dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,&
res1,epsijlip,epspeptube,epssctube,sigmapeptube, &
- sigmasctube
- integer :: ichir1,ichir2,ijunk
+ sigmasctube,krad2,ract
+ integer :: ichir1,ichir2,ijunk,irdiff
character*3 string
-
+ character*80 temp1,mychar
! 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))
!el allocate(v2_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
msc(:,:)=0.0d0
isc(:,:)=0.0d0
- allocate(msc(ntyp+1,5)) !(ntyp+1)
- allocate(isc(ntyp+1,5)) !(ntyp+1)
- allocate(restok(ntyp+1,5)) !(ntyp+1)
+ allocate(msc(-ntyp-1:ntyp+1,5)) !(ntyp+1)
+ allocate(isc(-ntyp-1:ntyp+1,5)) !(ntyp+1)
+ allocate(restok(-ntyp-1:ntyp+1,5)) !(ntyp+1)
read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp(1),ip(1),pstok(1)
do i=1,ntyp_molec(1)
- if (.not.allocated(ichargecat)) allocate (ichargecat(ntyp_molec(5)))
+ if (.not.allocated(ichargecat)) &
+ allocate (ichargecat(-ntyp_molec(5):ntyp_molec(5)))
+ ichargecat(:)=0
if (oldion.eq.1) then
do i=1,ntyp_molec(5)
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,liptranene(i)
enddo
close(iliptranpar)
+! water parmaters entalphy
+ allocate(awaterenta(0:400))
+ allocate(bwaterenta(0:400))
+ allocate(cwaterenta(0:400))
+ allocate(dwaterenta(0:400))
+ allocate(awaterentro(0:400))
+ allocate(bwaterentro(0:400))
+ allocate(cwaterentro(0:400))
+ allocate(dwaterentro(0:400))
+
+ read(iwaterwater,*) mychar
+ read(iwaterwater,*) ract,awaterenta(0),bwaterenta(0),&
+ cwaterenta(0),dwaterenta(0)
+ do i=1,398
+ read(iwaterwater,*) ract,awaterenta(i),bwaterenta(i),&
+ cwaterenta(i),dwaterenta(i)
+ irdiff=int((ract-2.06d0)*50.0d0)+1
+ if (i.ne.irdiff) print *,"WARTINING",i,ract, irdiff
+ enddo
+! water parmaters entrophy
+ read(iwaterwater,*) mychar
+ read(iwaterwater,*) ract,awaterentro(0),bwaterentro(0),&
+ cwaterentro(0),dwaterentro(0)
+ do i=1,398
+ read(iwaterwater,*) ract,awaterentro(i),bwaterentro(i),&
+ cwaterentro(i),dwaterentro(i)
+ irdiff=int((ract-2.06d0)*50.0d0)+1
+ if (i.ne.irdiff) print *,"WARTINING",i,ract, irdiff
+ enddo
+
#ifdef CRYST_THETA
!
