i) =b(5)
-! b1tilde(1,i)=0.0d0
-! b1tilde(2,i)=0.0d0
- B2(1,i) = b(2)
- B2(2,i) = b(4)
- B2(1,-i) =b(2)
- B2(2,-i) =-b(4)
-
-! b2(1,i)=0.0d0
-! b2(2,i)=0.0d0
- CC(1,1,i)= b(7)
- CC(2,2,i)=-b(7)
- CC(2,1,i)= b(9)
- CC(1,2,i)= b(9)
- CC(1,1,-i)= b(7)
- CC(2,2,-i)=-b(7)
- CC(2,1,-i)=-b(9)
- CC(1,2,-i)=-b(9)
+ B1(1,i) = buse(3)
+ B1(2,i) = buse(5)
+ B1(1,-i) = buse(3)
+ B1(2,-i) = -buse(5)
+! buse1(1,i)=0.0d0
+! buse1(2,i)=0.0d0
+ B1tilde(1,i) = buse(3)
+ B1tilde(2,i) =-buse(5)
+ B1tilde(1,-i) =-buse(3)
+ B1tilde(2,-i) =buse(5)
+! buse1tilde(1,i)=0.0d0
+! buse1tilde(2,i)=0.0d0
+ B2(1,i) = buse(2)
+ B2(2,i) = buse(4)
+ B2(1,-i) =buse(2)
+ B2(2,-i) =-buse(4)
+
+! buse2(1,i)=0.0d0
+! buse2(2,i)=0.0d0
+ CC(1,1,i)= buse(7)
+ CC(2,2,i)=-buse(7)
+ CC(2,1,i)= buse(9)
+ CC(1,2,i)= buse(9)
+ CC(1,1,-i)= buse(7)
+ CC(2,2,-i)=-buse(7)
+ CC(2,1,-i)=-buse(9)
+ CC(1,2,-i)=-buse(9)
! CC(1,1,i)=0.0d0
! CC(2,2,i)=0.0d0
! CC(2,1,i)=0.0d0
! CC(1,2,i)=0.0d0
- Ctilde(1,1,i)=b(7)
- Ctilde(1,2,i)=b(9)
- Ctilde(2,1,i)=-b(9)
- Ctilde(2,2,i)=b(7)
- Ctilde(1,1,-i)=b(7)
- Ctilde(1,2,-i)=-b(9)
- Ctilde(2,1,-i)=b(9)
- Ctilde(2,2,-i)=b(7)
+ Ctilde(1,1,i)=buse(7)
+ Ctilde(1,2,i)=buse(9)
+ Ctilde(2,1,i)=-buse(9)
+ Ctilde(2,2,i)=buse(7)
+ Ctilde(1,1,-i)=buse(7)
+ Ctilde(1,2,-i)=-buse(9)
+ Ctilde(2,1,-i)=buse(9)
+ Ctilde(2,2,-i)=buse(7)
! Ctilde(1,1,i)=0.0d0
! Ctilde(1,2,i)=0.0d0
! Ctilde(2,1,i)=0.0d0
! Ctilde(2,2,i)=0.0d0
- DD(1,1,i)= b(6)
- DD(2,2,i)=-b(6)
- DD(2,1,i)= b(8)
- DD(1,2,i)= b(8)
- DD(1,1,-i)= b(6)
- DD(2,2,-i)=-b(6)
- DD(2,1,-i)=-b(8)
- DD(1,2,-i)=-b(8)
+ DD(1,1,i)= buse(6)
+ DD(2,2,i)=-buse(6)
+ DD(2,1,i)= buse(8)
+ DD(1,2,i)= buse(8)
+ DD(1,1,-i)= buse(6)
+ DD(2,2,-i)=-buse(6)
+ DD(2,1,-i)=-buse(8)
+ DD(1,2,-i)=-buse(8)
! DD(1,1,i)=0.0d0
! DD(2,2,i)=0.0d0
! DD(2,1,i)=0.0d0
! DD(1,2,i)=0.0d0
- Dtilde(1,1,i)=b(6)
- Dtilde(1,2,i)=b(8)
- Dtilde(2,1,i)=-b(8)
- Dtilde(2,2,i)=b(6)
- Dtilde(1,1,-i)=b(6)
- Dtilde(1,2,-i)=-b(8)
- Dtilde(2,1,-i)=b(8)
- Dtilde(2,2,-i)=b(6)
+ Dtilde(1,1,i)=buse(6)
+ Dtilde(1,2,i)=buse(8)
+ Dtilde(2,1,i)=-buse(8)
+ Dtilde(2,2,i)=buse(6)
+ Dtilde(1,1,-i)=buse(6)
+ Dtilde(1,2,-i)=-buse(8)
+ Dtilde(2,1,-i)=buse(8)
+ Dtilde(2,2,-i)=buse(6)
! Dtilde(1,1,i)=0.0d0
! Dtilde(1,2,i)=0.0d0
! Dtilde(2,1,i)=0.0d0
! Dtilde(2,2,i)=0.0d0
- EE(1,1,i)= b(10)+b(11)
- EE(2,2,i)=-b(10)+b(11)
- EE(2,1,i)= b(12)-b(13)
- EE(1,2,i)= b(12)+b(13)
- EE(1,1,-i)= b(10)+b(11)
- EE(2,2,-i)=-b(10)+b(11)
- EE(2,1,-i)=-b(12)+b(13)
- EE(1,2,-i)=-b(12)-b(13)
+ EE(1,1,i)= buse(10)+buse(11)
+ EE(2,2,i)=-buse(10)+buse(11)
+ EE(2,1,i)= buse(12)-buse(13)
+ EE(1,2,i)= buse(12)+buse(13)
+ EE(1,1,-i)= buse(10)+buse(11)
+ EE(2,2,-i)=-buse(10)+buse(11)
+ EE(2,1,-i)=-buse(12)+buse(13)
+ EE(1,2,-i)=-buse(12)-buse(13)
! ee(1,1,i)=1.0d0
! ee(2,2,i)=1.0d0
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
