use geometry_data
use energy_data
- use control_data, only:maxtor,maxterm
+ use control_data, only:maxterm !,maxtor
use MD_data
use MPI_data
!el use map_data
real(kind=8) :: v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,si,&
dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,&
- res1
+ res1,epsijlip
integer :: ichir1,ichir2
! real(kind=8),dimension(maxterm,-maxtor:maxtor,-maxtor:maxtor,2) :: v1_el,v2_el !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
!el allocate(v1_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
allocate(isc(ntyp+1)) !(ntyp+1)
allocate(restok(ntyp+1)) !(ntyp+1)
allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
-
+ allocate(long_r_sidechain(ntyp))
+ allocate(short_r_sidechain(ntyp))
dsc(:)=0.0d0
dsc_inv(:)=0.0d0
endif
enddo
#else
- read (ibond,*) junk,vbldp0,akp,rjunk,mp,ip,pstok
+ read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp,ip,pstok
do i=1,ntyp
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),&
j=1,nbondterm(i)),msc(i),isc(i),restok(i)
theta0(:)=0.0D0
sig0(:)=0.0D0
sigc0(:)=0.0D0
+ allocate(liptranene(ntyp))
+!C reading lipid parameters
+ write (iout,*) "iliptranpar",iliptranpar
+ call flush(iout)
+ read(iliptranpar,*) pepliptran
+ print *,pepliptran
+ do i=1,ntyp
+ read(iliptranpar,*) liptranene(i)
+ print *,liptranene(i)
+ enddo
+ close(iliptranpar)
#ifdef CRYST_THETA
!
!----------------------------------------------------
allocate(ithetyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
- allocate(aa0thet(-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(aa0thet(-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(aathet(ntheterm,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(aathet(ntheterm,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxtheterm,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(bbthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ccthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ddthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(eethet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(bbthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ccthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ddthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(eethet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(ffthet(ndouble,ndouble,ntheterm3,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ggthet(ndouble,ndouble,ntheterm3,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(ffthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ggthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
do i=-ntyp,-1
itortyp(i)=-itortyp(-i)
enddo
-! itortyp(ntyp1)=ntortyp
-! itortyp(-ntyp1)=-ntortyp
+ itortyp(ntyp1)=ntortyp
+ itortyp(-ntyp1)=-ntortyp
do iblock=1,2
write (iout,*) 'ntortyp',ntortyp
do i=0,ntortyp-1
allocate(eps_scp(ntyp,2),rscp(ntyp,2)) !(ntyp,2)
allocate(sigma0(ntyp),rr0(ntyp),sigii(ntyp)) !(ntyp)
allocate(chip(ntyp1),alp(ntyp1)) !(ntyp)
-
+ allocate(epslip(ntyp,ntyp))
augm(:,:)=0.0D0
chip(:)=0.0D0
alp(:)=0.0D0
read (isidep,*,end=117,err=117)(sigii(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(chip(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(alp(i),i=1,ntyp)
+ do i=1,ntyp
+ read (isidep,*,end=117,err=117)(epslip(i,j),j=i,ntyp)
+ enddo
+
! For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
! Calculate the "working" parameters of SC interactions.
!el from module energy - COMMON.INTERACT-------
- allocate(aa(ntyp1,ntyp1),bb(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ allocate(aa_aq(ntyp1,ntyp1),bb_aq(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ allocate(aa_lip(ntyp1,ntyp1),bb_lip(ntyp1,ntyp1)) !(ntyp,ntyp)
allocate(sigma(0:ntyp1,0:ntyp1),r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
- aa(:,:)=0.0D0
- bb(:,:)=0.0D0
+ aa_aq(:,:)=0.0D0
+ bb_aq(:,:)=0.0D0
+ aa_lip(:,:)=0.0D0
+ bb_lip(:,:)=0.0D0
chi(:,:)=0.0D0
sigma(:,:)=0.0D0
r0(:,:)=0.0D0
do i=2,ntyp
do j=1,i-1
eps(i,j)=eps(j,i)
+ epslip(i,j)=epslip(j,i)
enddo
enddo
do i=1,ntyp
epsij=eps(i,j)
sigeps=dsign(1.0D0,epsij)
epsij=dabs(epsij)
- aa(i,j)=epsij*rrij*rrij
- bb(i,j)=-sigeps*epsij*rrij
- aa(j,i)=aa(i,j)
- bb(j,i)=bb(i,j)
+ aa_aq(i,j)=epsij*rrij*rrij
+ bb_aq(i,j)=-sigeps*epsij*rrij
+ aa_aq(j,i)=aa_aq(i,j)
+ bb_aq(j,i)=bb_aq(i,j)
+ epsijlip=epslip(i,j)
+ sigeps=dsign(1.0D0,epsijlip)
+ epsijlip=dabs(epsijlip)
+ aa_lip(i,j)=epsijlip*rrij*rrij
+ bb_lip(i,j)=-sigeps*epsijlip*rrij
+ aa_lip(j,i)=aa_lip(i,j)
+ bb_lip(j,i)=bb_lip(i,j)
+!C write(iout,*) aa_lip
if (ipot.gt.2) then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
endif
if (lprint) then
write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))') &
- restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),&
+ restyp(i),restyp(j),aa_aq(i,j),bb_aq(i,j),augm(i,j),&
sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
endif
enddo
goto 10
else if (card(:3).eq.'TER') then
! End current chain
- ires_old=ires+1
+ ires_old=ires+2
ishift1=ishift1+1
itype(ires_old)=ntyp1
+ itype(ires_old-1)=ntyp1
ibeg=2
! write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
enddo
else
call sccenter(ires,iii,sccor)
+! iii=0
endif
iii=0
endif
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires+ishift1-ishift-1)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
nres=ires
do i=2,nres-1
! write (iout,*) i,itype(i)
- if (itype(i).eq.ntyp1) then
+! if (itype(i).eq.ntyp1) then
! write (iout,*) "dummy",i,itype(i)
- do j=1,3
- c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
+! do j=1,3
+! c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
! c(j,i)=(c(j,i-1)+c(j,i+1))/2
- dc(j,i)=c(j,i)
- enddo
- endif
+! dc(j,i)=c(j,i)
+! enddo
+! endif
+ if (itype(i).eq.ntyp1) then
+ if (itype(i+1).eq.ntyp1) then
+! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+! first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+! second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+ 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
+ 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
+ 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
+ else !itype(i+1).eq.ntyp1
+ 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
+ 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+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 !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
+
enddo
! Calculate the CM of the last side chain.