allocate(ddnewtor(3,2,-nloctyp:nloctyp))
allocate(e0newtor(3,-nloctyp:nloctyp))
allocate(eenewtor(2,2,2,-nloctyp:nloctyp))
-
+ bnew1=0.0d0
+ bnew2=0.0d0
+ ccnew=0.0d0
+ ddnew=0.0d0
+ e0new=0.0d0
+ eenew=0.0d0
+ bnew1tor=0.0d0
+ bnew2tor=0.0d0
+ ccnewtor=0.0d0
+ ddnewtor=0.0d0
+ e0newtor=0.0d0
+ eenewtor=0.0d0
read (ifourier,*,end=115,err=115) (itype2loc(i),i=1,ntyp)
read (ifourier,*,end=115,err=115) (iloctyp(i),i=0,nloctyp-1)
itype2loc(ntyp1)=nloctyp
print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i), wqdip(1,i,j)
END DO
END DO
+ do i=1,ntyp
+ read (isidep,*,end=117,err=117)(epslip(i,j),j=i,ntyp)
+ enddo
do i=1,ntyp
do j=1,i
IF ((LaTeX).and.(i.gt.24)) then
allocate(alphapol_scbase(ntyp_molec(1),ntyp_molec(2)))
allocate(epsintab_scbase(ntyp_molec(1),ntyp_molec(2)))
-
+ write (iout,*) "ESCBASEPARM"
do i=1,ntyp_molec(1)
- do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
- write (*,*) "Im in ", i, " ", j
+ do j=1,ntyp_molec(2) ! without U then we will take T for U
+! write (*,*) "Im in ", i, " ", j
read(isidep_scbase,*) &
eps_scbase(i,j),sigma_scbase(i,j),chi_scbase(i,j,1),&
chi_scbase(i,j,2),chipp_scbase(i,j,1),chipp_scbase(i,j,2)
- write(*,*) "eps",eps_scbase(i,j)
+! write(*,*) "eps",eps_scbase(i,j)
read(isidep_scbase,*) &
(alphasur_scbase(k,i,j),k=1,4),sigmap1_scbase(i,j),sigmap2_scbase(i,j), &
chis_scbase(i,j,1),chis_scbase(i,j,2)
read(isidep_scbase,*) &
alphapol_scbase(i,j), &
epsintab_scbase(i,j)
+ if (chi_scbase(i,j,2).gt.0.9) chi_scbase(i,j,2)=0.9
+ if (chi_scbase(i,j,1).gt.0.9) chi_scbase(i,j,1)=0.9
+ if (chipp_scbase(i,j,2).gt.0.9) chipp_scbase(i,j,2)=0.9
+ if (chipp_scbase(i,j,1).gt.0.9) chipp_scbase(i,j,1)=0.9
+ if (chi_scbase(i,j,2).lt.-0.9) chi_scbase(i,j,2)=-0.9
+ if (chi_scbase(i,j,1).lt.-0.9) chi_scbase(i,j,1)=-0.9
+ if (chipp_scbase(i,j,2).lt.-0.9) chipp_scbase(i,j,2)=-0.9
+ if (chipp_scbase(i,j,1).lt.-0.9) chipp_scbase(i,j,1)=-0.9
+ write(iout,*) &
+ eps_scbase(i,j),sigma_scbase(i,j),chi_scbase(i,j,1),&
+ chi_scbase(i,j,2),chipp_scbase(i,j,1),chipp_scbase(i,j,2)
+ write(*,*) "eps",eps_scbase(i,j)
+ write(iout,*) &
+ (alphasur_scbase(k,i,j),k=1,4),sigmap1_scbase(i,j),sigmap2_scbase(i,j), &
+ chis_scbase(i,j,1),chis_scbase(i,j,2)
+ write(iout,*) &
+ dhead_scbasei(i,j), &
+ dhead_scbasej(i,j), &
+ rborn_scbasei(i,j),rborn_scbasej(i,j)
+ write(iout,*) &
+ (wdipdip_scbase(k,i,j),k=1,3), &
+ (wqdip_scbase(k,i,j),k=1,2)
+ write(iout,*) &
+ alphapol_scbase(i,j), &
+ epsintab_scbase(i,j)
+
END DO
+ j=4
+ write(iout,*) &
+ eps_scbase(i,j),sigma_scbase(i,j),chi_scbase(i,j,1),&
+ chi_scbase(i,j,2),chipp_scbase(i,j,1),chipp_scbase(i,j,2)
+ write(*,*) "eps",eps_scbase(i,j)
+ write(iout,*) &
+ (alphasur_scbase(k,i,j),k=1,4),sigmap1_scbase(i,j),sigmap2_scbase(i,j), &
+ chis_scbase(i,j,1),chis_scbase(i,j,2)
+ write(iout,*) &