+!-----------------READING SC BASE POTENTIALS-----------------------------
+ allocate(eps_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(sigma_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(chi_scbase(ntyp_molec(1),ntyp_molec(2),2))
+ allocate(chipp_scbase(ntyp_molec(1),ntyp_molec(2),2))
+ allocate(alphasur_scbase(4,ntyp_molec(1),ntyp_molec(2)))
+ allocate(sigmap1_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(sigmap2_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(chis_scbase(ntyp_molec(1),ntyp_molec(2),2))
+ allocate(dhead_scbasei(ntyp_molec(1),ntyp_molec(2)))
+ allocate(dhead_scbasej(ntyp_molec(1),ntyp_molec(2)))
+ allocate(rborn_scbasei(ntyp_molec(1),ntyp_molec(2)))
+ allocate(rborn_scbasej(ntyp_molec(1),ntyp_molec(2)))
+ allocate(wdipdip_scbase(3,ntyp_molec(1),ntyp_molec(2)))
+ allocate(wqdip_scbase(2,ntyp_molec(1),ntyp_molec(2)))
+ allocate(alphapol_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(epsintab_scbase(ntyp_molec(1),ntyp_molec(2)))
+
+
+ do i=1,ntyp_molec(1)
+ do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
+ write (*,*) "Im in ", i, " ", j
+ read(isidep_scbase,*) &
+ eps_scbase(i,j),sigma_scbase(i,j),chi_scbase(i,j,1),&
+ chi_scbase(i,j,2),chipp_scbase(i,j,1),chipp_scbase(i,j,2)
+ write(*,*) "eps",eps_scbase(i,j)
+ read(isidep_scbase,*) &
+ (alphasur_scbase(k,i,j),k=1,4),sigmap1_scbase(i,j),sigmap2_scbase(i,j), &
+ chis_scbase(i,j,1),chis_scbase(i,j,2)
+ read(isidep_scbase,*) &
+ dhead_scbasei(i,j), &
+ dhead_scbasej(i,j), &
+ rborn_scbasei(i,j),rborn_scbasej(i,j)
+ read(isidep_scbase,*) &
+ (wdipdip_scbase(k,i,j),k=1,3), &
+ (wqdip_scbase(k,i,j),k=1,2)
+ read(isidep_scbase,*) &
+ alphapol_scbase(i,j), &
+ epsintab_scbase(i,j)
+ END DO
+ END DO
+ allocate(aa_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(bb_scbase(ntyp_molec(1),ntyp_molec(2)))
+
+ do i=1,ntyp_molec(1)
+ do j=1,ntyp_molec(2)-1
+ epsij=eps_scbase(i,j)
+ rrij=sigma_scbase(i,j)
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_scbase(i,j)=epsij*rrij*rrij
+ bb_scbase(i,j)=-sigeps*epsij*rrij
+ enddo
+ enddo
+!-----------------READING PEP BASE POTENTIALS-------------------
+ allocate(eps_pepbase(ntyp_molec(2)))
+ allocate(sigma_pepbase(ntyp_molec(2)))
+ allocate(chi_pepbase(ntyp_molec(2),2))
+ allocate(chipp_pepbase(ntyp_molec(2),2))
+ allocate(alphasur_pepbase(4,ntyp_molec(2)))
+ allocate(sigmap1_pepbase(ntyp_molec(2)))
+ allocate(sigmap2_pepbase(ntyp_molec(2)))
+ allocate(chis_pepbase(ntyp_molec(2),2))
+ allocate(wdipdip_pepbase(3,ntyp_molec(2)))
+
+
+ do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
+ write (*,*) "Im in ", i, " ", j
+ read(isidep_pepbase,*) &
+ eps_pepbase(j),sigma_pepbase(j),chi_pepbase(j,1),&
+ chi_pepbase(j,2),chipp_pepbase(j,1),chipp_pepbase(j,2)
+ write(*,*) "eps",eps_pepbase(j)
+ read(isidep_pepbase,*) &
+ (alphasur_pepbase(k,j),k=1,4),sigmap1_pepbase(j),sigmap2_pepbase(j), &
