dsc_inv(i)=1.0D0/dsc(i)
endif
enddo
+! ip(1)=0.0001d0
+! isc(:,1)=0.0001d0
#endif
read (ibond_nucl,*) vbldp0_nucl,akp_nucl,mp(2),ip(2),pstok(2)
do i=1,ntyp_molec(2)
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
- ip(5)=0.2
+! ip(5)=0.2
! isc(5)=0.2
read (iion,*) ncatprotparm
allocate(catprm(ncatprotparm,4))
enddo
endif
enddo
+#ifdef SC_END
+ allocate(nterm_scend(2,ntyp))
+ allocate(arotam_end(0:6,2,ntyp))
+ nterm_scend=0
+ arotam_end=0.0d0
+ read (irotam_end,*) ijunk
+!c write (iout,*) "ijunk",ijunk
+ do i=1,ntyp
+ if (i.eq.10) cycle
+ do j=1,2
+ read (irotam_end,'(a)')
+ read (irotam_end,*) nterm_scend(j,i)
+!c write (iout,*) "i",i," j",j," nterm",nterm_scend(j,i)
+ do k=0,nterm_scend(j,i)
+ read (irotam_end,*) ijunk,arotam_end(k,j,i)
+!c write (iout,*) "k",k," arotam",arotam_end(k,j,i)
+ enddo
+ enddo
+ enddo
+!c lprint=.true.
+ if (lprint) then
+ write (iout,'(a)') &
+ "Parameters of the local potentials of sidechain ends"
+ do i=1,ntyp
+ write (iout,'(5x,9x,2hp-,a3,6x,9x,a3,2h-p)')&
+ restyp(i,1),restyp(i,1)
+ do j=0,max0(nterm_scend(1,i),nterm_scend(2,i))
+ write (iout,'(i5,2f20.10)') &
+ j,arotam_end(j,1,i),arotam_end(j,2,i)
+ enddo
+ enddo
+ endif
+!c lprint=.false.
+#endif
+
!---------reading nucleic acid parameters for rotamers-------------------
allocate(sc_parmin_nucl(9,ntyp_molec(2))) !(maxsccoef,ntyp)
do i=1,ntyp_molec(2)
sigiso2(i,j)=sigiso2(j,i)
! print *,"ATU",sigma(j,i),sigma(i,j),i,j
nstate(i,j) = nstate(j,i)
- dtail(1,i,j) = dtail(1,j,i)
- dtail(2,i,j) = dtail(2,j,i)
+ dtail(1,i,j) = dtail(2,j,i)
+ dtail(2,i,j) = dtail(1,j,i)
DO k = 1, 4
alphasur(k,i,j) = alphasur(k,j,i)
wstate(k,i,j) = wstate(k,j,i)
!HERE THE MASS of MARTINI
write(*,*) "before MARTINI PARAM"
do i=1,ntyp_molec(4)
- msc(i,4)=0.0d0
- mp(4)=72.0d0
+ msc(i,4)=72.0d0
+ mp(4)=0.0d0
isc(i,4)=0.d0
enddo
ip(4)=0.0
+ msc(ntyp_molec(4)+1,4)=0.1d0
!relative dielectric constant = 15 for implicit screening
k_coulomb_lip=332.0d0/15.0d0
!kbond = 1250 kJ/(mol*nm*2)
! Ions by Aga
- allocate(alphapolcat(ntyp,ntyp),epsheadcat(ntyp,ntyp),sig0headcat(ntyp,ntyp))
- allocate(alphapolcat2(ntyp,ntyp))
- allocate(sigiso1cat(ntyp,ntyp),rborn1cat(ntyp,ntyp),rborn2cat(ntyp,ntyp),sigmap1cat(ntyp,ntyp))
- allocate(sigmap2cat(ntyp,ntyp),sigiso2cat(ntyp,ntyp))
- allocate(chis1cat(ntyp,ntyp),chis2cat(ntyp,ntyp),wquadcat(ntyp,ntyp),chipp1cat(ntyp,ntyp),chipp2cat(ntyp,ntyp))
- allocate(epsintabcat(ntyp,ntyp))
- allocate(dtailcat(2,ntyp,ntyp))
- allocate(alphasurcat(4,ntyp,ntyp),alphisocat(4,ntyp,ntyp))
- allocate(wqdipcat(2,ntyp,ntyp))
- allocate(wstatecat(4,ntyp,ntyp))
- allocate(dheadcat(2,2,ntyp,ntyp))
- allocate(nstatecat(ntyp,ntyp))