+ dhead_scbasei(i,j), &
+ dhead_scbasej(i,j), &
+ rborn_scbasei(i,j),rborn_scbasej(i,j)
+ write(iout,*) &
+ (wdipdip_scbase(k,i,j),k=1,3), &
+ (wqdip_scbase(k,i,j),k=1,2)
+ write(iout,*) &
+ alphapol_scbase(i,j), &
+ epsintab_scbase(i,j)
+
END DO
allocate(aa_scbase(ntyp_molec(1),ntyp_molec(2)))
allocate(bb_scbase(ntyp_molec(1),ntyp_molec(2)))
allocate(chis_pepbase(ntyp_molec(2),2))
allocate(wdipdip_pepbase(3,ntyp_molec(2)))
+ write (iout,*) "EPEPBASEPARM"
- do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
+ do j=1,ntyp_molec(2) ! without U then we will take T for U
write (*,*) "Im in ", i, " ", j
read(isidep_pepbase,*) &
eps_pepbase(j),sigma_pepbase(j),chi_pepbase(j,1),&
chi_pepbase(j,2),chipp_pepbase(j,1),chipp_pepbase(j,2)
+ if (chi_pepbase(j,2).gt.0.9) chi_pepbase(j,2)=0.9
+ if (chi_pepbase(j,1).gt.0.9) chi_pepbase(j,1)=0.9
+ if (chipp_pepbase(j,2).gt.0.9) chipp_pepbase(j,2)=0.9
+ if (chipp_pepbase(j,1).gt.0.9) chipp_pepbase(j,1)=0.9
+ if (chi_pepbase(j,2).lt.-0.9) chi_pepbase(j,2)=-0.9
+ if (chi_pepbase(j,1).lt.-0.9) chi_pepbase(j,1)=-0.9
+ if (chipp_pepbase(j,2).lt.-0.9) chipp_pepbase(j,2)=-0.9
+ if (chipp_pepbase(j,1).lt.-0.9) chipp_pepbase(j,1)=-0.9
+
write(*,*) "eps",eps_pepbase(j)
read(isidep_pepbase,*) &
(alphasur_pepbase(k,j),k=1,4),sigmap1_pepbase(j),sigmap2_pepbase(j), &
chis_pepbase(j,1),chis_pepbase(j,2)
read(isidep_pepbase,*) &
(wdipdip_pepbase(k,j),k=1,3)
+ write(iout,*) eps_pepbase(j),sigma_pepbase(j),chi_pepbase(j,1),&
+ chi_pepbase(j,2),chipp_pepbase(j,1),chipp_pepbase(j,2)
+ write(iout,*) &
+ (alphasur_pepbase(k,j),k=1,4),sigmap1_pepbase(j),sigmap2_pepbase(j), &
+ chis_pepbase(j,1),chis_pepbase(j,2)
+ write(iout,*) &
+ (wdipdip_pepbase(k,j),k=1,3)
+
END DO
+ j=4
+ write(iout,*) eps_pepbase(j),sigma_pepbase(j),chi_pepbase(j,1),&
+ chi_pepbase(j,2),chipp_pepbase(j,1),chipp_pepbase(j,2)
+ write(iout,*) &
+ (alphasur_pepbase(k,j),k=1,4),sigmap1_pepbase(j),sigmap2_pepbase(j), &
+ chis_pepbase(j,1),chis_pepbase(j,2)
+ write(iout,*) &
+ (wdipdip_pepbase(k,j),k=1,3)
+
allocate(aa_pepbase(ntyp_molec(2)))
allocate(bb_pepbase(ntyp_molec(2)))
read(isidep_scpho,*) &
epsintab_scpho(j),alphapol_scpho(j),rborn_scphoi(j),rborn_scphoj(j), &
alphi_scpho(j)
+ if (chi_scpho(j,2).gt.0.9) chi_scpho(j,2)=0.9
+ if (chi_scpho(j,1).gt.0.9) chi_scpho(j,1)=0.9
+ if (chipp_scpho(j,2).gt.0.9) chipp_scpho(j,2)=0.9
+ if (chipp_scpho(j,1).gt.0.9) chipp_scpho(j,1)=0.9
+ if (chi_scpho(j,2).lt.-0.9) chi_scpho(j,2)=-0.9
+ if (chi_scpho(j,1).lt.-0.9) chi_scpho(j,1)=-0.9
+ if (chipp_scpho(j,2).lt.-0.9) chipp_scpho(j,2)=-0.9
+ if (chipp_scpho(j,1).lt.-0.9) chipp_scpho(j,1)=-0.9
+
END DO
allocate(aa_scpho(ntyp_molec(1)))
! v1ss=0.0d0
! v2ss=0.0d0
! v3ss=0.0d0
+! MARTINI PARAMETER
+ allocate(ichargelipid(ntyp_molec(4)))
+ allocate(lip_angle_force(ntyp_molec(4),ntyp_molec(4),ntyp_molec(4)))
