X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fio_config.F90;h=9b036aac1abd08b2730a8303a8a84446e72251f5;hb=545cf9507d923cdf917d80ed079c753702c68840;hp=c2f62bb1a287d5b6f05cfdace29f5d8846c08a01;hpb=bc23440fbe68672d430f71f22f46b11265f003db;p=unres4.git diff --git a/source/unres/io_config.F90 b/source/unres/io_config.F90 index c2f62bb..9b036aa 100644 --- a/source/unres/io_config.F90 +++ b/source/unres/io_config.F90 @@ -745,10 +745,10 @@ 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)) @@ -813,9 +813,9 @@ 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) @@ -870,7 +870,9 @@ - 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) @@ -929,6 +931,36 @@ 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 ! @@ -1586,7 +1618,18 @@ 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 @@ -2489,6 +2532,7 @@ si=-1.0d0 do k=1,nterm_sccor(i,j) + print *,"test",i,j,k,l read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j),& v2sccor(k,l,i,j) v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j) @@ -2702,6 +2746,9 @@ 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 @@ -3010,14 +3057,14 @@ 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) @@ -3031,7 +3078,52 @@ 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))) @@ -3061,19 +3153,46 @@ 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))) @@ -3123,6 +3242,15 @@ 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))) @@ -3254,6 +3382,97 @@ ! 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 @@ -3278,7 +3497,11 @@ 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 @@ -3287,16 +3510,16 @@ 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 @@ -3369,7 +3592,7 @@ 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) @@ -3410,8 +3633,37 @@ 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 @@ -3466,6 +3718,8 @@ 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) @@ -3530,7 +3784,7 @@ character(len=3) :: seq,res,res2 character(len=5) :: atom character(len=80) :: card - real(kind=8),dimension(3,20) :: sccor + real(kind=8),dimension(3,40) :: sccor integer :: kkk,lll,icha,kupa,molecule,counter,seqalingbegin !rescode, integer :: isugar,molecprev,firstion character*1 :: sugar @@ -3603,6 +3857,7 @@ 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 @@ -3614,6 +3869,13 @@ ! 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 @@ -3625,6 +3887,31 @@ 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, @@ -3788,6 +4075,7 @@ 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 @@ -3801,18 +4089,20 @@ 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 @@ -3921,6 +4211,7 @@ ! 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 @@ -4078,7 +4369,6 @@ 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 @@ -4091,6 +4381,9 @@ 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 @@ -4104,8 +4397,14 @@ 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 @@ -4451,6 +4750,7 @@ 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 @@ -4477,6 +4777,7 @@ 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) @@ -4488,7 +4789,11 @@ 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 @@ -4725,7 +5030,7 @@ ! ! 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 @@ -4756,6 +5061,7 @@ 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) @@ -4882,14 +5188,17 @@ 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 @@ -5333,7 +5642,8 @@ 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) @@ -5381,6 +5691,13 @@ 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) @@ -5436,12 +5753,22 @@ 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) @@ -6044,6 +6371,7 @@ return end subroutine write_stat_thread !----------------------------------------------------------------------------- +#endif subroutine readpdb_template(k) ! Read the PDB file for read_constr_homology with read2sigma ! and convert the peptide geometry into virtual-chain geometry. @@ -6068,7 +6396,7 @@ character*3 seq,res character*5 atom character*80 card - real(kind=8), dimension (3,20) :: sccor + real(kind=8), dimension (3,40) :: sccor ! integer rescode integer, dimension (:), allocatable :: iterter if(.not.allocated(iterter))allocate(iterter(nres)) @@ -6094,8 +6422,14 @@ ires_old=ires+2 itype(ires_old-1,1)=ntyp1 iterter(ires_old-1)=1 +#if defined(WHAM_RUN) || defined(CLUSTER) + if (ires_old.lt.nres) then +#endif itype(ires_old,1)=ntyp1 iterter(ires_old)=1 +#if defined(WHAM_RUN) || defined(CLUSTER) + endif +#endif ibeg=2 ! write (iout,*) "Chain ended",ires,ishift,ires_old if (unres_pdb) then @@ -6203,6 +6537,7 @@ ! Calculate dummy residue coordinates inside the "chain" of a multichain ! system nres=ires + write(2,*) "tutaj",ires,nres do i=2,nres-1 ! write (iout,*) i,itype(i),itype(i+1) if (itype(i,1).eq.ntyp1.and.iterter(i).eq.1) then @@ -6370,6 +6705,6 @@ return end subroutine readpdb_template !----------------------------------------------------------------------------- -#endif +!#endif !----------------------------------------------------------------------------- end module io_config