- allocate(debaykapcat(ntyp,ntyp))
-
- if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,0:ntyp1))
- if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,0:ntyp1))
+ allocate(alphapolcat(ntyp,-1:ntyp_molec(5)),epsheadcat(ntyp,-1:ntyp_molec(5)),sig0headcat(ntyp,-1:ntyp_molec(5)))
+ allocate(alphapolcat2(ntyp,-1:ntyp_molec(5)))
+ allocate(sigiso1cat(ntyp,-1:ntyp_molec(5)),rborn1cat(ntyp,-1:ntyp_molec(5)),rborn2cat(ntyp,-1:ntyp_molec(5)),sigmap1cat(ntyp,-1:ntyp_molec(5)))
+ allocate(sigmap2cat(ntyp,-1:ntyp_molec(5)),sigiso2cat(ntyp,-1:ntyp_molec(5)))
+ allocate(chis1cat(ntyp,-1:ntyp_molec(5)),chis2cat(ntyp,-1:ntyp_molec(5)),wquadcat(ntyp,-1:ntyp_molec(5)),chipp1cat(ntyp,-1:ntyp_molec(5)),chipp2cat(ntyp,-1:ntyp_molec(5)))
+ allocate(epsintabcat(ntyp,-1:ntyp_molec(5)))
+ allocate(dtailcat(2,ntyp,-1:ntyp_molec(5)))
+ allocate(alphasurcat(4,ntyp,-1:ntyp_molec(5)),alphisocat(4,ntyp,-1:ntyp_molec(5)))
+ allocate(wqdipcat(2,ntyp,-1:ntyp_molec(5)))
+ allocate(wstatecat(4,ntyp,-1:ntyp_molec(5)))
+ allocate(dheadcat(2,2,ntyp,-1:ntyp_molec(5)))
+ allocate(nstatecat(ntyp,-1:ntyp_molec(5)))
+ allocate(debaykapcat(ntyp,-1:ntyp_molec(5)))
+
+ if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,-1:ntyp1))
+ if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,-1:ntyp1))
! if (.not.allocated(chicat)) allocate(chicat(ntyp1,ntyp1)) !(ntyp,ntyp)
- if (.not.allocated(chi1cat)) allocate(chi1cat(ntyp1,ntyp1)) !(ntyp,ntyp)
- if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi1cat)) allocate(chi1cat(ntyp1,-1:ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,-1:ntyp1)) !(ntyp,ntyp)
if (.not.allocated(ichargecat))&
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
- ip(5)=0.2
+ ! ip(5)=0.2
! mp(5)=0.2
pstok(5)=3.0
!DIR$ NOUNROLL
- do j=1,ntyp_molec(5)-1 ! this is without Zn will be modified for ALL tranistion metals
+ do j=-1,ntyp_molec(5)-1 ! this is without Zn will be modified for ALL tranistion metals
+ if (j.eq.0) cycle
do i=1,ntyp
! do j=1,ntyp_molec(5)
! write (*,*) "Im in ALAB", i, " ", j
read(iion,*) &
epscat(i,j),sigmacat(i,j), &
! chicat(i,j),chicat(j,i),chippcat(i,j),chippcat(j,i), &
- chi1cat(i,j),chi2cat(i,j),chipp1cat(i,j),chipp2cat(i,j), &
+ chi1cat(i,j),chi2cat(i,j),chipp1cat(i,j),chipp2cat(i,j), & !6
- (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&
+ (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&!12
! chiscat(i,j),chiscat(j,i), &
chis1cat(i,j),chis2cat(i,j), &
- nstatecat(i,j),(wstatecat(k,i,j),k=1,4), & !5 w tej lini - 1 integer pierwszy
- dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&
+ nstatecat(i,j),(wstatecat(k,i,j),k=1,4), & !19 !5 w tej lini - 1 integer pierwszy
+ dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&!23
dtailcat(1,i,j),dtailcat(2,i,j), &
- epsheadcat(i,j),sig0headcat(i,j), &
+ epsheadcat(i,j),sig0headcat(i,j), &!27
!wdipcat = w1 , w2
! rborncat(i,j),rborncat(j,i),&
rborn1cat(i,j),rborn2cat(i,j),&
- (wqdipcat(k,i,j),k=1,2), &
- alphapolcat(i,j),alphapolcat2(j,i), &
+ (wqdipcat(k,i,j),k=1,2), &!31
+ alphapolcat(i,j),alphapolcat2(j,i), &!33
(alphisocat(k,i,j),k=1,4),sigiso1cat(i,j),sigiso2cat(i,j),epsintabcat(i,j),debaykapcat(i,j)
if (chi1cat(i,j).gt.0.9) write (*,*) "WTF ANISO", i,j, chi1cat(i,j)
END DO
END DO
- allocate(aa_aq_cat(-ntyp:ntyp,ntyp),bb_aq_cat(-ntyp:ntyp,ntyp))
+ allocate(aa_aq_cat(-ntyp:ntyp,-1:ntyp_molec(5)),&
+ bb_aq_cat(-ntyp:ntyp,-1:ntyp_molec(5)))
do i=1,ntyp
- do j=1,ntyp_molec(5)
+ do j=-1,ntyp_molec(5)
+ if (j.eq.0) cycle
epsij=epscat(i,j)
rrij=sigmacat(i,j)
rrij=rrij**expon
write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,&
' v3ss:',v3ss
endif
+
+!------------MARTINI-PROTEIN-parameters-------------------------
+ allocate(alphapolmart(ntyp,ntyp),epsheadmart(ntyp,ntyp_molec(4)),sig0headmart(ntyp,ntyp_molec(4)))
+ allocate(alphapolmart2(ntyp,ntyp))
+ allocate(sigiso1mart(ntyp,ntyp_molec(4)),rborn1mart(ntyp,ntyp_molec(4)),rborn2mart(ntyp,ntyp_molec(4)),sigmap1mart(ntyp,ntyp_molec(4)))
+ allocate(sigmap2mart(ntyp,ntyp_molec(4)),sigiso2mart(ntyp,ntyp_molec(4)))
+ allocate(chis1mart(ntyp,ntyp_molec(4)),chis2mart(ntyp,ntyp_molec(4)),wquadmart(ntyp,ntyp_molec(4)),chipp1mart(ntyp,ntyp_molec(4)),chipp2mart(ntyp,ntyp_molec(4)))
+ allocate(epsintabmart(ntyp,ntyp_molec(4)))
+ allocate(dtailmart(2,ntyp,ntyp_molec(4)))
+ allocate(alphasurmart(4,ntyp,ntyp_molec(4)),alphisomart(4,ntyp,ntyp_molec(4)))
+ allocate(wqdipmart(2,ntyp,ntyp_molec(4)))
+ allocate(wstatemart(4,ntyp,ntyp_molec(4)))
+ allocate(dheadmart(2,2,ntyp,ntyp_molec(4)))
+ allocate(nstatemart(ntyp,ntyp_molec(4)))
+ allocate(debaykapmart(ntyp,ntyp_molec(4)))
+
+ if (.not.allocated(epsmart)) allocate (epsmart(0:ntyp1,ntyp1))
+ if (.not.allocated(sigmamart)) allocate(sigmamart(0:ntyp1,ntyp1))
+! if (.not.allocated(chimart)) allomarte(chimart(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi1mart)) allocate(chi1mart(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi2mart)) allocate(chi2mart(ntyp1,ntyp1)) !(ntyp,ntyp)
+
+!DIR$ NOUNROLL
+ do i=1,ntyp-3 ! there are phosporylated missing
+ do j=1,ntyp_molec(4) ! this is without Zn will be modified for ALL tranistion metals
+! do j=1,ntyp_molec(5)
+ print *,"lipmart",i,j
+! write (*,*) "Im in ALAB", i, " ", j
+ read(imartprot,*) &
+ epsmart(i,j),sigmamart(i,j), &