+ allocate(lip_angle_angle(ntyp_molec(4),ntyp_molec(4),ntyp_molec(4)))
+ allocate(lip_bond(ntyp_molec(4),ntyp_molec(4)))
+ allocate(lip_eps(ntyp_molec(4),ntyp_molec(4)))
+ allocate(lip_sig(ntyp_molec(4),ntyp_molec(4)))
+ kjtokcal=0.2390057361
+ krad=57.295779513
+ !HERE THE MASS of MARTINI
+ write(*,*) "before MARTINI PARAM"
+ do i=1,ntyp_molec(4)
+ msc(i,4)=0.0d0
+ mp(4)=72.0d0
+ isc(i,4)=0.d0
+ enddo
+ ip(4)=0.0
+ !relative dielectric constant = 15 for implicit screening
+ k_coulomb_lip=332.0d0/15.0d0
+ !kbond = 1250 kJ/(mol*nm*2)
+ kbondlip=1250.0d0*kjtokcal/100.0d0
+ krad2=krad**2.0
+ lip_angle_force=0.0d0
+ if (DRY_MARTINI.gt.0) then
+ lip_angle_force(3,12,12)=35.0*kjtokcal!*krad2
+ lip_angle_force(3,12,18)=35.0*kjtokcal!*krad2
+ lip_angle_force(3,18,16)=35.0*kjtokcal!*krad2
+ lip_angle_force(12,18,16)=35.0*kjtokcal!*krad2
+ lip_angle_force(18,16,18)=45.0*kjtokcal!*krad2
+ lip_angle_force(16,18,18)=35.0*kjtokcal!*krad2
+ lip_angle_force(12,18,18)=35.0*kjtokcal!*krad2
+ lip_angle_force(18,18,18)=35.0*kjtokcal!*krad2
+ else
+ lip_angle_force(3,12,12)=25.0*kjtokcal!*krad2
+ lip_angle_force(3,12,18)=25.0*kjtokcal!*krad2
+ lip_angle_force(3,18,16)=25.0*kjtokcal!*krad2
+ lip_angle_force(12,18,16)=25.0*kjtokcal!*krad2
+ lip_angle_force(18,16,18)=45.0*kjtokcal!*krad2
+ lip_angle_force(16,18,18)=25.0*kjtokcal!*krad2
+ lip_angle_force(12,18,18)=25.0*kjtokcal!*krad2
+ lip_angle_force(18,18,18)=25.0*kjtokcal!*krad2
+ endif
+ lip_angle_angle=0.0d0
+ lip_angle_angle(3,12,12)=120.0/krad
+ lip_angle_angle(3,12,18)=180.0/krad
+ lip_angle_angle(3,18,16)=180.0/krad
+ lip_angle_angle(12,18,16)=180.0/krad
+ lip_angle_angle(18,16,18)=120.0/krad
+ lip_angle_angle(16,18,18)=180.0/krad
+ lip_angle_angle(12,18,18)=180.0/krad
+ lip_angle_angle(18,18,18)=180.0/krad
+ read(ilipbond,*) temp1
+ do i=1,18
+ read(ilipbond,*) temp1, lip_bond(i,1), &
+ lip_bond(i,2),lip_bond(i,3),lip_bond(i,4),lip_bond(i,5), &
+ lip_bond(i,6),lip_bond(i,7),lip_bond(i,8),lip_bond(i,9), &
+ lip_bond(i,10),lip_bond(i,11),lip_bond(i,12),lip_bond(i,13), &
+ lip_bond(i,14),lip_bond(i,15),lip_bond(i,16),lip_bond(i,17), &
+ lip_bond(i,18)
+ do j=1,18
+ lip_bond(i,j)=lip_bond(i,j)*10
+ enddo
+ enddo
+
+ read(ilipnonbond,*) (ichargelipid(i),i=1,ntyp_molec(4))
+ read(ilipnonbond,*) temp1
+ do i=1,18
+ read(ilipnonbond,*) temp1, lip_eps(i,1), &
+ lip_eps(i,2),lip_eps(i,3),lip_eps(i,4),lip_eps(i,5), &
+ lip_eps(i,6),lip_eps(i,7),lip_eps(i,8),lip_eps(i,9), &
+ lip_eps(i,10),lip_eps(i,11),lip_eps(i,12),lip_eps(i,13), &
+ lip_eps(i,14),lip_eps(i,15),lip_eps(i,16),lip_eps(i,17), &
+ lip_eps(i,18)
+! write(*,*) i, lip_eps(i,18)
+ do j=1,18
+ lip_eps(i,j)=lip_eps(i,j)*kjtokcal
+ enddo
+ enddo
+ read(ilipnonbond,*) temp1
+ do i=1,18
+ read(ilipnonbond,*) temp1,lip_sig(i,1), &