+ chis_pepbase(j,1),chis_pepbase(j,2)
+ read(isidep_pepbase,*) &
+ (wdipdip_pepbase(k,j),k=1,3)
+ END DO
+ allocate(aa_pepbase(ntyp_molec(2)))
+ allocate(bb_pepbase(ntyp_molec(2)))
+
+ do j=1,ntyp_molec(2)-1
+ epsij=eps_pepbase(j)
+ rrij=sigma_pepbase(j)
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_pepbase(j)=epsij*rrij*rrij
+ bb_pepbase(j)=-sigeps*epsij*rrij
+ enddo
+!--------------READING SC PHOSPHATE-------------------------------------
+ allocate(eps_scpho(ntyp_molec(1)))
+ allocate(sigma_scpho(ntyp_molec(1)))
+ allocate(chi_scpho(ntyp_molec(1),2))
+ allocate(chipp_scpho(ntyp_molec(1),2))
+ allocate(alphasur_scpho(4,ntyp_molec(1)))
+ allocate(sigmap1_scpho(ntyp_molec(1)))
+ allocate(sigmap2_scpho(ntyp_molec(1)))
+ allocate(chis_scpho(ntyp_molec(1),2))
+ allocate(wqq_scpho(ntyp_molec(1)))
+ allocate(wqdip_scpho(2,ntyp_molec(1)))
+ allocate(alphapol_scpho(ntyp_molec(1)))
+ allocate(epsintab_scpho(ntyp_molec(1)))
+ allocate(dhead_scphoi(ntyp_molec(1)))
+ allocate(rborn_scphoi(ntyp_molec(1)))
+ allocate(rborn_scphoj(ntyp_molec(1)))
+
+! j=1
+ do j=1,ntyp_molec(1) ! without U then we will take T for U
+ write (*,*) "Im in scpho ", i, " ", j
+ read(isidep_scpho,*) &
+ eps_scpho(j),sigma_scpho(j),chi_scpho(j,1),&
+ chi_scpho(j,2),chipp_scpho(j,1),chipp_scpho(j,2)
+ write(*,*) "eps",eps_scpho(j)
+ read(isidep_scpho,*) &
+ (alphasur_scpho(k,j),k=1,4),sigmap1_scpho(j),sigmap2_scpho(j), &
+ chis_scpho(j,1),chis_scpho(j,2)
+ read(isidep_scpho,*) &
+ (wqdip_scpho(k,j),k=1,2),wqq_scpho(j),dhead_scphoi(j)
+ read(isidep_scpho,*) &
+ epsintab_scpho(j),alphapol_scpho(j),rborn_scphoi(j),rborn_scphoj(j)
+
+ END DO
+ allocate(aa_scpho(ntyp_molec(1)))
+ allocate(bb_scpho(ntyp_molec(1)))
+
+ do j=1,ntyp_molec(1)
+ epsij=eps_scpho(j)
+ rrij=sigma_scpho(j)
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_scpho(j)=epsij*rrij*rrij
+ bb_scpho(j)=-sigeps*epsij*rrij
+ enddo
+
+
+ read(isidep_peppho,*) &
+ eps_peppho,sigma_peppho
+ read(isidep_peppho,*) &
+ (alphasur_peppho(k),k=1,4),sigmap1_peppho,sigmap2_peppho
+ read(isidep_peppho,*) &
+ (wqdip_peppho(k),k=1,2)
+
+ epsij=eps_peppho
+ rrij=sigma_peppho
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_peppho=epsij*rrij*rrij
+ bb_peppho=-sigeps*epsij*rrij
+
allocate(aad(ntyp,2),bad(ntyp,2)) !(ntyp,2)
bad(:,:)=0.0D0
! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
! 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
+! if (unres_pdb) then
! 2/15/2013 by Adam: corrected insertion of the last dummy residue
! print *,i,'tu dochodze'
- call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
- if (fail) then
- e2(1)=0.0d0
- e2(2)=1.0d0
- e2(3)=0.0d0
- endif !fail
+! call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+! if (fail) then
+! e2(1)=0.0d0
+! e2(2)=1.0d0
+! e2(3)=0.0d0
+! endif !fail
! print *,i,'a tu?'
