X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Fenergy_p_new.F;h=fb18913435cc4daf46f956bdf7c2a19b66cf1132;hb=48f04f24e913a3e10867d2038b30efcd48a60a9f;hp=7217542b604fb7236557707fe99542d61f5cc2f6;hpb=1e3c2bda475e5d4031b8dab868bb8bf379a9e388;p=unres.git diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F index 7217542..fb18913 100644 --- a/source/wham/src-M/energy_p_new.F +++ b/source/wham/src-M/energy_p_new.F @@ -22,6 +22,8 @@ cMS$ATTRIBUTES C :: proc_proc include 'COMMON.INTERACT' include 'COMMON.SBRIDGE' include 'COMMON.CHAIN' + include 'COMMON.SHIELD' + include 'COMMON.CONTROL' double precision fact(6) cd write(iout, '(a,i2)')'Calling etotal ipot=',ipot cd print *,'nnt=',nnt,' nct=',nct @@ -48,7 +50,13 @@ C write(iout,*) 'po elektostatyce' C C Calculate electrostatic (H-bonding) energy of the main chain. C - 106 call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4) + 106 continue + if (shield_mode.eq.1) then + call set_shield_fac + else if (shield_mode.eq.2) then + call set_shield_fac2 + endif + call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4) C write(iout,*) 'po eelec' C Calculate excluded-volume interaction energy between peptide groups @@ -70,8 +78,9 @@ cd print *,'EHPB exitted succesfully.' C C Calculate the virtual-bond-angle energy. C - call ebend(ebe) C print *,'Bend energy finished.' + call ebend(ebe,ethetacnstr) +cd print *,'Bend energy finished.' C C Calculate the SC local energy. C @@ -90,6 +99,11 @@ C C 21/5/07 Calculate local sicdechain correlation energy C call eback_sc_corr(esccor) + + if (wliptran.gt.0) then + call Eliptransfer(eliptran) + endif + C C 12/1/95 Multi-body terms C @@ -101,29 +115,61 @@ c print *,"calling multibody_eello" call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1) c write (*,*) 'n_corr=',n_corr,' n_corr1=',n_corr1 c print *,ecorr,ecorr5,ecorr6,eturn6 + else + ecorr=0.0d0 + ecorr5=0.0d0 + ecorr6=0.0d0 + eturn6=0.0d0 endif if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1) endif c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t #ifdef SPLITELE + if (shield_mode.gt.0) then + etot=fact(1)*wsc*(evdw+fact(6)*evdw_t)+fact(1)*wscp*evdw2 + & +welec*fact(1)*ees + & +fact(1)*wvdwpp*evdw1 + & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 + & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 + & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + else etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees & +wvdwpp*evdw1 & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d - & +wbond*estr+wsccor*fact(1)*esccor + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + endif #else + if (shield_mode.gt.0) then + etot=fact(1)wsc*(evdw+fact(6)*evdw_t)+fact(1)*wscp*evdw2 + & +welec*fact(1)*(ees+evdw1) + & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 + & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 + & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + else etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2 & +welec*fact(1)*(ees+evdw1) & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d - & +wbond*estr+wsccor*fact(1)*esccor + & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr + & +wliptran*eliptran + endif #endif energia(0)=etot energia(1)=evdw @@ -157,6 +203,8 @@ c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t energia(19)=esccor energia(20)=edihcnstr energia(21)=evdw_t + energia(24)=ethetacnstr + energia(22)=eliptran c detecting NaNQ #ifdef ISNAN #ifdef AIX @@ -176,6 +224,11 @@ c detecting NaNQ #ifdef MPL c endif #endif +#define DEBUG +#ifdef DEBUG + call enerprint(energia,fact) +#endif +#undef DEBUG if (calc_grad) then C C Sum up the components of the Cartesian gradient. @@ -183,6 +236,7 @@ C #ifdef SPLITELE do i=1,nct do j=1,3 + if (shield_mode.eq.0) then gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+ & welec*fact(1)*gelc(j,i)+wvdwpp*gvdwpp(j,i)+ & wbond*gradb(j,i)+ @@ -195,14 +249,57 @@ C & wcorr6*fact(5)*gradcorr6(j,i)+ & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(2)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + else + gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i) + & +fact(1)*wscp*gvdwc_scp(j,i)+ + & welec*fact(1)*gelc(j,i)+fact(1)*wvdwpp*gvdwpp(j,i)+ + & wbond*gradb(j,i)+ + & wstrain*ghpbc(j,i)+ + & wcorr*fact(3)*gradcorr(j,i)+ + & wel_loc*fact(2)*gel_loc(j,i)+ + & wturn3*fact(2)*gcorr3_turn(j,i)+ + & wturn4*fact(3)*gcorr4_turn(j,i)+ + & wcorr5*fact(4)*gradcorr5(j,i)+ + & wcorr6*fact(5)*gradcorr6(j,i)+ + & wturn6*fact(5)*gcorr6_turn(j,i)+ + & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) + & +welec*gshieldc(j,i) + & +welec*gshieldc_loc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wcorr*gshieldc_loc_ec(j,i) + & +wturn3*gshieldc_t3(j,i) + & +wturn3*gshieldc_loc_t3(j,i) + & +wturn4*gshieldc_t4(j,i) + & +wturn4*gshieldc_loc_t4(j,i) + & +wel_loc*gshieldc_ll(j,i) + & +wel_loc*gshieldc_loc_ll(j,i) + + gradx(j,i,icg)=fact(1)*wsc*gvdwx(j,i) + & +fact(1)*wscp*gradx_scp(j,i)+ + & wbond*gradbx(j,i)+ + & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ + & wsccor*fact(2)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + & +welec*gshieldx(j,i) + & +wcorr*gshieldx_ec(j,i) + & +wturn3*gshieldx_t3(j,i) + & +wturn4*gshieldx_t4(j,i) + & +wel_loc*gshieldx_ll(j,i) + + + endif enddo #else do i=1,nct do j=1,3 + if (shield_mode.eq.0) then gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+ & welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+ & wbond*gradb(j,i)+ @@ -214,10 +311,50 @@ C & wcorr6*fact(5)*gradcorr6(j,i)+ & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(1)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + else + gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i)+ + & fact(1)*wscp*gvdwc_scp(j,i)+ + & welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+ + & wbond*gradb(j,i)+ + & wcorr*fact(3)*gradcorr(j,i)+ + & wel_loc*fact(2)*gel_loc(j,i)+ + & wturn3*fact(2)*gcorr3_turn(j,i)+ + & wturn4*fact(3)*gcorr4_turn(j,i)+ + & wcorr5*fact(4)*gradcorr5(j,i)+ + & wcorr6*fact(5)*gradcorr6(j,i)+ + & wturn6*fact(5)*gcorr6_turn(j,i)+ + & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) + & +welec*gshieldc(j,i) + & +welec*gshieldc_loc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wcorr*gshieldc_loc_ec(j,i) + & +wturn3*gshieldc_t3(j,i) + & +wturn3*gshieldc_loc_t3(j,i) + & +wturn4*gshieldc_t4(j,i) + & +wturn4*gshieldc_loc_t4(j,i) + & +wel_loc*gshieldc_ll(j,i) + & +wel_loc*gshieldc_loc_ll(j,i) + + gradx(j,i,icg)=fact(1)*wsc*gvdwx(j,i)+ + & fact(1)*wscp*gradx_scp(j,i)+ + & wbond*gradbx(j,i)+ + & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ + & wsccor*fact(1)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) + & +welec*gshieldx(j,i) + & +wcorr*gshieldx_ec(j,i) + & +wturn3*gshieldx_t3(j,i) + & +wturn4*gshieldx_t4(j,i) + & +wel_loc*gshieldx_ll(j,i) + + endif enddo #endif enddo @@ -231,8 +368,11 @@ C & +wturn3*fact(2)*gel_loc_turn3(i) & +wturn6*fact(5)*gel_loc_turn6(i) & +wel_loc*fact(2)*gel_loc_loc(i) +c & +wsccor*fact(1)*gsccor_loc(i) +c BYLA ROZNICA Z CLUSTER< OSTATNIA LINIA DODANA enddo endif + if (dyn_ss) call dyn_set_nss return end C------------------------------------------------------------------------ @@ -270,6 +410,8 @@ C------------------------------------------------------------------------ esccor=energia(19) edihcnstr=energia(20) estr=energia(18) + ethetacnstr=energia(24) + eliptran=energia(22) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1, & wvdwpp, @@ -278,7 +420,8 @@ C------------------------------------------------------------------------ & ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),ecorr6,wcorr6*fact(5), & eel_loc,wel_loc*fact(2),eello_turn3,wturn3*fact(2), & eello_turn4,wturn4*fact(3),eello_turn6,wturn6*fact(5), - & esccor,wsccor*fact(1),edihcnstr,ebr*nss,etot + & esccor,wsccor*fact(1),edihcnstr,ethetacnstr,ebr*nss, + & eliptran,wliptran,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -300,7 +443,9 @@ C------------------------------------------------------------------------ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ + & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'ETOT= ',1pE16.6,' (total)') #else write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),estr,wbond, @@ -309,7 +454,7 @@ C------------------------------------------------------------------------ & ecorr6,wcorr6*fact(5),eel_loc,wel_loc*fact(2), & eello_turn3,wturn3*fact(2),eello_turn4,wturn4*fact(3), & eello_turn6,wturn6*fact(5),esccor*fact(1),wsccor, - & edihcnstr,ebr*nss,etot + & edihcnstr,ethetacnstr,ebr*nss,eliptran,wliptran,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -330,7 +475,9 @@ C------------------------------------------------------------------------ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ + & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'ETOT= ',1pE16.6,' (total)') #endif return @@ -362,11 +509,14 @@ C integer icant external icant cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon +c ROZNICA z cluster do i=1,210 do j=1,2 eneps_temp(j,i)=0.0d0 enddo enddo +cROZNICA + evdw=0.0D0 evdw_t=0.0d0 do i=iatsc_s,iatsc_e @@ -396,19 +546,22 @@ C Change 12/1/95 to calculate four-body interactions c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj eps0ij=eps(itypi,itypj) fac=rrij**expon2 - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e1+e2 ij=icant(itypi,itypj) +c ROZNICA z cluster eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij) eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij +c + cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj) cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)') cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm, cd & (c(k,i),k=1,3),(c(k,j),k=1,3) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij @@ -566,8 +719,8 @@ C rij=1.0D0/r_inv_ij r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj)) fac=r_shift_inv**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e_augm+e1+e2 ij=icant(itypi,itypj) eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm) @@ -580,7 +733,7 @@ cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), cd & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm, cd & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij, cd & (c(k,i),k=1,3),(c(k,j),k=1,3) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij @@ -712,8 +865,8 @@ C Calculate the angle-dependent terms of energy & contributions to derivatives. C Calculate whole angle-dependent part of epsilon and contributions C to its derivatives fac=(rrij*sigsq)**expon2 - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt @@ -723,15 +876,15 @@ C to its derivatives eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux & /dabs(eps(itypi,itypj)) eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij endif if (calc_grad) then if (lprn) then - sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) - epsi=bb(itypi,itypj)**2/aa(itypi,itypj) + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa write (iout,'(2(a3,i3,2x),15(0pf7.3))') & restyp(itypi),i,restyp(itypj),j, & epsi,sigm,chi1,chi2,chip1,chip2, @@ -778,9 +931,10 @@ C include 'COMMON.ENEPS' include 'COMMON.IOUNITS' include 'COMMON.CALC' + include 'COMMON.SBRIDGE' logical lprn common /srutu/icall - integer icant + integer icant,xshift,yshift,zshift external icant do i=1,210 do j=1,2 @@ -807,6 +961,28 @@ C returning the ith atom to box if (yi.lt.0) yi=yi+boxysize zi=mod(zi,boxzsize) if (zi.lt.0) zi=zi+boxzsize + if ((zi.gt.bordlipbot) + &.and.(zi.lt.bordliptop)) then +C the energy transfer exist + if (zi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) @@ -817,6 +993,26 @@ C Calculate SC interaction energy. C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) + IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN + call dyn_ssbond_ene(i,j,evdwij) + evdw=evdw+evdwij +C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)') +C & 'evdw',i,j,evdwij,' ss',evdw,evdw_t +C triple bond artifac removal + do k=j+1,iend(i,iint) +C search over all next residues + if (dyn_ss_mask(k)) then +C check if they are cysteins +C write(iout,*) 'k=',k + call triple_ssbond_ene(i,j,k,evdwij) +C call the energy function that removes the artifical triple disulfide +C bond the soubroutine is located in ssMD.F + evdw=evdw+evdwij +C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)') +C & 'evdw',i,j,evdwij,'tss',evdw,evdw_t + endif!dyn_ss_mask(k) + enddo! k + ELSE ind=ind+1 itypj=iabs(itype(j)) if (itypj.eq.ntyp1) cycle @@ -851,6 +1047,40 @@ C returning jth atom to box if (yj.lt.0) yj=yj+boxysize zj=mod(zj,boxzsize) if (zj.lt.0) zj=zj+boxzsize + if ((zj.gt.bordlipbot) + &.and.(zj.lt.bordliptop)) then +C the energy transfer exist + if (zj.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zj-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipj=sscalelip(fracinbuf) + ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick + elseif (zj.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick) + sslipj=sscalelip(fracinbuf) + ssgradlipj=sscagradlip(fracinbuf)/lipbufthick + else + sslipj=1.0d0 + ssgradlipj=0.0 + endif + else + sslipj=0.0d0 + ssgradlipj=0.0 + endif + aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 +C if (aa.ne.aa_aq(itypi,itypj)) then + +C write(iout,*) "tu,", i,j,aa_aq(itypi,itypj)-aa, +C & bb_aq(itypi,itypj)-bb, +C & sslipi,sslipj +C endif + +C write(iout,*),aa,aa_lip(itypi,itypj),aa_aq(itypi,itypj) C checking the distance dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 xj_safe=xj @@ -896,6 +1126,7 @@ c write (iout,*) i,j,xj,yj,zj if (sss.le.0.0) cycle C Calculate angle-dependent terms of energy and contributions to their C derivatives. + call sc_angular sigsq=1.0D0/sigsq sig=sig0ij*dsqrt(sigsq) @@ -909,13 +1140,13 @@ C I hate to put IF's in the loops, but here don't have another choice!!!! c--------------------------------------------------------------- rij_shift=1.0D0/rij_shift fac=rij_shift**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt evdwij=evdwij*eps2rt*eps3rt - if (bb(itypi,itypj).gt.0) then + if (bb.gt.0) then evdw=evdw+evdwij*sss else evdw_t=evdw_t+evdwij*sss @@ -929,8 +1160,9 @@ c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj, c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)), c & aux*e2/eps(itypi,itypj) c if (lprn) then - sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) - epsi=bb(itypi,itypj)**2/aa(itypi,itypj) + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa +C#define DEBUG #ifdef DEBUG write (iout,'(2(a3,i3,2x),17(0pf7.3))') & restyp(itypi),i,restyp(itypj),j, @@ -940,6 +1172,7 @@ c if (lprn) then & evdwij write (iout,*) "partial sum", evdw, evdw_t #endif +C#undef DEBUG c endif if (calc_grad) then C Calculate gradient components. @@ -955,6 +1188,8 @@ C Calculate the radial part of the gradient C Calculate angular part of the gradient. call sc_grad endif +C write(iout,*) "partial sum", evdw, evdw_t + ENDIF ! dyn_ss enddo ! j enddo ! iint enddo ! i @@ -1060,15 +1295,15 @@ C I hate to put IF's in the loops, but here don't have another choice!!!! c--------------------------------------------------------------- rij_shift=1.0D0/rij_shift fac=rij_shift**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt fac_augm=rrij**expon e_augm=augm(itypi,itypj)*fac_augm evdwij=evdwij*eps2rt*eps3rt - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij+e_augm else evdw_t=evdw_t+evdwij+e_augm @@ -1779,6 +2014,8 @@ c print *,"itilde3 i iti iti1",i,iti,iti1 do k=1,2 mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1) enddo +C write (iout,*) 'mumu',i,b1(1,iti),Ub2(1,i-2) + C Vectors and matrices dependent on a single virtual-bond dihedral. call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1)) call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2)) @@ -1838,6 +2075,7 @@ C include 'COMMON.TORSION' include 'COMMON.VECTORS' include 