+ lip_sig(i,2),lip_sig(i,3),lip_sig(i,4),lip_sig(i,5), &
+ lip_sig(i,6),lip_sig(i,7),lip_sig(i,8),lip_sig(i,9), &
+ lip_sig(i,10),lip_sig(i,11),lip_sig(i,12),lip_sig(i,13), &
+ lip_sig(i,14),lip_sig(i,15),lip_sig(i,16),lip_sig(i,17), &
+ lip_sig(i,18)
+ do j=1,18
+ lip_sig(i,j)=lip_sig(i,j)*10.0
+ enddo
+ enddo
+ write(*,*) "after MARTINI PARAM"
! Ions by Aga
if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
- if (.not.allocated(ichargecat)) allocate (ichargecat(ntyp_molec(5)))
+ if (.not.allocated(ichargecat))&
+ allocate (ichargecat(-ntyp_molec(5):ntyp_molec(5)))
+ write(*,*) "before ions",oldion
+ ichargecat(:)=0
+
! 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
else
read(iion,*) ijunk
endif
-
- do i=1,ntyp_molec(5)
+ print *,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
! mp(5)=0.2
- ! pstok(5)=1.0
+ pstok(5)=3.0
!DIR$ NOUNROLL
- do j=1,ntyp_molec(5)
+ do j=1,ntyp_molec(5)-1 ! this is without Zn will be modified for ALL tranistion metals
do i=1,ntyp
! do j=1,ntyp_molec(5)
! write (*,*) "Im in ALAB", i, " ", j
enddo
do i=1,ntyp
- do j=1,ntyp_molec(5)
+ do j=1,ntyp_molec(5)-1
if (i.eq.10) then
write (iout,*) 'i= ', i, ' j= ', j
write (iout,*) 'epsi0= ', epscat(i,j)
enddo
endif
-
-
+! read number of Zn2+
+! 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,*,err=123,end=123) (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
if(me.eq.king) then
write (iout,'(/a)') "Disulfide bridge parameters:"
write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
119 write (iout,*) "Error reading SCCOR parameters"
go to 999
121 write (iout,*) "Error in Czybyshev parameters"
+ go to 999
+ 123 write(iout,*) "Error in transition metal parameters"
999 continue
#ifdef MPI
call MPI_Finalize(Ierror)
itype(ires_old,molecule)=ntyp1_molec(molecule)
itype(ires_old-1,molecule)=ntyp1_molec(molecule)
nres_molec(molecule)=nres_molec(molecule)+2
+! if (molecule.eq.4) ires=ires+2
ibeg=2
! write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
! iii=0
endif
iii=0
+ else if (card(:3).eq.'BRA') then
+ molecule=4
+ ires=ires+1
+ ires_old=ires+1
+ itype(ires,molecule)=ntyp1_molec(molecule)-1
+ nres_molec(molecule)=nres_molec(molecule)+1
+
endif
! Read free energy
if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
read (card(12:16),*) atom
! write (iout,*) "! ",atom," !",ires
! if (atom.eq.'CA' .or. atom.eq.'CH3') then
+ if (card(14:16).eq.'LIP') then
+! reading lipid
+ if (ibeg.eq.1) then
+ molecule=4
+ ires=ires+1
+ nres_molec(molecule)=nres_molec(molecule)+1
+ itype(ires,molecule)=ntyp1_molec(molecule)
+ ibeg=0
+ endif
+ if (ibeg.eq.2) then
+ ibeg=0
+ ires=ires+2
+ endif
+
+ molecule=4
+ nres_molec(molecule)=nres_molec(molecule)+1
+ read (card(18:20),'(a3)') res
+ ires=ires+1
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+ if (UNRES_PDB) then!