- do j=1,3
- c(j,i)=c(j,i-1)-1.9d0*e2(j)
- enddo
- else !unres_pdb
+! do j=1,3
+! c(j,i)=c(j,i-1)-1.9d0*e2(j)
+! enddo
+! else !unres_pdb
do j=1,3
dcj=(c(j,i-2)-c(j,i-3))/2.0
if (dcj.eq.0) dcj=1.23591524223
c(j,i)=c(j,i-1)+dcj
c(j,nres+i)=c(j,i)
enddo
- endif !unres_pdb
+! endif !unres_pdb
else !itype(i+1,1).eq.ntyp1
- if (unres_pdb) then
+! 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)
- if (fail) then
- e2(1)=0.0d0
- e2(2)=1.0d0
- e2(3)=0.0d0
- endif
+! call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+! if (fail) then
+! e2(1)=0.0d0
+! e2(2)=1.0d0
+! e2(3)=0.0d0
+! endif
do j=1,3
c(j,i)=c(j,i+1)-1.9d0*e2(j)
enddo
- else !unres_pdb
+! else !unres_pdb
do j=1,3
dcj=(c(j,i+3)-c(j,i+2))/2.0
if (dcj.eq.0) dcj=1.23591524223
c(j,i)=c(j,i+1)-dcj
c(j,nres+i)=c(j,i)
enddo
- endif !unres_pdb
+! endif !unres_pdb
endif !itype(i+1,1).eq.ntyp1
endif !itype.eq.ntyp1
if (molecule.eq.5) molecule=molecprev
itype(nres,molecule)=ntyp1_molec(molecule)
nres_molec(molecule)=nres_molec(molecule)+1
- if (unres_pdb) then
+! 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)
- if (fail) then
- e2(1)=0.0d0
- e2(2)=1.0d0
- e2(3)=0.0d0
- endif
- do j=1,3
- c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
- enddo
- else
+! call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+! if (fail) then
+! e2(1)=0.0d0
+! e2(2)=1.0d0
+! e2(3)=0.0d0
+! endif
+! do j=1,3
+! 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))/2.0
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
- endif
+! endif
endif
! print *,'I have',nres, nres_molec(:)
! NOW LETS ROCK! SORTING
allocate(c_temporary(3,2*nres))
allocate(itype_temporary(nres,5))
- allocate(molnum(nres))
+ allocate(molnum(nres+1))
allocate(istype_temp(nres))
itype_temporary(:,:)=0
seqalingbegin=1
open (itordp_nucl,file=tordname_nucl,status='old',action='read')
call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
open (isidep_nucl,file=sidename_nucl,status='old',action='read')
+ call getenv_loc('SIDEPAR_SCBASE',sidename_scbase)
+ open (isidep_scbase,file=sidename_scbase,status='old',action='read')
+ call getenv_loc('PEPPAR_PEPBASE',pepname_pepbase)
+ open (isidep_pepbase,file=pepname_pepbase,status='old',action='read')
+ call getenv_loc('SCPAR_PHOSPH',pepname_scpho)
+ open (isidep_scpho,file=pepname_scpho,status='old',action='read')
+ call getenv_loc('PEPPAR_PHOSPH',pepname_peppho)
+ open (isidep_peppho,file=pepname_peppho,status='old',action='read')
+
call getenv_loc('LIPTRANPAR',liptranname)
open (iliptranpar,file=liptranname,status='old',action='read')
projects / unres4.git / blobdiff