open (iscpp_nucl,file=scpname_nucl,status='old')
call mygetenv('IONPAR_NUCL',ionnuclname)
open (iionnucl,file=ionnuclname,status='old')
+ call mygetenv('IONPAR_TRAN',iontranname)
+ open (iiontran,file=iontranname,status='old',action='read')
#ifndef OLDSCP
call reada(controlcard,"DTRISS",dtriss,1.001D0)
call reada(controlcard,"SSSCALE",ssscale,1.0D0)
dyn_ss=(index(controlcard,'DYN_SS').gt.0)
-
+ call reada(controlcard,"LIPSCALE",lipscale,1.0D0)
allocate(ww(max_eneW))
do i=1,n_eneW
key = wname(i)(:ilen(wname(i)))
wscpho=ww(48)
wpeppho=ww(49)
wcatnucl=ww(50)
+ wcat_tran=ww(56)
! print *,"KURWA",ww(48)
! "WSCBASE ","WPEPBASE ","WSCPHO ","WPEPPHO "
! "WVDWPP ","WELPP ","WVDWPSB ","WELPSB ","WVDWSB ",&
weights(48) =wscpho
weights(49) =wpeppho
weights(50) =wcatnucl
+ weights(56)=wcat_tran
! el--------
call card_concat(controlcard,.false.)
enddo
enddo
endif
- if (.not. allocated(msc)) allocate(msc(ntyp1,5))
- if (.not. allocated(restok)) allocate(restok(ntyp1,5))
+ if (.not. allocated(msc)) allocate(msc(-ntyp1:ntyp1,5))
+ if (.not. allocated(restok)) allocate(restok(-ntyp1:ntyp1,5))
if (oldion.eq.1) then
do i=1,ntyp_molec(5)
if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
- allocate (ichargecat(ntyp_molec(5)))
+ allocate (ichargecat(-ntyp_molec(5):ntyp_molec(5)))
! i to SC, j to jon, isideocat - nazwa pliku z ktorego czytam parametry
if (oldion.eq.0) then
if (.not.allocated(icharge)) then ! this mean you are oprating in old sc-sc mode
read(iion,*) ijunk
endif
- do i=1,ntyp_molec(5)
+ do i=-ntyp_molec(5),ntyp_molec(5)
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
ip(5)=0.2
!DIR$ NOUNROLL
- do j=1,ntyp_molec(5)
+ do j=1,ntyp_molec(5)-1
do i=1,ntyp
! do j=1,ntyp_molec(5)
! write (*,*) "Im in ALAB", i, " ", j
END DO
allocate(aa_aq_cat(-ntyp:ntyp,ntyp),bb_aq_cat(-ntyp:ntyp,ntyp))
do i=1,ntyp
- do j=1,ntyp_molec(5)
+ do j=1,ntyp_molec(5)-1 !without zinc
epsij=epscat(i,j)
rrij=sigmacat(i,j)
rrij=rrij**expon
enddo
endif
-
+! here two denotes the Zn2+ and Cu2+
+ write(iout,*) "before TRANPARM"
+ allocate(aomicattr(0:3,2))
+ allocate(athetacattran(0:6,5,2))
+ allocate(agamacattran(3,5,2))
+ allocate(acatshiftdsc(5,2))
+ allocate(bcatshiftdsc(5,2))
+ allocate(demorsecat(5,2))
+ allocate(alphamorsecat(5,2))
+ allocate(x0catleft(5,2))
+ allocate(x0catright(5,2))
+ allocate(x0cattrans(5,2))
+ allocate(ntrantyp(2))
+ do i=1,1 ! currently only Zn2+
+
+ read(iiontran,*) ntrantyp(i)
+!ntrantyp=4
+!| ao0 ao1 ao2 ao3
+!ASP| a1 a2 a3 aa0 aa1 aa2 aa3 aa4 aa5 aa6 ad bd De alpha x0 -1 -.5
+!CYS| a1 a2 a3 aa0 aa1 aa2 aa3 aa4 aa5 aa6 ad bd De alpha x0left x0right x0transi
+!GLU| a1 a2 a3 aa0 aa1 aa2 aa3 aa4 aa5 aa6 ad bd De alpha x0 -1 -0.5
+!HIS| a1 a2 a3 aa0 aa1 aa2 aa3 aa4 aa5 aa6 ad bd De alpha x0 -1 -.5
+ read(iiontran,*) (aomicattr(j,i),j=0,3)
+ do j=1,ntrantyp(i)
+ read (iiontran,*) (agamacattran(k,j,i),k=1,3),&
+ (athetacattran(k,j,i),k=0,6),acatshiftdsc(j,i),bcatshiftdsc(j,i),&
+ demorsecat(j,i),alphamorsecat(j,i),x0catleft(j,i),x0catright(j,i),&
+ x0cattrans(j,i)
+ enddo
+ enddo
#ifdef CLUSTER
!