+ itype(ires,molecule)=rescode(ires,res,0,molecule)
+ else
+ itype(ires,molecule)=rescode_lip(res,ires)
+ endif
+ else
read (card(23:26),*) ires
read (card(18:20),'(a3)') res
! write (iout,*) "ires",ires,ires-ishift+ishift1,
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
endif
endif
+ endif !LIP
! print *,"IONS",ions,card(1:6)
else if ((ions).and.(card(1:6).eq.'HETATM')) then
if (firstion.eq.0) then
endif ! unres_pdb
endif !firstion
read (card(12:16),*) atom
-! print *,"HETATOM", atom
+ print *,"HETATOM", atom(1:2)
read (card(18:20),'(a3)') res
+ if (atom(3:3).eq.'H') cycle
if ((atom(1:2).eq.'NA').or.(atom(1:2).eq.'CL').or.&
(atom(1:2).eq.'CA').or.(atom(1:2).eq.'MG') &
- .or.(atom(1:2).eq.'K ')) &
- then
+ .or.(atom(1:2).eq.'K ').or.(atom(1:2).eq.'ZN').or.&
+ (atom(1:2).eq.'O ')) then
ires=ires+1
+ print *,"I have water"
if (molecule.ne.5) molecprev=molecule
molecule=5
nres_molec(molecule)=nres_molec(molecule)+1
print *,"HERE",nres_molec(molecule)
- res=res(2:3)//' '
+ if (res.ne.'WAT') res=res(2:3)//' '
itype(ires,molecule)=rescode(ires,res,0,molecule)
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
endif! NA
! print *,"molecule",molecule
if ((itype(nres,1).ne.10)) then
nres=nres+1
+ nsup=nsup+1
if (molecule.eq.5) molecule=molecprev
itype(nres,molecule)=ntyp1_molec(molecule)
nres_molec(molecule)=nres_molec(molecule)+1
do j=1,3
c_temporary(j,seqalingbegin)=c(j,i)
c_temporary(j,seqalingbegin+nres)=c(j,i+nres)
-
enddo
itype_temporary(seqalingbegin,k)=itype(i,k)
print *,i,k,itype(i,k),itype_temporary(seqalingbegin,k),seqalingbegin
do i=1,2*nres
do j=1,3
c(j,i)=c_temporary(j,i)
+ if (i.gt.nres) then
+ if ((molnum(i-nres).eq.4)) c(j,i)=0.0d0
+ endif
enddo
enddo
do k=1,5
molnum(1)=5
itype(1,5)=itype(2,5)
itype(1,1)=0
- do i=2,nres
+ do j=1,3
+ c(j,1)=c(j,2)
+ enddo
+ do i=2,nres-1
itype(i,5)=itype(i+1,5)
+ do j=1,3
+ c(j,i)=c(j,i+1)
+ enddo
enddo
itype(nres,5)=0
nres=nres-1
with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
protein=index(controlcard,"PROTEIN").gt.0
ions=index(controlcard,"IONS").gt.0
+ fodson=index(controlcard,"FODSON").gt.0
call readi(controlcard,'OLDION',oldion,1)
nucleic=index(controlcard,"NUCLEIC").gt.0
write (iout,*) "with_theta_constr ",with_theta_constr
call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
call reada(controlcard,"RTUBE",tubeR0,0.0d0)
+ call reada(controlcard,"VNANO",velnanoconst,0.0d0)
call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
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
-! Lipidic parameters
+ 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)
+
+! Lipidec parameters
call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
if (lipthick.gt.0.0d0) then
!
