call int_from_cart1(.false.)
do j=nnt+1,nct-1
mnum=molnum(j)
-! write (iout,*) "Check atom",j
+ write (iout,*) "Check atom",j,itype(j,mnum),vbld(j)
if (mnum.ne.1) cycle
if (itype(j,mnum).eq.ntyp1_molec(mnum)) cycle
- if (itype(j+1,molnum(j+1)).eq.ntyp1_molec(molnum(j+1))) cycle
+ if (itype(j-1,molnum(j-1)).eq.ntyp1_molec(molnum(j-1))) cycle
if ((vbld(j).lt.2.0d0 .or. vbld(j).gt.5.0d0).and.(mnum.ne.5)) then
if (j.gt.2) then
if (itel(j).ne.0 .and. itel(j-1).ne.0) then
- write (iout,*) "Conformation",jjj,jj+1
+ write (iout,*) "Conformation",jjj,jj+1,itype(j-1,molnum(j-1)),itype(j,mnum)
write (iout,*) "Bad CA-CA bond length",j," ",vbld(j),itel(j),&
chalen
write (iout,*) "The Cartesian geometry is:"
use control_data, only: titel,outpdb,outmol2,refstr,pdbref,&
iscode,symetr,punch_dist,print_dist,nstart,nend,&
caonly,iopt,efree,lprint_cart,lprint_int,rlamb_ele,&
- r_cut_ele,nclust,tor_mode,scelemode
+ r_cut_ele,nclust,tor_mode,scelemode,r_cut_mart,r_cut_ang,&
+ rlamb_mart
+ use geometry_data, only:bordliptop,bordlipbot,&
+ bufliptop,buflipbot,lipthick,lipbufthick
! implicit none
! include 'DIMENSIONS'
! include 'sizesclu.dat'
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
+
call readi(controlcard,'NCLUST',nclust,5)
! ions=index(controlcard,"IONS").gt.0
call readi(controlcard,"SCELEMODE",scelemode,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)
call readi(controlcard,'NEND',nend,0)
call reada(controlcard,'ECUT',ecut,10.0d0)
call reada(controlcard,'PROB',prob_limit,0.99d0)
call reada(weightcard,'WPEPBASE',wpepbase,1.0d0)
call reada(weightcard,'WSCPHO',wscpho,0.0d0)
call reada(weightcard,'WPEPPHO',wpeppho,0.0d0)
-
+ call reada(weightcard,'WCATNUCL',wcatnucl,0.0d0)
+ call reada(weightcard,'WCATTRAN',wcat_tran,0.0d0)
call reada(weightcard,"D0CM",d0cm,3.78d0)
call reada(weightcard,"AKCM",akcm,15.1d0)
call reada(weightcard,"AKTH",akth,11.0d0)
call reada(weightcard,"DTRISS",dtriss,1.001D0)
call reada(weightcard,"SSSCALE",ssscale,1.0D0)
dyn_ss=(index(weightcard,'DYN_SS').gt.0)
+ call reada(weightcard,"LIPSCALE",lipscale,1.0D0)
+ call reada(weightcard,"WTL",wliptran,1.0D0)
call reada(weightcard,"HT",Ht,0.0D0)
if (dyn_ss) then
weights(46)=wscbase
weights(47)=wscpho
weights(48)=wpeppho
-
+ weights(49)=wpeppho
+ weights(50)=wcatnucl
+ weights(56)=wcat_tran
+ weights(22)=wliptran
write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wturn3,&
open (itube,file=tubename,status='old')
call getenv('IONPAR',ionname)
open (iion,file=ionname,status='old')
+ call getenv('IONPAR_NUCL',ionnuclname)
+ open (iionnucl,file=ionnuclname,status='old')
+ call getenv('IONPAR_TRAN',iontranname)
+ open (iiontran,file=iontranname,status='old')
+
#ifndef OLDSCP
!
character(len=50) :: tytul
character(len=1) :: chainid(10)=(/'A','B','C','D','E','F',&
'G','H','I','J'/)
- integer :: ica(nres),k,iti1
+ integer :: ica(nres),k,iti1,ki
real(kind=8) :: etot,rmsd
integer :: iatom,ichain,ires,i,j,iti,mnum,mnum1,boxxxshift(3)
real(kind=8) :: boxxxx(3),cbeg(3),Rdist(3)
write (ipdb,'(a)') 'TER'
else
ires=ires+1
- if (ires.eq.2) then
- do j=1,3
- cbeg(j)=c(j,i-1)
- enddo
- endif
+! if (molnum(i).ge.1) then
+ if (i.le.3) then
+ ki=2
+ else
+ if (itype(i,mnum).ne.ntyp1_molec(mnum)) then
+ ki=ki+1
+ endif
+ endif
+! endif
+! print *,"tu2",i,k
+ if (itype(ki,mnum).eq.ntyp1_molec(mnum)) ki=ki+1
+ if (itype(ki,mnum).eq.ntyp1_molec(mnum)) ki=ki+1
+ do j=1,3
+ cbeg(j)=c(j,ki)
+ enddo
iatom=iatom+1
ica(i)=iatom
call to_box(c(1,i),c(2,i),c(3,i))
projects / unres4.git / blobdiff