use names
!-----------------------------------------------------------------------------
! Max. number of energy intervals
- integer,parameter :: max_ene=21 !10
+ integer,parameter :: max_ene=49 !10
!-----------------------------------------------------------------------------
! Maximum number of terms in SC bond-stretching potential
integer,parameter :: maxbondterm=3
!-----------------------------------------------------------------------------
! Max. number of contacts per residue
integer :: maxconts
+ integer,parameter :: maxcontsshi=50
!-----------------------------------------------------------------------------
! Max. number of SC contacts
integer :: maxcont
integer :: rescale_mode
real(kind=8) :: wsc,wscp,welec,wbond,wstrain,wtor,wtor_d,wang,&
wscloc,wcorr,wcorr4,wcorr5,wcorr6,wsccor,wel_loc,wturn3,wturn4,&
- wturn6,wvdwpp,wliptran,wshield,lipscale,wtube
+ wturn6,wvdwpp,wliptran,wshield,lipscale,wtube, &
+ wbond_nucl,wang_nucl,wcorr_nucl,wcorr3_nucl,welpp,wtor_nucl,&
+ wtor_d_nucl,welsb,wsbloc,wvdwsb,welpsb,wvdwpp_nucl,wvdwpsb,wcatprot,&
+ wcatcat,wscbase,wpepbase,wscpho,wpeppho
#ifdef CLUSTER
real(kind=8) :: scalscp
#endif
real(kind=8),dimension(:),allocatable :: weights !(n_ene)
real(kind=8) :: temp0,scal14,cutoff_corr,delt_corr,r0_corr
- integer :: ipot
+ integer :: ipot,ipot_nucl
! common /potentials/
character(len=3),dimension(5) :: potname = &
(/'LJ ','LJK','BP ','GB ','GBV'/)
real(kind=8),dimension(:,:),allocatable :: aa_aq,bb_aq,augm,aa_lip,bb_lip !(ntyp,ntyp)
real(kind=8),dimension(:),allocatable :: sc_aa_tube_par,sc_bb_tube_par,&
acavtub,bcavtub,ccavtub,dcavtub,tubetranene
+ real(kind=8),dimension(:,:),allocatable :: aa_nucl,bb_nucl
real(kind=8) :: acavtubpep,bcavtubpep,ccavtubpep,dcavtubpep, &
tubetranenepep,pep_aa_tube,pep_bb_tube,tubeR0
real(kind=8),dimension(3) :: tubecenter
real(kind=8),dimension(:,:),allocatable :: aad,bad !(ntyp,2)
real(kind=8),dimension(2,2) :: app,bpp,ael6,ael3
+ real(kind=8),dimension(:),allocatable :: aad_nucl,bad_nucl !(ntyp,2)
+ real(kind=8),dimension(2,2) :: app_nucl,bpp_nucl
+ real(kind=8),dimension(:,:),allocatable :: ael6_nucl,&
+ ael3_nucl,ael32_nucl,ael63_nucl
integer :: expon,expon2, nnt,nct,itypro
+ integer,dimension(5) :: nnt_molec,nct_molec
integer,dimension(:,:),allocatable :: istart,iend !(maxres,maxint_gr)
integer,dimension(:),allocatable :: nint_gr,itel,&
ielstart,ielend,ielstart_vdw,ielend_vdw,nscp_gr !(maxres)
+ integer,dimension(:,:),allocatable :: istart_nucl,iend_nucl !(maxres,maxint_gr)
+ integer,dimension(:),allocatable :: nint_gr_nucl,itel_nucl,&
+ ielstart_nucl,ielend_nucl,ielstart_vdw_nucl,ielend_vdw_nucl,nscp_gr_nucl !(maxres)
+ integer,dimension(:,:),allocatable :: iscpstart_nucl,iscpend_nucl !(maxres,maxint_gr)
+
+ integer,dimension(:),allocatable :: istype,molnum
integer,dimension(:,:),allocatable :: itype ! now itype has more molecule types
integer,dimension(:,:),allocatable :: iscpstart,iscpend !(maxres,maxint_gr)
integer :: iatsc_s,iatsc_e,iatel_s,iatel_e,iatel_s_vdw,&
iatel_e_vdw,iatscp_s,iatscp_e,ispp,iscp
+ integer :: iatsc_s_nucl,iatsc_e_nucl,iatel_s_nucl,iatel_e_nucl,&
+ iatel_s_vdw_nucl,iatel_e_vdw_nucl,iatscp_s_nucl,iatscp_e_nucl,&
+ ispp_nucl,iscp_nucl
+
! 12/1/95 Array EPS included in the COMMON block.
