allocate(nss_all(maxstr_proc)) !(maxstr_proc)
allocate(ihpb_all(maxss,maxstr_proc),jhpb_all(maxss,maxstr_proc))!(maxss,maxstr_proc)
allocate(iscore(maxconf)) !(maxconf)
-
+ nss_all=0
+ ihpb_all=0
+ jhpb_all=0
#ifdef CHUJ
ICON=1
! call flush(iout)
if (iret.eq.0) goto 101
call xdrfint(ixdrf, nss, iret)
-! write (iout,*) "iret",iret
-! write (iout,*) "nss",nss
+ write (iout,*) "iret",iret
+! write (iout,*) "nss",nss,i,"TUTU"
call flush(iout)
if (iret.eq.0) goto 101
do k=1,nss
if (iret.eq.0) goto 101
call xdrfint(ixdrf, jhpb(k), iret)
if (iret.eq.0) goto 101
+! write(iout,*), ihpb(k),jhpb(k),"TUTU"
enddo
call xdrffloat(ixdrf,reini,iret)
if (iret.eq.0) goto 101
+! write(iout,*) "TUTU", reini
call xdrffloat(ixdrf,refree,iret)
+! write(iout,*) "TUTU", refree
if (iret.eq.0) goto 101
call xdrffloat(ixdrf,rmsdev,iret)
if (iret.eq.0) goto 101
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:"
!------------------------------------------------------------------------------
subroutine daread_ccoords(istart_conf,iend_conf)
+ use energy_data, only: dyn_ss
+
! implicit none
! include "DIMENSIONS"
! include "sizesclu.dat"
write (iout,*) "Reading binary file, record",iii," ii",ii
call flush(iout)
#endif
+ if (dyn_ss) then
+ read(icbase,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres), &
+ ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),&
+ entfac(ii),rmstb(ii)
+ else
read(icbase,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres),&
- ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),&
- nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss),&
- entfac(ii),rmstb(ii)
+ ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),&
+ nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss),&
+ entfac(ii),rmstb(ii)
+ endif
+
#ifdef DEBUG
write (iout,*) ii,iii,ij,entfac(ii)
write (iout,'(8f10.5)') ((allcart(j,i,ij),j=1,3),i=1,nres)
! implicit none
! include "DIMENSIONS"
! include "sizesclu.dat"
+ use energy_data, only: dyn_ss
+
#ifdef MPI
use MPI_data
include "mpif.h"
write (iout,*) "Writing binary file, record",iii," ii",ii
call flush(iout)
#endif
+ if (dyn_ss) then
write(unit_out,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres),&
- ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),&
- nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss_all(ij)),&
- entfac(ii),rmstb(ii)
+ ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),&
+ entfac(ii),rmstb(ii)
+ else
+ write(unit_out,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres), &
+ ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),&
+ nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss_all(ij)),&
+ entfac(ii),rmstb(ii)
+ endif
+
#ifdef DEBUG
write (iout,'(8f10.5)') ((allcart(j,i,ij),j=1,3),i=1,nres)
write (iout,'(8f10.4)') ((allcart(j,i,ij),j=1,3),i=nnt+nres,&
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 readi(controlcard,'TORMODE',tor_mode,0)
!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
write(iout,*) "torsional and valence angle mode",tor_mode
- call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
+ 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)
character(len=800) :: weightcard
! integer rescode
real(kind=8) :: x(6*nres) !(maxvar)
+ real(kind=8) :: ssscale
integer :: itype_pdb(nres) !(maxres)
! logical seq_comp
integer :: i,j,kkk,mnum
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,"AKCT",akct,12.0d0)
+ call reada(weightcard,"V1SS",v1ss,-1.08d0)
+ call reada(weightcard,"V2SS",v2ss,7.61d0)
+ call reada(weightcard,"V3SS",v3ss,13.7d0)
+ call reada(weightcard,"EBR",ebr,-5.50D0)
+ call reada(weightcard,"ATRISS",atriss,0.301D0)
+ call reada(weightcard,"BTRISS",btriss,0.021D0)
+ call reada(weightcard,"CTRISS",ctriss,1.001D0)
+ 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
+ ss_depth=(ebr/wsc-0.25*eps(1,1))*ssscale
+ Ht=(Ht/wsc-0.25*eps(1,1))*ssscale
+ akcm=akcm/wsc*ssscale
+ akth=akth/wsc*ssscale
+ akct=akct/wsc*ssscale
+ v1ss=v1ss/wsc*ssscale
+ v2ss=v2ss/wsc*ssscale
+ v3ss=v3ss/wsc*ssscale
+ else
+ ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ endif
if (wcorr4.gt.0.0d0) wcorr=wcorr4
weights(1)=wsc
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,&
write(iout,*)"przed setup var"
call setup_var
write(iout,*)"po setup var"
+ if (ns.gt.0.and.dyn_ss) then
+ do i=nss+1,nhpb
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ link_start=1
+ link_end=nhpb
+! call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ enddo
+ endif
+
write (iout,*) "molread: REFSTR",refstr
if (refstr) then
if (.not.pdbref) then
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
!