! Read MD settings
!
- use control_data, only: r_cut,rlamb,out1file
+ use control_data, only: r_cut,rlamb,out1file,r_cut_mart,rlamb_mart
use energy_data
use geometry_data, only: pi
use MPI_data
call readi(controlcard,"NSTEP",n_timestep,1000000)
call readi(controlcard,"NTWE",ntwe,100)
call readi(controlcard,"NTWX",ntwx,1000)
+ call readi(controlcard,"NFOD",nfodstep,100)
call reada(controlcard,"DT",d_time,1.0d-1)
call reada(controlcard,"DVMAX",dvmax,2.0d1)
call reada(controlcard,"DAMAX",damax,1.0d1)
enddo
if(me.eq.king.or..not.out1file)then
+ do j=1,5
write (iout,'(/2a/)') &
"Radii of site types and friction coefficients and std's of",&
" stochastic forces of fully exposed sites"
- write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp(1),stdfp*dsqrt(gamp(1))
+ write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp(j),stdfp*dsqrt(gamp(j))
+
do i=1,ntyp
- write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i,1),&
- gamsc(i,1),stdfsc(i,1)*dsqrt(gamsc(i,1))
+ write (iout,'(a5,f5.2,2f10.5)') restyp(i,j),restok(i,j),&
+ gamsc(i,j),stdfsc(i,j)*dsqrt(gamsc(i,j))
enddo
+ enddo
endif
else if (tbf) then
if(me.eq.king.or..not.out1file)then
open (itube,file=tubename,status='old',action='read')
call getenv_loc('IONPAR',ionname)
open (iion,file=ionname,status='old',action='read')
-
+ call getenv_loc('IONPAR_TRAN',iontranname)
+ open (iiontran,file=iontranname,status='old',action='read')
! print *,"Processor",myrank," opened file ISIDEP"
! print *,"Processor",myrank," opened parameter files"
#elif (defined G77)
open (iion,file=ionname,status='old')
call getenv_loc('IONPAR_NUCL',ionnuclname)
open (iionnucl,file=ionnuclname,status='old')
+ call getenv_loc('IONPAR_TRAN',iontranname)
+ open (iiontran,file=iontranname,status='old')
+ call getenv_loc('WATWAT',iwaterwatername)
+ open (iwaterwater,file=iwaterwatername,status='old')
+ call getenv_loc('WATPROT',iwaterscname)
+ open (iwatersc,file=iwaterscname,status='old')
+
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
readonly)
call getenv_loc('LIPTRANPAR',liptranname)
open (iliptranpar,file=liptranname,status='old',action='read')
+ call getenv_loc('LIPBOND',lipbondname)
+ open (ilipbond,file=lipbondname,status='old',action='read')
+ call getenv_loc('LIPNONBOND',lipnonbondname)
+ open (ilipnonbond,file=lipnonbondname,status='old',action='read')
call getenv_loc('TUBEPAR',tubename)
open (itube,file=tubename,status='old',action='read')
call getenv_loc('IONPAR',ionname)
open (iion,file=ionname,status='old',action='read')
call getenv_loc('IONPAR_NUCL',ionnuclname)
open (iionnucl,file=ionnuclname,status='old',action='read')
+ call getenv_loc('IONPAR_TRAN',iontranname)
+ open (iiontran,file=iontranname,status='old',action='read')
+ call getenv_loc('WATWAT',iwaterwatername)
+ open (iwaterwater,file=iwaterwatername,status='old',action='read')
+ call getenv_loc('WATPROT',iwaterscname)
+ open (iwatersc,file=iwaterscname,status='old',action='read')
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
projects / unres4.git / blobdiff