! common /body/
real(kind=8),dimension(:,:),allocatable :: sigma !(0:ntyp1,0:ntyp1)
real(kind=8),dimension(:),allocatable :: chip,alp,sigma0,&
sigii,rr0 !(ntyp)
real(kind=8),dimension(2,2) :: rpp,epp,elpp6,elpp3
+ real(kind=8),dimension(:,:),allocatable :: sigma_nucl !(0:ntyp1,0:ntyp1)
+ real(kind=8),dimension(:,:),allocatable :: eps_nucl,sigmaii_nucl,&
+ chi_nucl,r0_nucl, chip_nucl !(ntyp,ntyp) r0e !!! nie używane
+ real(kind=8),dimension(:),allocatable :: alp_nucl,sigma0_nucl,&
+ sigii_nucl,rr0_nucl !(ntyp)
+ real(kind=8),dimension(2,2) :: rpp_nucl,epp_nucl
+ real(kind=8),dimension(:,:),allocatable ::elpp6_nucl,&
+ elpp3_nucl,elpp32_nucl,elpp63_nucl
+ real(kind=8):: r0pp,epspp,AEES,BEES
+
real(kind=8),dimension(:,:),allocatable :: r0d,eps_scp,rscp !(ntyp,2) r0d !!! nie używane
+ real(kind=8),dimension(:),allocatable :: eps_scp_nucl,rscp_nucl!(ntyp,2) r0d !!! nie używane
+
! 12/5/03 modified 09/18/03 Bond stretching parameters.
! common /stretch/
real(kind=8) :: vbldp0,akp,distchainmax,vbldpDUM
real(kind=8),dimension(:,:),allocatable :: vbldsc0,aksc,abond0 !(maxbondterm,ntyp)
+ real(kind=8) :: vbldp0_nucl,akp_nucl
+ real(kind=8),dimension(:,:),allocatable :: vbldsc0_nucl,&
+ aksc_nucl,abond0_nucl !(maxbondterm,ntyp)
+
integer,dimension(:),allocatable :: nbondterm !(ntyp)
+ integer,dimension(:),allocatable :: nbondterm_nucl !(ntyp)
+
!-----------------------------------------------------------------------------
! common.local
! Parameters of ab initio-derived potential of virtual-bond-angle bending
integer :: nthetyp,ntheterm,ntheterm2,ntheterm3,nsingle,&
ndouble,nntheterm
integer,dimension(:),allocatable :: ithetyp !(-ntyp1:ntyp1)
+ integer,dimension(:,:),allocatable :: nstate !(-ntyp1:ntyp1)
real(kind=8),dimension(:,:,:,:),allocatable :: aa0thet
!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
real(kind=8),dimension(:,:,:,:,:),allocatable :: aathet
ccthet,ddthet,eethet
!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
real(kind=8),dimension(:,:,:,:,:,:,:),allocatable :: ffthet,ggthet
+
+!-----------nucleic acid parameters--------------------------
+ integer :: nthetyp_nucl,ntheterm_nucl,ntheterm2_nucl,&
+ ntheterm3_nucl,nsingle_nucl,&
+ ndouble_nucl,nntheterm_nucl
+ integer,dimension(:),allocatable :: ithetyp_nucl !(-ntyp1:ntyp1)
+ real(kind=8),dimension(:,:,:),allocatable :: aa0thet_nucl
+!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ real(kind=8),dimension(:,:,:,:),allocatable :: aathet_nucl
+ real(kind=8),dimension(:,:,:,:,:),allocatable :: bbthet_nucl,&
+ ccthet_nucl,ddthet_nucl,eethet_nucl
+!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ real(kind=8),dimension(:,:,:,:,:,:),allocatable :: ffthet_nucl,ggthet_nucl
+
!(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
! Parameters of the virtual-bond-angle probability distribution
! common /thetas/
iturn3_start,iturn3_end,iturn4_start,iturn4_end,iint_start,&
iint_end,iphi1_start,iphi1_end,itau_start,itau_end,&
ilip_start,ilip_end,itube_start,itube_end
+ integer :: ibond_nucl_start,ibond_nucl_end,iphi_nucl_start,&
+ iphi_nucl_end,iphid_nucl_start,iphid_nucl_end,&
+ ibondp_nucl_start,ibondp_nucl_end,ithet_nucl_start,ithet_nucl_end,&
+ loc_start_nucl,loc_end_nucl
integer,dimension(:),allocatable :: ibond_displ,ibond_count,&
ithet_displ,ithet_count,iphi_displ,iphi_count,iphi1_displ,&
iphi1_count,ivec_displ,ivec_count,iset_displ,iset_count,&
! Parameters of the SC rotamers (local) term
! common/scrot/
real(kind=8),dimension(:,:),allocatable :: sc_parmin !(maxsccoef,ntyp)
+ real(kind=8),dimension(:,:),allocatable :: sc_parmin_nucl !(maxsccoef,ntyp)
+
!-----------------------------------------------------------------------------