subroutine pdboutC(etot,rmsd,tytul)
use energy_data, only: ihpb,jhpb,itype,molnum
+ use energy, only:boxshift,to_box
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.CONTROL'
character(len=50) :: tytul
character(len=1) :: chainid(10)=(/'A','B','C','D','E','F',&
'G','H','I','J'/)
- integer :: ica(nres)
+ 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)
+ real(kind=8) :: boxxxx(3),cbeg(3),Rdist(3)
write (ipdb,'(3a,1pe15.5,a,0pf7.2)') 'REMARK ',tytul(:20),&
' ENERGY ',etot,' RMS ',rmsd
iatom=0
ichain=1
ires=0
- boxxxshift(1)=int(c(1,nnt)/boxxsize)
+! boxxxshift(1)=int(c(1,nnt)/boxxsize)
! if (c(1,nnt).lt.0) boxxxshift(1)=boxxxshift(1)-1
- boxxxshift(2)=int(c(2,nnt)/boxzsize)
+! boxxxshift(2)=int(c(2,nnt)/boxzsize)
! if (c(2,nnt).lt.0) boxxxshift(2)=boxxxshift(2)-1
- boxxxshift(3)=int(c(3,nnt)/boxzsize)
+! boxxxshift(3)=int(c(3,nnt)/boxzsize)
! if (c(3,nnt).lt.0) boxxxshift(3)=boxxxshift(3)-1
-
+! do i=1,3
+! if (boxxxshift(i).gt.2) boxxxshift(i)=2
+! if (boxxxshift(i).lt.-2) boxxxshift(i)=-2
+!
+! enddo
+ do j=1,3
+ cbeg(j)=c(j,nnt)
+ enddo
+ call to_box(cbeg(1),cbeg(2),cbeg(3))
boxxxx(1)=boxxsize
boxxxx(2)=boxysize
boxxxx(3)=boxzsize
do i=nnt,nct
mnum=molnum(i)
iti=itype(i,mnum)
+ if (i.ne.nct) then
+ iti1=itype(i+1,mnum)
+ mnum1=molnum(i+1)
+ if ((iti.eq.ntyp1_molec(mnum)).and.(iti1.eq.ntyp1_molec(mnum1))) cycle
+ endif
if (iti.eq.ntyp1_molec(mnum)) then
ichain=ichain+1
ires=0
write (ipdb,'(a)') 'TER'
else
ires=ires+1
+! 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
- if (mnum.eq.5) then
- do j=1,3
- if ((c(j,i).gt.0).and.(c(j,nnt).lt.0)) then
- c(j,i)=dmod(c(j,i),boxxxx(j))+(boxxxshift(j)-1)*boxxxx(j)
- else if ((c(j,i).lt.0).and.(c(j,nnt).gt.0)) then
- c(j,i)=dmod(c(j,i),boxxxx(j))+(boxxxshift(j)+1)*boxxxx(j)
- else
- c(j,i)=dmod(c(j,i),boxxxx(j))+(boxxxshift(j))*boxxxx(j)
- endif
- enddo
- endif
+ call to_box(c(1,i),c(2,i),c(3,i))
+
+ DO k=1,3
+ Rdist(k) = boxshift(c(k,i) - cbeg(k),boxxxx(k))
+ c(k,i)=cbeg(k)+Rdist(k)
+ ENDDO
+ if ((itype(i,molnum(i)).ne.10).and.(molnum(i).ne.5)) then
+ call to_box(c(1,i+nres),c(2,i+nres),c(3,i+nres))
+ DO k=1,3
+ Rdist(k) = boxshift(c(k,i+nres) - cbeg(k),boxxxx(k))
+ c(k,i+nres)=cbeg(k)+Rdist(k)
+ ENDDO
+ endif
write (ipdb,10) iatom,restyp(iti,mnum),chainid(ichain),&
ires,(c(j,i),j=1,3),1.0d0,tempfac(1,i)
if ((iti.ne.10).and.(mnum.ne.5)) then
projects / unres4.git / blobdiff