From: Adam Sieradzan Date: Mon, 30 Apr 2018 07:49:32 +0000 (+0200) Subject: Merge branch 'UCGM' of mmka.chem.univ.gda.pl:unres4 into UCGM X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;ds=sidebyside;h=10689ab7d813dfbdbb0c6e631d90234d78ea306a;hp=-c;p=unres4.git Merge branch 'UCGM' of mmka.chem.univ.gda.pl:unres4 into UCGM --- 10689ab7d813dfbdbb0c6e631d90234d78ea306a diff --combined source/unres/io_config.f90 index b3492fe,b52f157..87ddf94 --- a/source/unres/io_config.f90 +++ b/source/unres/io_config.f90 @@@ -2771,31 -2771,6 +2771,31 @@@ write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,& ' v3ss:',v3ss endif + if (shield_mode.gt.0) then + pi=4.0D0*datan(1.0D0) +!C VSolvSphere the volume of solving sphere + 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*(4.50d0)**3 + VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3 + write (iout,*) VSolvSphere,VSolvSphere_div +!C long axis of side chain + do i=1,ntyp + long_r_sidechain(i)=vbldsc0(1,i) +! if (scelemode.eq.0) then + short_r_sidechain(i)=sigma(i,i)/sqrt(2.0) + if (short_r_sidechain(i).eq.0.0) short_r_sidechain(i)=0.2 +! else +! short_r_sidechain(i)=sigma(i,i) +! endif + write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),& + sigma0(i) + enddo + buff_shield=1.0d0 + endif + return 111 write (iout,*) "Error reading bending energy parameters." goto 999 @@@ -2858,7 -2833,7 +2858,7 @@@ use control_data use compare_data use MPI_data - use control, only: rescode,sugarcode + ! use control, only: rescode,sugarcode ! implicit real*8 (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.LOCAL' @@@ -2924,7 -2899,7 +2924,7 @@@ if(.not. allocated(istype)) allocate(istype(maxres)) do i=1,100000 read (ipdbin,'(a80)',end=10) card - ! write (iout,'(a)') card + write (iout,'(a)') card if (card(:5).eq.'HELIX') then nhfrag=nhfrag+1 lsecondary=.true. @@@ -3387,10 -3362,10 +3387,10 @@@ if (lprn) then write (iout,'(/a)') & "Cartesian coordinates of the reference structure" - write (iout,'(a,3(3x,a5),5x,3(3x,a5))') & + write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)" do ires=1,nres - write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') & + write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') & (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),& (c(j,ires+nres),j=1,3) enddo @@@ -3401,7 -3376,7 +3401,7 @@@ write (iout,'(a)') & "Backbone and SC coordinates as read from the PDB" do ires=1,nres - write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') & + write (iout,'(i5,i3,2x,a,3f8.3,5x,3f8.3)') & ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),& (c(j,nres+ires),j=1,3) enddo @@@ -3468,10 -3443,10 +3468,10 @@@ if (lprn) then write (iout,'(/a)') & "Cartesian coordinates of the reference structure after sorting" - write (iout,'(a,3(3x,a5),5x,3(3x,a5))') & + write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)" do ires=1,nres - write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') & + write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') & (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),& (c(j,ires+nres),j=1,3) enddo @@@ -3559,7 -3534,7 +3559,7 @@@ write (iout,*) "symetr", symetr do i=1,nres lll=lll+1 - !c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3) + ! 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 @@@ -3588,7 -3563,7 +3588,7 @@@ ! write (iout,*) "spraw lancuchy",chain_length,symetr ! do i=1,4 ! do kkk=1,chain_length - ! write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3) + ! write (iout,*) itype(kkk,1),(chain_rep(j,kkk,i), j=1,3) ! enddo ! enddo ! enddiagnostic @@@ -3611,7 -3586,7 +3611,7 @@@ cou=0 do kkk=1,symetr icha=tabperm(i,kkk) - ! write (iout,*) i,icha + write (iout,*) i,icha do lll=1,chain_length cou=cou+1 if (cou.le.nres) then @@@ -3619,7 -3594,7 +3619,7 @@@ kupa=mod(lll,chain_length) iprzes=(kkk-1)*chain_length+lll if (kupa.eq.0) kupa=chain_length - ! write (iout,*) "kupa", kupa + 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 @@@ -3638,11 -3613,11 +3638,11 @@@ cref(3,i,kkk),cref(1,nres+i,kkk),& cref(2,nres+i,kkk),cref(3,nres+i,kkk) enddo - 100 format (//' alpha-carbon coordinates ',& + 100 format (//' alpha-carbon coordinates ',& ' centroid coordinates'/ & ' ', 6X,'X',11X,'Y',11X,'Z', & 10X,'X',11X,'Y',11X,'Z') - 110 format (a,'(',i3,')',6f12.5) + 110 format (a,'(',i5,')',6f12.5) enddo !c enddiag @@@ -3916,22 -3891,22 +3916,22 @@@ write (iout,'(2a)') diagmeth(kdiag),& ' routine used to diagonalize matrices.' if (shield_mode.gt.0) then - pi=3.141592d0 + pi=4.0D0*datan(1.0D0) !C VSolvSphere the volume of solving sphere -!C print *,pi,"pi" + 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 + VSolvSphere=4.0/3.0*pi*(4.50d0)**3 + VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**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 +! 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 @@@ -4091,6 -4066,10 +4091,10 @@@ large = index(controlcard,"LARGE").gt.0 print_compon = index(controlcard,"PRINT_COMPON").gt.0 rattle = index(controlcard,"RATTLE").gt.0 + preminim=(index(controlcard,'PREMINIM').gt.0) + write (iout,*) "PREMINIM ",preminim + dccart=(index(controlcard,'CART').gt.0) + if (preminim) call read_minim ! if performing umbrella sampling, fragments constrained are read from the fragment file nset=0 if(usampl) then