! common.torcnstr
! common /torcnstr/
integer,dimension(:),allocatable :: idih_constr,idih_nconstr,itheta_constr !(maxdih_constr)
integer :: idihconstr_start,idihconstr_end, &
ithetaconstr_start,ithetaconstr_end
- real(kind=8) :: ftors
+! real(kind=8) :: ftors
real(kind=8),dimension(:),allocatable :: drange,theta_constr0,theta_drange !(maxdih_constr)
- real(kind=8),dimension(:),allocatable :: phi0 !(maxdih_constr)
+ real(kind=8),dimension(:),allocatable :: phi0,ftors !(maxdih_constr)
real(kind=8),dimension(:),allocatable :: for_thet_constr !(maxdih_constr)
!-----------------------------------------------------------------------------
integer,dimension(:),allocatable :: itortyp !(-ntyp1:ntyp1)
integer,dimension(:,:,:),allocatable :: nterm,nlor !(-maxtor:maxtor,-maxtor:maxtor,2)
integer :: ntortyp,nterm_old
+!------torsion nucleic
+ real(kind=8),dimension(:,:),allocatable :: v0_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
+ real(kind=8),dimension(:,:,:),allocatable :: v1_nucl,v2_nucl !(maxterm,-maxtor:maxtor,-maxtor:maxtor)
+ real(kind=8),dimension(:,:,:),allocatable :: vlor1_nucl !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
+ real(kind=8),dimension(:,:,:),allocatable :: vlor2_nucl,vlor3_nucl !(maxlor,maxtor,maxtor)
+ integer,dimension(:),allocatable :: itortyp_nucl !(-ntyp1:ntyp1)
+ integer,dimension(:,:),allocatable :: nterm_nucl,nlor_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
+ integer :: ntortyp_nucl,nterm_old_nucl
+
! 6/23/01 - constants for double torsionals
! common /torsiond/
real(kind=8),dimension(:,:,:,:,:,:),allocatable :: v1c,v1s
integer :: nloctyp
! common/fourier/ z wham
real(kind=8),dimension(:,:),allocatable :: b !(13,0:maxtor)
+!---------------MOMO---------------------------------------------------
+ integer,dimension(:),allocatable :: icharge
+ real(kind=8),dimension(:,:),allocatable :: alphapol,epshead,&
+ sig0head,sigiso1,sigiso2,rborn,sigmap1,sigmap2,chis,wquad,chipp,&
+ epsintab
+ real(kind=8),dimension(:,:,:),allocatable :: alphasur,alphiso,&
+ wqdip,wstate,dtail
+ real(kind=8),dimension(:,:,:,:),allocatable :: dhead
!-----------------------------------------------------------------------------
! 24 Apr 2017
! Varibles for cutoff on electorstatic
! AFM
real(kind=8) :: distafminit,forceAFMconst,velAFMconst
integer :: afmend,afmbeg
+ real(kind=8),dimension(:,:), allocatable :: catprm
+
+ real(kind=8),dimension(:,:), allocatable :: eps_scbase, &
+ sigma_scbase, &
+ sigmap1_scbase,sigmap2_scbase, &
+ dhead_scbasei, dhead_scbasej, epshead_scbase,&
+ sig0head_scbase, rborn_scbasei,rborn_scbasej,alphapol_scbase,epsintab_scbase,&
+ aa_scbase,bb_scbase
+ real(kind=8),dimension(:,:,:), allocatable :: alphasur_scbase, &
+ wdipdip_scbase,wqdip_scbase,chi_scbase,chipp_scbase,chis_scbase
+ real(kind=8),dimension(:), allocatable :: eps_pepbase, &
+ sigma_pepbase, &
+ sigmap1_pepbase,sigmap2_pepbase,&
+ aa_pepbase,bb_pepbase
+ real(kind=8),dimension(:,:), allocatable :: alphasur_pepbase, &
+ wdipdip_pepbase,chi_pepbase,chipp_pepbase,chis_pepbase
+ real(kind=8),dimension(:), allocatable :: eps_scpho, &
+ sigma_scpho, &
+ sigmap1_scpho,sigmap2_scpho,&
+ aa_scpho,bb_scpho,wqq_scpho,epsintab_scpho,alphapol_scpho,&
+ rborn_scphoi,rborn_scphoj,dhead_scphoi,alphi_scpho
+ real(kind=8),dimension(:,:), allocatable :: alphasur_scpho, &
+ chi_scpho,chipp_scpho,chis_scpho, &
+ wqdip_scpho
+ real(kind=8) ,dimension(4) :: alphasur_peppho
+ real(kind=8) ,dimension(2) :: wqdip_peppho
+ real(kind=8) :: eps_peppho,sigma_peppho,sigmap1_peppho,sigmap2_peppho, &
+ aa_peppho,bb_peppho
end module energy_data
projects / unres4.git / blobdiff