if (iii.gt.0) then
e2(3)=0.0d0
endif
do j=1,3
- c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ 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)
+ 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
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ c(j,1)=c(j,2)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,4)-c(j,3)
+ dcj=(c(j,4)-c(j,3))/2.0
c(j,1)=c(j,2)-dcj
c(j,nres+1)=c(j,1)
enddo
! enddiagnostic
! makes copy of chains
write (iout,*) "symetr", symetr
+ do j=1,3
+ dc(j,0)=c(j,1)
+ enddo
if (symetr.gt.1) then
call permut(symetr)
character(len=640) :: controlcard
real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
-
+ integer i
nglob_csa=0
eglob_csa=1d99
timem=timlim
modecalc=0
call reada(controlcard,"T_BATH",t_bath,300.0d0)
+!C SHIELD keyword sets if the shielding effect of side-chains is used
+!C 0 denots no shielding is used all peptide are equally despite the
+!C solvent accesible area
+!C 1 the newly introduced function
+!C 2 reseved for further possible developement
+ call readi(controlcard,'SHIELD',shield_mode,0)
+!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "shield_mode",shield_mode
+!C Varibles set size of box
+ call reada(controlcard,'BOXX',boxxsize,100.0d0)
+ call reada(controlcard,'BOXY',boxysize,100.0d0)
+ call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+! CUTOFFF ON ELECTROSTATICS
+ call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
+ call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
+ write(iout,*) "R_CUT_ELE=",r_cut_ele
+! Lipidic parameters
+ 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
+ write (iout,*) "SHIELD MODE",shield_mode
+
+!C-------------------------
minim=(index(controlcard,'MINIMIZE').gt.0)
dccart=(index(controlcard,'CART').gt.0)
overlapsc=(index(controlcard,'OVERLAP').gt.0)
if(me.eq.king.or..not.out1file) &
write (iout,'(2a)') diagmeth(kdiag),&
' routine used to diagonalize matrices.'
+ if (shield_mode.gt.0) then
+ pi=3.141592d0
+!C VSolvSphere the volume of solving sphere
+!C print *,pi,"pi"
+!C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
+!C there will be no distinction between proline peptide group and normal peptide
+!C group in case of shielding parameters
+ VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+ write (iout,*) VSolvSphere,VSolvSphere_div
+!C long axis of side chain
+ do i=1,ntyp
+ long_r_sidechain(i)=vbldsc0(1,i)
+ short_r_sidechain(i)=sigma0(i)
+ write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
+ sigma0(i)
+ enddo
+ buff_shield=1.0d0
+ endif
return
end subroutine read_control
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
subroutine openunits
- use energy_data, only: usampl
+ use MD_data, only: usampl
use csa_data
use MPI_data
use control_data, only:out1file
! print *,"Processor",myrank," opened file IELEP"
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',action='read')
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
! print *,"Processor",myrank," opened file ISIDEP"
! print *,"Processor",myrank," opened parameter files"
#elif (defined G77)
open (ielep,file=elename,status='old')
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old')
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
readonly)
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
open (irotam_pdb,file=rotname_pdb,status='old',action='read')
subroutine readrst
use geometry_data, only: nres,dc
- use energy_data, only: usampl,iset
use MD_data
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
- do i=1,2*nres
+! do i=1,2*nres
+! AL 4/17/17: Now reading d_t(0,:) too
+ do i=0,2*nres
read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
enddo
- do i=1,2*nres
+! do i=1,2*nres
+! AL 4/17/17: Now reading d_c(0,:) too
+ do i=0,2*nres
read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
enddo
if(usampl) then
projects / unres4.git / blobdiff