! Define the SC-p interaction constants
subroutine read_general_data(*)
use control_data, only:indpdb,symetr,r_cut_ele,rlamb_ele,ions,&
- scelemode,TUBEmode,tor_mode,energy_dec
+ scelemode,TUBEmode,tor_mode,energy_dec,r_cut_ang,r_cut_mart,&
+ rlamb_mart
use energy_data, only:distchainmax,tubeR0,tubecenter,dyn_ss,constr_homology
use geometry_data, only:boxxsize,boxysize,boxzsize,bordtubetop,&
- bordtubebot,tubebufthick,buftubebot,buftubetop
+ bordtubebot,tubebufthick,buftubebot,buftubetop,buflipbot, bufliptop,bordlipbot,bordliptop, &
+ lipbufthick,lipthick
! implicit none
! include "DIMENSIONS"
! include "DIMENSIONS.ZSCOPT"
! include "COMMON.FREE"
! include "COMMON.CONTROL"
! include "COMMON.ENERGIES"
+
character(len=800) :: controlcard
integer :: i,j,k,ii,n_ene_found
integer :: ind,itype1,itype2,itypf,itypsc,itypp
call reada(controlcard,'BOXX',boxxsize,100.0d0)
call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ 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
+
energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
call readi(controlcard,"SCELEMODE",scelemode,0)
call readi(controlcard,"OLDION",oldion,0)
call reada(controlcard,"R_CUT_ELE",r_cut_ele,25.0d0)
call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
write(iout,*) "R_CUT_ELE=",r_cut_ele
+ call reada(controlcard,"R_CUT_MART",r_cut_mart,15.0d0)
+ call reada(controlcard,"LAMBDA_MART",rlamb_mart,0.3d0)
+ call reada(controlcard,"R_CUT_ANG",r_cut_ang,4.2d0)
check_conf=index(controlcard,"NO_CHECK_CONF").eq.0
call reada(controlcard,'DISTCHAINMAX',distchainmax,50.0d0)
call readi(controlcard,'SYM',symetr,1)
do i=nnt,nct
mnum=molnum(i)
iti=itype(i,mnum)
- if (iti.eq.ntyp1) then
- if (itype(i-1,molnum(i-1)).eq.ntyp1) then
+ if (iti.eq.ntyp1_molec(mnum)) then
+ if (itype(i-1,molnum(i-1)).eq.ntyp1_molec(mnum)) then
ichain=ichain+1
ires=0
write (ipdb,'(a)') 'TER'
write (ipdb,'(a)') 'TER'
do i=nnt,nct-1
mnum=molnum(i)
- if (itype(i,mnum).eq.ntyp1) cycle
+ if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
if (itype(i,mnum).eq.10 .and. itype(i+1,mnum).ne.ntyp1_molec(mnum)) then
write (ipdb,30) ica(i),ica(i+1)
else if (itype(i,mnum).ne.10 .and. itype(i+1,mnum).ne.ntyp1_molec(mnum)) then
projects / unres4.git / blobdiff