'COMMON.FFIELD' + include 'COMMON.SHIELD' dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3), & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3) double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4), @@ -1908,15 +2146,15 @@ C write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e gcorr_loc(i)=0.0d0 enddo do i=iatel_s,iatel_e - if (i.eq.1) then +C if (i.eq.1) then if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1 - & .or. itype(i+2).eq.ntyp1) cycle - else - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 - & .or. itype(i+2).eq.ntyp1 - & .or. itype(i-1).eq.ntyp1 +C & .or. itype(i+2).eq.ntyp1) cycle +C else +C if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C & .or. itype(i+2).eq.ntyp1 +C & .or. itype(i-1).eq.ntyp1 &) cycle - endif +C endif if (itel(i).eq.0) goto 1215 dxi=dc(1,i) dyi=dc(2,i) @@ -1936,16 +2174,16 @@ C write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e num_conti=0 C write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) do j=ielstart(i),ielend(i) - if (j.eq.1) then - if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1 - & .or.itype(j+2).eq.ntyp1 - &) cycle - else + if (j.le.1) cycle +C if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1 +C & .or.itype(j+2).eq.ntyp1 +C &) cycle +C else if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1 - & .or.itype(j+2).eq.ntyp1 - & .or.itype(j-1).eq.ntyp1 +C & .or.itype(j+2).eq.ntyp1 +C & .or.itype(j-1).eq.ntyp1 &) cycle - endif +C endif C C) cycle if (itel(j).eq.0) goto 1216 @@ -1978,7 +2216,7 @@ C End diagnostics if (yj.lt.0) yj=yj+boxysize zj=mod(zj,boxzsize) if (zj.lt.0) zj=zj+boxzsize - dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 xj_safe=xj yj_safe=yj zj_safe=zj @@ -1989,7 +2227,7 @@ C End diagnostics xj=xj_safe+xshift*boxxsize yj=yj_safe+yshift*boxysize zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 if(dist_temp.lt.dist_init) then dist_init=dist_temp xj_temp=xj @@ -2009,7 +2247,6 @@ C End diagnostics yj=yj_safe-ymedi zj=zj_safe-zmedi endif - rij=xj*xj+yj*yj+zj*zj sss=sscale(sqrt(rij)) sssgrad=sscagrad(sqrt(rij)) @@ -2035,7 +2272,25 @@ c 4/26/02 - AL scaling down 1,4 repulsive VDW interactions c write (iout,*) "i",i,iteli," j",j,itelj," eesij",eesij C 12/26/95 - for the evaluation of multi-body H-bonding interactions ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg) + if (shield_mode.gt.0) then +C#define DEBUG +#ifdef DEBUG + write(iout,*) "ees_compon",i,j,el1,el2, + & fac_shield(i),fac_shield(j) +#endif +C#undef DEBUG +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + el1=el1*fac_shield(i)**2*fac_shield(j)**2 + el2=el2*fac_shield(i)**2*fac_shield(j)**2 + eesij=(el1+el2) ees=ees+eesij + else + fac_shield(i)=1.0 + fac_shield(j)=1.0 + eesij=(el1+el2) + ees=ees+eesij + endif evdw1=evdw1+evdwij*sss c write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)') c &'evdw1',i,j,evdwij @@ -2063,6 +2318,60 @@ C ggg(1)=facel*xj ggg(2)=facel*yj ggg(3)=facel*zj + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eesij/fac_shield(i) + & *2.0 + gshieldx(k,iresshield)=gshieldx(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i)*2.0 + gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield +C gshieldc_loc(k,iresshield)=gshieldc_loc(k,iresshield) +C & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i) +C if (iresshield.gt.i) then +C do ishi=i+1,iresshield-1 +C gshieldc(k,ishi)=gshieldc(k,ishi)+rlocshield +C & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i) +C +C enddo +C else +C do ishi=iresshield,i +C gshieldc(k,ishi)=gshieldc(k,ishi)-rlocshield +C & -grad_shield_loc(k,ilist,i)*eesij/fac_shield(i) +C +C enddo +C endif + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eesij/fac_shield(j) + & *2.0 + gshieldx(k,iresshield)=gshieldx(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)*2.0 + gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield + enddo + enddo + + do k=1,3 + gshieldc(k,i)=gshieldc(k,i)+ + & grad_shield(k,i)*eesij/fac_shield(i)*2.0 + gshieldc(k,j)=gshieldc(k,j)+ + & grad_shield(k,j)*eesij/fac_shield(j)*2.0 + gshieldc(k,i-1)=gshieldc(k,i-1)+ + & grad_shield(k,i)*eesij/fac_shield(i)*2.0 + gshieldc(k,j-1)=gshieldc(k,j-1)+ + & grad_shield(k,j)*eesij/fac_shield(j)*2.0 + + enddo + endif + do k=1,3 ghalf=0.5D0*ggg(k) gelc(k,i)=gelc(k,i)+ghalf @@ -2146,15 +2455,19 @@ cd print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3), cd & (dcosg(k),k=1,3) do k=1,3 ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k) + & *fac_shield(i)**2*fac_shield(j)**2 enddo do k=1,3 ghalf=0.5D0*ggg(k) gelc(k,i)=gelc(k,i)+ghalf & +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i)) & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) + & *fac_shield(i)**2*fac_shield(j)**2 + gelc(k,j)=gelc(k,j)+ghalf & +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j)) & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) + & *fac_shield(i)**2*fac_shield(j)**2 enddo do k=i+1,j-1 do l=1,3 @@ -2400,20 +2713,78 @@ C Check the loc-el terms by numerical integration C Contribution to the local-electrostatic energy coming from the i-j pair eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3) & +a33*muij(4) + if (shield_mode.eq.0) then + fac_shield(i)=1.0 + fac_shield(j)=1.0 +C else +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + endif + eel_loc_ij=eel_loc_ij + & *fac_shield(i)*fac_shield(j) c write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij -c write (iout,'(a6,2i5,0pf7.3)') -c & 'eelloc',i,j,eel_loc_ij +C write (iout,'(a6,2i5,0pf7.3)') +C & 'eelloc',i,j,eel_loc_ij +C write(iout,*) 'muije=',i,j,muij(1),muij(2),muij(3),muij(4) c write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3) +C eel_loc=eel_loc+eel_loc_ij + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eel_loc_ij + & /fac_shield(i) +C & *2.0 + gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eel_loc_ij/fac_shield(i) + gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eel_loc_ij + & /fac_shield(j) +C & *2.0 + gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eel_loc_ij/fac_shield(j) + gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1) + & +rlocshield + + enddo + enddo + do k=1,3 + gshieldc_ll(k,i)=gshieldc_ll(k,i)+ + & grad_shield(k,i)*eel_loc_ij/fac_shield(i) + gshieldc_ll(k,j)=gshieldc_ll(k,j)+ + & grad_shield(k,j)*eel_loc_ij/fac_shield(j) + gshieldc_ll(k,i-1)=gshieldc_ll(k,i-1)+ + & grad_shield(k,i)*eel_loc_ij/fac_shield(i) + gshieldc_ll(k,j-1)=gshieldc_ll(k,j-1)+ + & grad_shield(k,j)*eel_loc_ij/fac_shield(j) + enddo + endif eel_loc=eel_loc+eel_loc_ij + C Partial derivatives in virtual-bond dihedral angles gamma if (calc_grad) then if (i.gt.1) & gel_loc_loc(i-1)=gel_loc_loc(i-1)+ - & a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j) - & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j) + & (a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j) + & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)) + & *fac_shield(i)*fac_shield(j) + gel_loc_loc(j-1)=gel_loc_loc(j-1)+ - & a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j) - & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j) + & (a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j) + & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j)) + & *fac_shield(i)*fac_shield(j) + cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij) cd write(iout,*) 'agg ',agg cd write(iout,*) 'aggi ',aggi @@ -2423,8 +2794,10 @@ cd write(iout,*) 'aggj1',aggj1 C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2) do l=1,3 - ggg(l)=agg(l,1)*muij(1)+ - & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4) + ggg(l)=(agg(l,1)*muij(1)+ + & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + enddo do k=i+2,j2 do l=1,3 @@ -2433,14 +2806,22 @@ C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2) enddo C Remaining derivatives of eello do l=1,3 - gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+ - & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4) - gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+ - & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4) - gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+ - & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4) - gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+ - & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4) + gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+ + & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + + gel_loc(l,i+1)=gel_loc(l,i+1)+(aggi1(l,1)*muij(1)+ + & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + + gel_loc(l,j)=gel_loc(l,j)+(aggj(l,1)*muij(1)+ + & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + + gel_loc(l,j1)=gel_loc(l,j1)+(aggj1(l,1)*muij(1)+ + & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)) + & *fac_shield(i)*fac_shield(j) + enddo endif ENDIF @@ -2547,8 +2928,20 @@ c fac3=dsqrt(-ael6i)/r0ij**3 ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1) ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2) c ees0mij=0.0D0 + if (shield_mode.eq.0) then + fac_shield(i)=1.0d0 + fac_shield(j)=1.0d0 + else + ees0plist(num_conti,i)=j +C fac_shield(i)=0.4d0 +C fac_shield(j)=0.6d0 + endif ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij) + & *fac_shield(i)*fac_shield(j) + ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij) + & *fac_shield(i)*fac_shield(j) + C Diagnostics. Comment out or remove after debugging! c ees0p(num_conti,i)=0.5D0*fac3*ees0pij c ees0m(num_conti,i)=0.5D0*fac3*ees0mij @@ -2613,17 +3006,29 @@ C Derivatives due to the contact function gacontp_hb1(k,num_conti,i)=ghalfp & +(ecosap*(dc_norm(k,j)-cosa*dc_norm(k,i)) & + ecosbp*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) + & *fac_shield(i)*fac_shield(j) + gacontp_hb2(k,num_conti,i)=ghalfp & +(ecosap*(dc_norm(k,i)-cosa*dc_norm(k,j)) & + ecosgp*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) + & *fac_shield(i)*fac_shield(j) + gacontp_hb3(k,num_conti,i)=gggp(k) + & *fac_shield(i)*fac_shield(j) + gacontm_hb1(k,num_conti,i)=ghalfm & +(ecosam*(dc_norm(k,j)-cosa*dc_norm(k,i)) & + ecosbm*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1) + & *fac_shield(i)*fac_shield(j) + gacontm_hb2(k,num_conti,i)=ghalfm & +(ecosam*(dc_norm(k,i)-cosa*dc_norm(k,j)) & + ecosgm*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1) + & *fac_shield(i)*fac_shield(j) + gacontm_hb3(k,num_conti,i)=gggm(k) + & *fac_shield(i)*fac_shield(j) + enddo endif C Diagnostics. Comment out or remove after debugging! @@ -2669,6 +3074,8 @@ C Third- and fourth-order contributions from turns include 'COMMON.TORSION' include 'COMMON.VECTORS' include 'COMMON.FFIELD' + include 'COMMON.SHIELD' + include 'COMMON.CONTROL' dimension ggg(3) double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2), & e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2), @@ -2677,6 +3084,18 @@ C Third- and fourth-order contributions from turns & aggj(3,4),aggj1(3,4),a_temp(2,2) common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2 if (j.eq.i+2) then + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds +C & .or.((i+5).gt.nres) +C & .or.((i-1).le.0) +C end of changes suggested by Ana + & .or. itype(i+2).eq.ntyp1 + & .or. itype(i+3).eq.ntyp1 +C & .or. itype(i+5).eq.ntyp1 +C & .or. itype(i).eq.ntyp1 +C & .or. itype(i-1).eq.ntyp1 + & ) goto 179 + CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C Third-order contributions @@ -2691,22 +3110,80 @@ cd call checkint_turn3(i,a_temp,eello_turn3_num) call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1)) call transpose2(auxmat(1,1),auxmat1(1,1)) call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) + if (shield_mode.eq.0) then + fac_shield(i)=1.0 + fac_shield(j)=1.0 +C else +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + endif + eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + eello_t3=0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + cd write (2,*) 'i,',i,' j',j,'eello_turn3', cd & 0.5d0*(pizda(1,1)+pizda(2,2)), cd & ' eello_turn3_num',4*eello_turn3_num if (calc_grad) then +C Derivatives in shield mode + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eello_t3/fac_shield(i) +C & *2.0 + gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eello_t3/fac_shield(i) + gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eello_t3/fac_shield(j) +C & *2.0 + gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eello_t3/fac_shield(j) + gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1) + & +rlocshield + + enddo + enddo + + do k=1,3 + gshieldc_t3(k,i)=gshieldc_t3(k,i)+ + & grad_shield(k,i)*eello_t3/fac_shield(i) + gshieldc_t3(k,j)=gshieldc_t3(k,j)+ + & grad_shield(k,j)*eello_t3/fac_shield(j) + gshieldc_t3(k,i-1)=gshieldc_t3(k,i-1)+ + & grad_shield(k,i)*eello_t3/fac_shield(i) + gshieldc_t3(k,j-1)=gshieldc_t3(k,j-1)+ + & grad_shield(k,j)*eello_t3/fac_shield(j) + enddo + endif + C Derivatives in gamma(i) call matmat2(EUgder(1,1,i+1),EUg(1,1,i+2),auxmat2(1,1)) call transpose2(auxmat2(1,1),pizda(1,1)) call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1)) gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) C Derivatives in gamma(i+1) call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1)) call transpose2(auxmat2(1,1),pizda(1,1)) call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1)) gel_loc_turn3(i+1)=gel_loc_turn3(i+1) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + C Cartesian derivatives do l=1,3 a_temp(1,1)=aggi(l,1) @@ -2716,6 +3193,8 @@ C Cartesian derivatives call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,i)=gcorr3_turn(l,i) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) a_temp(2,1)=aggi1(l,3) @@ -2723,6 +3202,8 @@ C Cartesian derivatives call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) a_temp(2,1)=aggj(l,3) @@ -2730,6 +3211,8 @@ C Cartesian derivatives call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,j)=gcorr3_turn(l,j) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) a_temp(2,1)=aggj1(l,3) @@ -2737,9 +3220,23 @@ C Cartesian derivatives call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1)) gcorr3_turn(l,j1)=gcorr3_turn(l,j1) & +0.5d0*(pizda(1,1)+pizda(2,2)) + & *fac_shield(i)*fac_shield(j) + enddo endif + 179 continue else if (j.eq.i+3 .and. itype(i+2).ne.ntyp1) then + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds +C & .or.((i+5).gt.nres) +C & .or.((i-1).le.0) +C end of changes suggested by Ana + & .or. itype(i+3).eq.ntyp1 + & .or. itype(i+4).eq.ntyp1 +C & .or. itype(i+5).eq.ntyp1 + & .or. itype(i).eq.ntyp1 +C & .or. itype(i-1).eq.ntyp1 + & ) goto 178 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C Fourth-order contributions @@ -2767,11 +3264,64 @@ cd call checkint_turn4(i,a_temp,eello_turn4_num) call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1)) call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) + if (shield_mode.eq.0) then + fac_shield(i)=1.0 + fac_shield(j)=1.0 +C else +C fac_shield(i)=0.4 +C fac_shield(j)=0.6 + endif + eello_turn4=eello_turn4-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + eello_t4=-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3), cd & ' eello_turn4_num',8*eello_turn4_num C Derivatives in gamma(i) if (calc_grad) then + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (shield_mode.gt.0)) then +C print *,i,j + + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,i)*eello_t4/fac_shield(i) +C & *2.0 + gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,i)*eello_t4/fac_shield(i) + gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do k=1,3 + rlocshield=grad_shield_side(k,ilist,j)*eello_t4/fac_shield(j) +C & *2.0 + gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+ + & rlocshield + & +grad_shield_loc(k,ilist,j)*eello_t4/fac_shield(j) + gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1) + & +rlocshield + + enddo + enddo + + do k=1,3 + gshieldc_t4(k,i)=gshieldc_t4(k,i)+ + & grad_shield(k,i)*eello_t4/fac_shield(i) + gshieldc_t4(k,j)=gshieldc_t4(k,j)+ + & grad_shield(k,j)*eello_t4/fac_shield(j) + gshieldc_t4(k,i-1)=gshieldc_t4(k,i-1)+ + & grad_shield(k,i)*eello_t4/fac_shield(i) + gshieldc_t4(k,j-1)=gshieldc_t4(k,j-1)+ + & grad_shield(k,j)*eello_t4/fac_shield(j) + enddo + endif call transpose2(EUgder(1,1,i+1),e1tder(1,1)) call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1)) call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1)) @@ -2779,6 +3329,8 @@ C Derivatives in gamma(i) call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3) + & *fac_shield(i)*fac_shield(j) + C Derivatives in gamma(i+1) call transpose2(EUgder(1,1,i+2),e2tder(1,1)) call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1)) @@ -2787,6 +3339,8 @@ C Derivatives in gamma(i+1) call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3) + & *fac_shield(i)*fac_shield(j) + C Derivatives in gamma(i+2) call transpose2(EUgder(1,1,i+3),e3tder(1,1)) call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1)) @@ -2798,7 +3352,10 @@ C Derivatives in gamma(i+2) call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + C Cartesian derivatives + C Derivatives of this turn contributions in DC(i+2) if (j.lt.nres-1) then do l=1,3 @@ -2817,6 +3374,8 @@ C Derivatives of this turn contributions in DC(i+2) s3=0.5d0*(pizda(1,1)+pizda(2,2)) ggg(l)=-(s1+s2+s3) gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + enddo endif C Remaining derivatives of this turn contribution @@ -2835,6 +3394,8 @@ C Remaining derivatives of this turn contribution call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) a_temp(2,1)=aggi1(l,3) @@ -2849,6 +3410,8 @@ C Remaining derivatives of this turn contribution call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) a_temp(2,1)=aggj(l,3) @@ -2863,6 +3426,8 @@ C Remaining derivatives of this turn contribution call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) a_temp(2,1)=aggj1(l,3) @@ -2877,8 +3442,11 @@ C Remaining derivatives of this turn contribution call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1)) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3) + & *fac_shield(i)*fac_shield(j) + enddo endif + 178 continue endif return end @@ -3096,10 +3664,13 @@ C include 'COMMON.DERIV' include 'COMMON.VAR' include 'COMMON.INTERACT' + include 'COMMON.CONTROL' + include 'COMMON.IOUNITS' dimension ggg(3) ehpb=0.0D0 cd print *,'edis: nhpb=',nhpb,' fbr=',fbr cd print *,'link_start=',link_start,' link_end=',link_end +C write(iout,*) link_end, "link_end" if (link_end.eq.0) return do i=link_start,link_end C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a @@ -3116,25 +3687,98 @@ C iii and jjj point to the residues for which the distance is assigned. endif C 24/11/03 AL: SS bridges handled separately because of introducing a specific C distance and angle dependent SS bond potential. - if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. +C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. +C & iabs(itype(jjj)).eq.1) then +C write(iout,*) constr_dist,"const" + if (.not.dyn_ss .and. i.le.nss) then + if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. & iabs(itype(jjj)).eq.1) then call ssbond_ene(iii,jjj,eij) ehpb=ehpb+2*eij - else -C Calculate the distance between the two points and its difference from the -C target distance. - dd=dist(ii,jj) - rdis=dd-dhpb(i) + endif !ii.gt.neres + else if (ii.gt.nres .and. jj.gt.nres) then +c Restraints from contact prediction + dd=dist(ii,jj) + if (constr_dist.eq.11) then +C ehpb=ehpb+fordepth(i)**4.0d0 +C & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + ehpb=ehpb+fordepth(i)**4.0d0 + & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)**4.0d0 + & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd +C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, +C & ehpb,fordepth(i),dd +C write(iout,*) ehpb,"atu?" +C ehpb,"tu?" +C fac=fordepth(i)**4.0d0 +C & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd + else + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +c write (iout,*) "beta nmr", +c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else + dd=dist(ii,jj) + rdis=dd-dhpb(i) +C Get the force constant corresponding to this distance. + waga=forcon(i) +C Calculate the contribution to energy. + ehpb=ehpb+waga*rdis*rdis +c write (iout,*) "beta reg",dd,waga*rdis*rdis +C +C Evaluate gradient. +C + fac=waga*rdis/dd + endif !end dhpb1(i).gt.0 + endif !end const_dist=11 + do j=1,3 + ggg(j)=fac*(c(j,jj)-c(j,ii)) + enddo + do j=1,3 + ghpbx(j,iii)=ghpbx(j,iii)-ggg(j) + ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j) + enddo + do k=1,3 + ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) + ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) + enddo + else !ii.gt.nres +C write(iout,*) "before" + dd=dist(ii,jj) +C write(iout,*) "after",dd + if (constr_dist.eq.11) then + ehpb=ehpb+fordepth(i)**4.0d0 + & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)**4.0d0 + & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd +C ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i)) +C fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd +C print *,ehpb,"tu?" +C write(iout,*) ehpb,"btu?", +C & dd,dhpb(i),dhpb1(i),fordepth(i),forcon(i) +C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, +C & ehpb,fordepth(i),dd + else + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +c write (iout,*) "alph nmr", +c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else + rdis=dd-dhpb(i) C Get the force constant corresponding to this distance. - waga=forcon(i) + waga=forcon(i) C Calculate the contribution to energy. - ehpb=ehpb+waga*rdis*rdis + ehpb=ehpb+waga*rdis*rdis +c write (iout,*) "alpha reg",dd,waga*rdis*rdis C C Evaluate gradient. C - fac=waga*rdis/dd -cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd, -cd & ' waga=',waga,' fac=',fac + fac=waga*rdis/dd + endif + endif + do j=1,3 ggg(j)=fac*(c(j,jj)-c(j,ii)) enddo @@ -3154,7 +3798,7 @@ C Cartesian gradient in the SC vectors (ghpbx). enddo endif enddo - ehpb=0.5D0*ehpb + if (constr_dist.ne.11) ehpb=0.5D0*ehpb return end C-------------------------------------------------------------------------- @@ -3278,6 +3922,7 @@ C & gnmr1(vbld(i),-1.0d0,distchainmax) C else if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then diff = vbld(i)-vbldpDUM +C write(iout,*) i,diff else diff = vbld(i)-vbldp0 c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff @@ -3330,8 +3975,8 @@ C & AKSC(1,iti),AKSC(1,iti)*diff*diff usum=usum+uprod1 usumsqder=usumsqder+ud(j)*uprod2 enddo - write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), - & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) +c write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), +c & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) estr=estr+uprod/usum do j=1,3 gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres) @@ -3343,7 +3988,7 @@ C & AKSC(1,iti),AKSC(1,iti)*diff*diff end #ifdef CRYST_THETA C-------------------------------------------------------------------------- - subroutine ebend(etheta) + subroutine ebend(etheta,ethetacnstr) C C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral C angles gamma and its derivatives in consecutive thetas and gammas. @@ -3360,13 +4005,14 @@ C include 'COMMON.IOUNITS' include 'COMMON.NAMES' include 'COMMON.FFIELD' + include 'COMMON.TORCNSTR' common /calcthet/ term1,term2,termm,diffak,ratak, & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq, & delthe0,sig0inv,sigtc,sigsqtc,delthec,it double precision y(2),z(2) delta=0.02d0*pi - time11=dexp(-2*time) - time12=1.0d0 +c time11=dexp(-2*time) +c time12=1.0d0 etheta=0.0D0 c write (iout,*) "nres",nres c write (*,'(a,i2)') 'EBEND ICG=',icg @@ -3399,8 +4045,8 @@ C Zero the energy function and its derivative at 0 or pi. if (i.gt.3 .and. itype(i-3).ne.ntyp1) then #ifdef OSF