+! chimart(i,j),chimart(j,i),chippmart(i,j),chippmart(j,i), &
+ chi1mart(i,j),chi2mart(i,j),chipp1mart(i,j),chipp2mart(i,j), & !6
+
+ (alphasurmart(k,i,j),k=1,4),sigmap1mart(i,j),sigmap2mart(i,j),&!12
+! chismart(i,j),chismart(j,i), &
+ chis1mart(i,j),chis2mart(i,j), &
+
+ nstatemart(i,j),(wstatemart(k,i,j),k=1,4), & !19 !5 w tej lini - 1 integer pierwszy
+ dheadmart(1,1,i,j),dheadmart(1,2,i,j),dheadmart(2,1,i,j),dheadmart(2,2,i,j),&!23
+ dtailmart(1,i,j),dtailmart(2,i,j), &
+ epsheadmart(i,j),sig0headmart(i,j), &!27
+!wdipmart = w1 , w2
+! rbornmart(i,j),rbornmart(j,i),&
+ rborn1mart(i,j),rborn2mart(i,j),&
+ (wqdipmart(k,i,j),k=1,2), &!31
+ alphapolmart(i,j),alphapolmart2(j,i), &!33
+ (alphisomart(k,i,j),k=1,4),sigiso1mart(i,j),sigiso2mart(i,j),epsintabmart(i,j),debaykapmart(i,j)
+ enddo
+ enddo
+ allocate(aa_aq_mart(-ntyp:ntyp,ntyp_molec(4)),&
+ bb_aq_mart(-ntyp:ntyp,ntyp_molec(4)))
+ do i=1,ntyp-3 ! still no phophorylated residues
+ do j=1,ntyp_molec(4)
+ if (j.eq.0) cycle
+ epsij=epsmart(i,j)
+ rrij=sigmamart(i,j)
+ rrij=rrij**expon
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_aq_mart(i,j)=epsij*rrij*rrij
+ bb_aq_mart(i,j)=-sigeps*epsij*rrij
+ enddo
+ enddo
+
+
+
+
+
+
+
+
+
+
+
if (shield_mode.gt.0) then
pi=4.0D0*datan(1.0D0)
!C VSolvSphere the volume of solving sphere
cou=1
write (iout,*) "symetr", symetr
do i=1,nres
- lll=lll+1
+ lll=lll+1
! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
- if (i.gt.1) then
- if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
- chain_length=lll-1
- kkk=kkk+1
+! if (i.gt.1) then
+! if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
+! chain_length=lll-1
+! kkk=kkk+1
! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
- lll=1
- endif
- endif
+! lll=1
+! endif
+! endif
do j=1,3
cref(j,i,cou)=c(j,i)
cref(j,i+nres,cou)=c(j,i+nres)
endif
enddo
enddo
- write (iout,*) chain_length
- if (chain_length.eq.0) chain_length=nres
- do j=1,3
- chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
- chain_rep(j,chain_length+nres,symetr) &
- =chain_rep(j,chain_length+nres,1)
- enddo
! diagnostic
! write (iout,*) "spraw lancuchy",chain_length,symetr
! do i=1,4
dc(j,0)=c(j,1)
enddo
- if (symetr.gt.1) then
- call permut(symetr)
- nperm=1
- do i=1,symetr
- nperm=nperm*i
- enddo
- do i=1,nperm
- write(iout,*) (tabperm(i,kkk),kkk=1,4)
- enddo
- do i=1,nperm
- cou=0
- do kkk=1,symetr
- icha=tabperm(i,kkk)
- write (iout,*) i,icha
- do lll=1,chain_length
- cou=cou+1
- if (cou.le.nres) then
- do j=1,3
- kupa=mod(lll,chain_length)
- iprzes=(kkk-1)*chain_length+lll
- if (kupa.eq.0) kupa=chain_length
- write (iout,*) "kupa", kupa
- cref(j,iprzes,i)=chain_rep(j,kupa,icha)
- cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
- enddo
- endif
- enddo
- enddo
- enddo
- endif
+! if (symetr.gt.1) then
+! call permut(symetr)
+! nperm=1
+! do i=1,symetr
+! nperm=nperm*i
+! enddo
+! do i=1,nperm
+! write(iout,*) (tabperm(i,kkk),kkk=1,4)
+! enddo
+! do i=1,nperm
+! cou=0
+! do kkk=1,symetr
+! icha=tabperm(i,kkk)
+! write (iout,*) i,icha
+! do lll=1,chain_length
+! cou=cou+1
+! if (cou.le.nres) then
+! do j=1,3
+! kupa=mod(lll,chain_length)
+! iprzes=(kkk-1)*chain_length+lll
+! if (kupa.eq.0) kupa=chain_length
+! write (iout,*) "kupa", kupa
+! cref(j,iprzes,i)=chain_rep(j,kupa,icha)
+! cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
+! enddo
+! endif
+! enddo
+! enddo
+! enddo
+! endif
!-koniec robienia kopii
! diag
do kkk=1,nperm
! CUTOFFF ON ELECTROSTATICS
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
+
+ write(iout,*) "R_CUT_ELE=",r_cut_ele,rlamb_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 reada(controlcard,"DELTA",graddelta,1.0d-5)
! Lipidec parameters
call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
! print *,"Processor",myrank," opened file ITHEP"
call getenv_loc('ROTPAR',rotname)
open (irotam,file=rotname,status='old',action='read')
+#ifdef SC_END
+ call getenv_loc('ROTPAR_END',rotname_end)
+ open (irotam_end,file=rotname_end,status='old',action='read')
+#endif
! print *,"Processor",myrank," opened file IROTAM"
call getenv_loc('TORPAR',torname)
open (itorp,file=torname,status='old',action='read')
open (ithep,file=thetname,status='old')
call getenv_loc('ROTPAR',rotname)
open (irotam,file=rotname,status='old')
+#ifdef SC_END
+ call getenv_loc('ROTPAR_END',rotname_end)
+ open (irotam_end,file=rotname_end,status='old')
+#endif
call getenv_loc('TORPAR',torname)
open (itorp,file=torname,status='old')
call getenv_loc('TORDPAR',tordname)
open (ithep,file=thetname,status='old',action='read')
call getenv_loc('ROTPAR',rotname)
open (irotam,file=rotname,status='old',action='read')
+#ifdef SC_END
+ call getenv_loc('ROTPAR_END',rotname_end)
+ open (irotam_end,file=rotname_end,status='old',action='read')
+#endif
call getenv_loc('TORPAR',torname)
open (itorp,file=torname,status='old',action='read')
call getenv_loc('TORDPAR',tordname)
open (ilipbond,file=lipbondname,status='old',action='read')
call getenv_loc('LIPNONBOND',lipnonbondname)
open (ilipnonbond,file=lipnonbondname,status='old',action='read')
+ call getenv_loc('LIPPROT',lipprotname)
+ open (imartprot,file=lipprotname,status='old',action='read')
+
call getenv_loc('TUBEPAR',tubename)
open (itube,file=tubename,status='old',action='read')
call getenv_loc('IONPAR',ionname)
projects / unres4.git / blobdiff