phii=phi(i) - icrc=0 - call proc_proc(phii,icrc) +c icrc=0 +c call proc_proc(phii,icrc) if (icrc.eq.1) phii=150.0 #else phii=phi(i) @@ -3415,8 +4061,8 @@ C Zero the energy function and its derivative at 0 or pi. if (i.lt.nres .and. itype(i+1).ne.ntyp1) then #ifdef OSF phii1=phi(i+1) - icrc=0 - call proc_proc(phii1,icrc) +c icrc=0 +c call proc_proc(phii1,icrc) if (icrc.eq.1) phii1=150.0 phii1=pinorm(phii1) z(1)=cos(phii1) @@ -3486,7 +4132,34 @@ c & rad2deg*phii,rad2deg*phii1,ethetai if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1 if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2 gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett) - 1215 continue +c 1215 continue + enddo + ethetacnstr=0.0d0 +C print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=1,ntheta_constr + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif +C if (energy_dec) then +C write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", +C & i,itheta,rad2deg*thetiii, +C & rad2deg*theta_constr0(i), rad2deg*theta_drange(i), +C & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, +C & gloc(itheta+nphi-2,icg) +C endif enddo C Ufff.... We've done all this!!! return @@ -3601,7 +4274,7 @@ C "Thank you" to MAPLE (probably spared one day of hand-differentiation). end #else C-------------------------------------------------------------------------- - subroutine ebend(etheta) + subroutine ebend(etheta,ethetacnstr) C C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral C angles gamma and its derivatives in consecutive thetas and gammas. @@ -3621,6 +4294,7 @@ C include 'COMMON.NAMES' include 'COMMON.FFIELD' include 'COMMON.CONTROL' + include 'COMMON.TORCNSTR' double precision coskt(mmaxtheterm),sinkt(mmaxtheterm), & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle), & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble), @@ -3667,8 +4341,9 @@ C if (itype(i-1).eq.ntyp1) cycle enddo else phii=0.0d0 - ityp1=nthetyp+1 +c ityp1=nthetyp+1 do k=1,nsingle + ityp1=ithetyp((itype(i-2))) cosph1(k)=0.0d0 sinph1(k)=0.0d0 enddo @@ -3689,7 +4364,8 @@ C if (itype(i-1).eq.ntyp1) cycle enddo else phii1=0.0d0 - ityp3=nthetyp+1 +c ityp3=nthetyp+1 + ityp3=ithetyp((itype(i))) do k=1,nsingle cosph2(k)=0.0d0 sinph2(k)=0.0d0 @@ -3806,7 +4482,36 @@ c call flush(iout) etheta=etheta+ethetai if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1 - gloc(nphi+i-2,icg)=wang*dethetai +c gloc(nphi+i-2,icg)=wang*dethetai + gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*dethetai + enddo +C now constrains + ethetacnstr=0.0d0 +C print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=1,ntheta_constr + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif +C if (energy_dec) then +C write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", +C & i,itheta,rad2deg*thetiii, +C & rad2deg*theta_constr0(i), rad2deg*theta_drange(i), +C & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, +C & gloc(itheta+nphi-2,icg) +C endif enddo return end @@ -4576,15 +5281,16 @@ c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) difi=phii-phi0(i) if (difi.gt.drange(i)) then difi=difi-drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 else if (difi.lt.-drange(i)) then difi=difi+drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 endif -! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii, -! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) +C write (iout,'(a6,2i5,2f8.3,2e14.5)') "edih", +C & i,itori,rad2deg*phii, +C & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg) enddo ! write (iout,*) 'edihcnstr',edihcnstr return @@ -4674,21 +5380,24 @@ c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) edihi=0.0d0 if (difi.gt.drange(i)) then difi=difi-drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 - edihi=0.25d0*ftors*difi**4 + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 + edihi=0.25d0*ftors(i)*difi**4 else if (difi.lt.-drange(i)) then difi=difi+drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 - edihi=0.25d0*ftors*difi**4 + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 + edihi=0.25d0*ftors(i)*difi**4 else difi=0.0d0 endif + write (iout,'(a6,2i5,2f8.3,2e14.5)') "edih", + & i,itori,rad2deg*phii, + & rad2deg*difi,0.25d0*ftors(i)*difi**4 c write (iout,'(2i5,4f10.5,e15.5)') i,itori,phii,phi0(i),difi, c & drange(i),edihi ! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii, -! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) +! & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg) enddo ! write (iout,*) 'edihcnstr',edihcnstr return @@ -4835,6 +5544,7 @@ c 3 = SC...Ca...Ca...SCi esccor=esccor+v1ij*cosphi+v2ij*sinphi gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) enddo +C write (iout,*)"EBACK_SC_COR",esccor,i c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp, c & nterm_sccor(isccori,isccori1),isccori,isccori1 c gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci @@ -5214,6 +5924,7 @@ C This subroutine calculates multi-body contributions to hydrogen-bonding C Set lprn=.true. for debugging lprn=.false. eturn6=0.0d0 + ecorr6=0.0d0 #ifdef MPL n_corr=0 n_corr1=0 @@ -5403,7 +6114,11 @@ cd & dabs(eello6(i,j,i+1,j1,jj,kk)) cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1 eturn6=eturn6+eello_turn6(i,jj,kk) cd write (2,*) 'multibody_eello:eturn6',eturn6 + else if ((wturn6.eq.0.0d0).and.(wcorr6.eq.0.0d0)) then + eturn6=0.0d0 + ecorr6=0.0d0 endif + ENDIF 1111 continue else if (j1.eq.j) then @@ -5424,6 +6139,7 @@ c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0) enddo ! kk enddo ! jj enddo ! i + write (iout,*) "eturn6",eturn6,ecorr6 return end c------------------------------------------------------------------------------ @@ -5434,6 +6150,8 @@ c------------------------------------------------------------------------------ include 'COMMON.DERIV' include 'COMMON.INTERACT' include 'COMMON.CONTACTS' + include 'COMMON.CONTROL' + include 'COMMON.SHIELD' double precision gx(3),gx1(3) logical lprn lprn=.false. @@ -5457,7 +6175,7 @@ c write (iout,*)'Contacts have occurred for peptide groups', c & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees C Calculate the multi-body contribution to energy. - ecorr=ecorr+ekont*ees +C ecorr=ecorr+ekont*ees if (calc_grad) then C Calculate multi-body contributions to the gradient. do ll=1,3 @@ -5491,7 +6209,85 @@ C Calculate multi-body contributions to the gradient. & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+ & coeffm*ees0mij*gacontm_hb3(ll,kk,k)) enddo - enddo + enddo + if (shield_mode.gt.0) then + j=ees0plist(jj,i) + l=ees0plist(kk,k) +C print *,i,j,fac_shield(i),fac_shield(j), +C &fac_shield(k),fac_shield(l) + if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. + & (fac_shield(k).gt.0).and.(fac_shield(l).gt.0)) then + do ilist=1,ishield_list(i) + iresshield=shield_list(ilist,i) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,i)*ehbcorr/fac_shield(i) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,i)*ehbcorr/fac_shield(i) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + &+rlocshield + enddo + enddo + do ilist=1,ishield_list(j) + iresshield=shield_list(ilist,j) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,j)*ehbcorr/fac_shield(j) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,j)*ehbcorr/fac_shield(j) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(k) + iresshield=shield_list(ilist,k) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,k)*ehbcorr/fac_shield(k) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,k)*ehbcorr/fac_shield(k) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + & +rlocshield + enddo + enddo + do ilist=1,ishield_list(l) + iresshield=shield_list(ilist,l) + do m=1,3 + rlocshield=grad_shield_side(m,ilist,l)*ehbcorr/fac_shield(l) +C & *2.0 + gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+ + & rlocshield + & +grad_shield_loc(m,ilist,l)*ehbcorr/fac_shield(l) + gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1) + & +rlocshield + enddo + enddo +C print *,gshieldx(m,iresshield) + do m=1,3 + gshieldc_ec(m,i)=gshieldc_ec(m,i)+ + & grad_shield(m,i)*ehbcorr/fac_shield(i) + gshieldc_ec(m,j)=gshieldc_ec(m,j)+ + & grad_shield(m,j)*ehbcorr/fac_shield(j) + gshieldc_ec(m,i-1)=gshieldc_ec(m,i-1)+ + & grad_shield(m,i)*ehbcorr/fac_shield(i) + gshieldc_ec(m,j-1)=gshieldc_ec(m,j-1)+ + & grad_shield(m,j)*ehbcorr/fac_shield(j) + + gshieldc_ec(m,k)=gshieldc_ec(m,k)+ + & grad_shield(m,k)*ehbcorr/fac_shield(k) + gshieldc_ec(m,l)=gshieldc_ec(m,l)+ + & grad_shield(m,l)*ehbcorr/fac_shield(l) + gshieldc_ec(m,k-1)=gshieldc_ec(m,k-1)+ + & grad_shield(m,k)*ehbcorr/fac_shield(k) + gshieldc_ec(m,l-1)=gshieldc_ec(m,l-1)+ + & grad_shield(m,l)*ehbcorr/fac_shield(l) + + enddo + endif + endif endif ehbcorr=ekont*ees return @@ -7597,6 +8393,125 @@ cd write (2,*) 'eel_turn6',ekont*eel_turn6 return end crc------------------------------------------------- +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + subroutine Eliptransfer(eliptran) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.GEO' + include 'COMMON.VAR' + include 'COMMON.LOCAL' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' +C this is done by Adasko +C print *,"wchodze" +C structure of box: +C water +C--bordliptop-- buffore starts +C--bufliptop--- here true lipid starts +C lipid +C--buflipbot--- lipid ends buffore starts +C--bordlipbot--buffore ends + eliptran=0.0 + do i=1,nres +C do i=1,1 + if (itype(i).eq.ntyp1) cycle + + positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize)) + if (positi.le.0) positi=positi+boxzsize +C print *,i +C first for peptide groups +c for each residue check if it is in lipid or lipid water border area + if ((positi.gt.bordlipbot) + &.and.(positi.lt.bordliptop)) then +C the energy transfer exist + if (positi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((positi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslip=sscalelip(fracinbuf) + ssgradlip=-sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*pepliptran + gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0 + gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0 +C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran + elseif (positi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick) + sslip=sscalelip(fracinbuf) + ssgradlip=sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*pepliptran + gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0 + gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0 +C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran +C print *, "doing sscalefor top part" +C print *,i,sslip,fracinbuf,ssgradlip + else + eliptran=eliptran+pepliptran +C print *,"I am in true lipid" + endif +C else +C eliptran=elpitran+0.0 ! I am in water + endif + enddo +C print *, "nic nie bylo w lipidzie?" +C now multiply all by the peptide group transfer factor +C eliptran=eliptran*pepliptran +C now the same for side chains +CV do i=1,1 + do i=1,nres + if (itype(i).eq.ntyp1) cycle + positi=(mod(c(3,i+nres),boxzsize)) + if (positi.le.0) positi=positi+boxzsize +C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop +c for each residue check if it is in lipid or lipid water border area +C respos=mod(c(3,i+nres),boxzsize) +C print *,positi,bordlipbot,buflipbot + if ((positi.gt.bordlipbot) + & .and.(positi.lt.bordliptop)) then +C the energy transfer exist + if (positi.lt.buflipbot) then + fracinbuf=1.0d0- + & ((positi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslip=sscalelip(fracinbuf) + ssgradlip=-sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*liptranene(itype(i)) + gliptranx(3,i)=gliptranx(3,i) + &+ssgradlip*liptranene(itype(i)) + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i)) +C print *,"doing sccale for lower part" + elseif (positi.gt.bufliptop) then + fracinbuf=1.0d0- + &((bordliptop-positi)/lipbufthick) + sslip=sscalelip(fracinbuf) + ssgradlip=sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*liptranene(itype(i)) + gliptranx(3,i)=gliptranx(3,i) + &+ssgradlip*liptranene(itype(i)) + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i)) +C print *, "doing sscalefor top part",sslip,fracinbuf + else + eliptran=eliptran+liptranene(itype(i)) +C print *,"I am in true lipid" + endif + endif ! if in lipid or buffor +C else +C eliptran=elpitran+0.0 ! I am in water + enddo + return + end + + +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + SUBROUTINE MATVEC2(A1,V1,V2) implicit real*8 (a-h,o-z) include 'DIMENSIONS' @@ -7760,4 +8675,370 @@ C----------------------------------------------------------------------- return end C----------------------------------------------------------------------- +C----------------------------------------------------------------------- + double precision function sscalelip(r) + double precision r,gamm + include "COMMON.SPLITELE" +C if(r.lt.r_cut-rlamb) then +C sscale=1.0d0 +C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then +C gamm=(r-(r_cut-rlamb))/rlamb + sscalelip=1.0d0+r*r*(2*r-3.0d0) +C else +C sscale=0d0 +C endif + return + end +C----------------------------------------------------------------------- + double precision function sscagradlip(r) + double precision r,gamm + include "COMMON.SPLITELE" +C if(r.lt.r_cut-rlamb) then +C sscagrad=0.0d0 +C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then +C gamm=(r-(r_cut-rlamb))/rlamb + sscagradlip=r*(6*r-6.0d0) +C else +C sscagrad=0.0d0 +C endif + return + end + +C----------------------------------------------------------------------- + subroutine set_shield_fac + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.SHIELD' + include 'COMMON.INTERACT' +C this is the squar root 77 devided by 81 the epislion in lipid (in protein) + double precision div77_81/0.974996043d0/, + &div4_81/0.2222222222d0/,sh_frac_dist_grad(3) + +C the vector between center of side_chain and peptide group + double precision pep_side(3),long,side_calf(3), + &pept_group(3),costhet_grad(3),cosphi_grad_long(3), + &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3) +C the line belowe needs to be changed for FGPROC>1 + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle + ishield_list(i)=0 +Cif there two consequtive dummy atoms there is no peptide group between them +C the line below has to be changed for FGPROC>1 + VolumeTotal=0.0 + do k=1,nres + if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle + dist_pep_side=0.0 + dist_side_calf=0.0 + do j=1,3 +C first lets set vector conecting the ithe side-chain with kth side-chain + pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0 +C pep_side(j)=2.0d0 +C and vector conecting the side-chain with its proper calfa + side_calf(j)=c(j,k+nres)-c(j,k) +C side_calf(j)=2.0d0 + pept_group(j)=c(j,i)-c(j,i+1) +C lets have their lenght + dist_pep_side=pep_side(j)**2+dist_pep_side + dist_side_calf=dist_side_calf+side_calf(j)**2 + dist_pept_group=dist_pept_group+pept_group(j)**2 + enddo + dist_pep_side=dsqrt(dist_pep_side) + dist_pept_group=dsqrt(dist_pept_group) + dist_side_calf=dsqrt(dist_side_calf) + do j=1,3 + pep_side_norm(j)=pep_side(j)/dist_pep_side + side_calf_norm(j)=dist_side_calf + enddo +C now sscale fraction + sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield +C print *,buff_shield,"buff" +C now sscale + if (sh_frac_dist.le.0.0) cycle +C If we reach here it means that this side chain reaches the shielding sphere +C Lets add him to the list for gradient + ishield_list(i)=ishield_list(i)+1 +C ishield_list is a list of non 0 side-chain that contribute to factor gradient +C this list is essential otherwise problem would be O3 + shield_list(ishield_list(i),i)=k +C Lets have the sscale value + if (sh_frac_dist.gt.1.0) then + scale_fac_dist=1.0d0 + do j=1,3 + sh_frac_dist_grad(j)=0.0d0 + enddo + else + scale_fac_dist=-sh_frac_dist*sh_frac_dist + & *(2.0*sh_frac_dist-3.0d0) + fac_help_scale=6.0*(sh_frac_dist-sh_frac_dist**2) + & /dist_pep_side/buff_shield*0.5 +C remember for the final gradient multiply sh_frac_dist_grad(j) +C for side_chain by factor -2 ! + do j=1,3 + sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) +C print *,"jestem",scale_fac_dist,fac_help_scale, +C & sh_frac_dist_grad(j) + enddo + endif +C if ((i.eq.3).and.(k.eq.2)) then +C print *,i,sh_frac_dist,dist_pep,fac_help_scale,scale_fac_dist +C & ,"TU" +C endif + +C this is what is now we have the distance scaling now volume... + short=short_r_sidechain(itype(k)) + long=long_r_sidechain(itype(k)) + costhet=1.0d0/dsqrt(1.0+short**2/dist_pep_side**2) +C now costhet_grad +C costhet=0.0d0 + costhet_fac=costhet**3*short**2*(-0.5)/dist_pep_side**4 +C costhet_fac=0.0d0 + do j=1,3 + costhet_grad(j)=costhet_fac*pep_side(j) + enddo +C remember for the final gradient multiply costhet_grad(j) +C for side_chain by factor -2 ! +C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1 +C pep_side0pept_group is vector multiplication + pep_side0pept_group=0.0 + do j=1,3 + pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j) + enddo + cosalfa=(pep_side0pept_group/ + & (dist_pep_side*dist_side_calf)) + fac_alfa_sin=1.0-cosalfa**2 + fac_alfa_sin=dsqrt(fac_alfa_sin) + rkprim=fac_alfa_sin*(long-short)+short +C now costhet_grad + cosphi=1.0d0/dsqrt(1.0+rkprim**2/dist_pep_side**2) + cosphi_fac=cosphi**3*rkprim**2*(-0.5)/dist_pep_side**4 + + do j=1,3 + cosphi_grad_long(j)=cosphi_fac*pep_side(j) + &+cosphi**3*0.5/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa/ + &((dist_pep_side*dist_side_calf))* + &((side_calf(j))-cosalfa* + &((pep_side(j)/dist_pep_side)*dist_side_calf)) + + cosphi_grad_loc(j)=cosphi**3*0.5/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa + &/((dist_pep_side*dist_side_calf))* + &(pep_side(j)- + &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side) + enddo + + VofOverlap=VSolvSphere/2.0d0*(1.0-costhet)*(1.0-cosphi) + & /VSolvSphere_div + & *wshield +C now the gradient... +C grad_shield is gradient of Calfa for peptide groups +C write(iout,*) "shield_compon",i,k,VSolvSphere,scale_fac_dist, +C & costhet,cosphi +C write(iout,*) "cosphi_compon",i,k,pep_side0pept_group, +C & dist_pep_side,dist_side_calf,c(1,k+nres),c(1,k),itype(k) + do j=1,3 + grad_shield(j,i)=grad_shield(j,i) +C gradient po skalowaniu + & +(sh_frac_dist_grad(j) +C gradient po costhet + &-scale_fac_dist*costhet_grad(j)/(1.0-costhet) + &-scale_fac_dist*(cosphi_grad_long(j)) + &/(1.0-cosphi) )*div77_81 + &*VofOverlap +C grad_shield_side is Cbeta sidechain gradient + grad_shield_side(j,ishield_list(i),i)= + & (sh_frac_dist_grad(j)*-2.0d0 + & +scale_fac_dist*costhet_grad(j)*2.0d0/(1.0-costhet) + & +scale_fac_dist*(cosphi_grad_long(j)) + & *2.0d0/(1.0-cosphi)) + & *div77_81*VofOverlap + + grad_shield_loc(j,ishield_list(i),i)= + & scale_fac_dist*cosphi_grad_loc(j) + & *2.0d0/(1.0-cosphi) + & *div77_81*VofOverlap + enddo + VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist + enddo + fac_shield(i)=VolumeTotal*div77_81+div4_81 +C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i) + enddo + return + end +C-------------------------------------------------------------------------- +C first for shielding is setting of function of side-chains + subroutine set_shield_fac2 + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.SHIELD' + include 'COMMON.INTERACT' +C this is the squar root 77 devided by 81 the epislion in lipid (in protein) + double precision div77_81/0.974996043d0/, + &div4_81/0.2222222222d0/,sh_frac_dist_grad(3) + +C the vector between center of side_chain and peptide group + double precision pep_side(3),long,side_calf(3), + &pept_group(3),costhet_grad(3),cosphi_grad_long(3), + &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3) +C the line belowe needs to be changed for FGPROC>1 + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle + ishield_list(i)=0 +Cif there two consequtive dummy atoms there is no peptide group between them +C the line below has to be changed for FGPROC>1 + VolumeTotal=0.0 + do k=1,nres + if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle + dist_pep_side=0.0 + dist_side_calf=0.0 + do j=1,3 +C first lets set vector conecting the ithe side-chain with kth side-chain + pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0 +C pep_side(j)=2.0d0 +C and vector conecting the side-chain with its proper calfa + side_calf(j)=c(j,k+nres)-c(j,k) +C side_calf(j)=2.0d0 + pept_group(j)=c(j,i)-c(j,i+1) +C lets have their lenght + dist_pep_side=pep_side(j)**2+dist_pep_side + dist_side_calf=dist_side_calf+side_calf(j)**2 + dist_pept_group=dist_pept_group+pept_group(j)**2 + enddo + dist_pep_side=dsqrt(dist_pep_side) + dist_pept_group=dsqrt(dist_pept_group) + dist_side_calf=dsqrt(dist_side_calf) + do j=1,3 + pep_side_norm(j)=pep_side(j)/dist_pep_side + side_calf_norm(j)=dist_side_calf + enddo +C now sscale fraction + sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield +C print *,buff_shield,"buff" +C now sscale + if (sh_frac_dist.le.0.0) cycle +C If we reach here it means that this side chain reaches the shielding sphere +C Lets add him to the list for gradient + ishield_list(i)=ishield_list(i)+1 +C ishield_list is a list of non 0 side-chain that contribute to factor gradient +C this list is essential otherwise problem would be O3 + shield_list(ishield_list(i),i)=k +C Lets have the sscale value + if (sh_frac_dist.gt.1.0) then + scale_fac_dist=1.0d0 + do j=1,3 + sh_frac_dist_grad(j)=0.0d0 + enddo + else + scale_fac_dist=-sh_frac_dist*sh_frac_dist + & *(2.0d0*sh_frac_dist-3.0d0) + fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2) + & /dist_pep_side/buff_shield*0.5d0 +C remember for the final gradient multiply sh_frac_dist_grad(j) +C for side_chain by factor -2 ! + do j=1,3 + sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) +C sh_frac_dist_grad(j)=0.0d0 +C scale_fac_dist=1.0d0 +C print *,"jestem",scale_fac_dist,fac_help_scale, +C & sh_frac_dist_grad(j) + enddo + endif +C this is what is now we have the distance scaling now volume... + short=short_r_sidechain(itype(k)) + long=long_r_sidechain(itype(k)) + costhet=1.0d0/dsqrt(1.0d0+short**2/dist_pep_side**2) + sinthet=short/dist_pep_side*costhet +C now costhet_grad +C costhet=0.6d0 +C sinthet=0.8 + costhet_fac=costhet**3*short**2*(-0.5d0)/dist_pep_side**4 +C sinthet_fac=costhet**2*0.5d0*(short**3/dist_pep_side**4*costhet +C & -short/dist_pep_side**2/costhet) +C costhet_fac=0.0d0 + do j=1,3 + costhet_grad(j)=costhet_fac*pep_side(j) + enddo +C remember for the final gradient multiply costhet_grad(j) +C for side_chain by factor -2 ! +C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1 +C pep_side0pept_group is vector multiplication + pep_side0pept_group=0.0d0 + do j=1,3 + pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j) + enddo + cosalfa=(pep_side0pept_group/ + & (dist_pep_side*dist_side_calf)) + fac_alfa_sin=1.0d0-cosalfa**2 + fac_alfa_sin=dsqrt(fac_alfa_sin) + rkprim=fac_alfa_sin*(long-short)+short +C rkprim=short + +C now costhet_grad + cosphi=1.0d0/dsqrt(1.0d0+rkprim**2/dist_pep_side**2) +C cosphi=0.6 + cosphi_fac=cosphi**3*rkprim**2*(-0.5d0)/dist_pep_side**4 + sinphi=rkprim/dist_pep_side/dsqrt(1.0d0+rkprim**2/ + & dist_pep_side**2) +C sinphi=0.8 + do j=1,3 + cosphi_grad_long(j)=cosphi_fac*pep_side(j) + &+cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa/ + &((dist_pep_side*dist_side_calf))* + &((side_calf(j))-cosalfa* + &((pep_side(j)/dist_pep_side)*dist_side_calf)) +C cosphi_grad_long(j)=0.0d0 + cosphi_grad_loc(j)=cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa + &/((dist_pep_side*dist_side_calf))* + &(pep_side(j)- + &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side) +C cosphi_grad_loc(j)=0.0d0 + enddo +C print *,sinphi,sinthet + VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet)) + & /VSolvSphere_div +C & *wshield +C now the gradient... + do j=1,3 + grad_shield(j,i)=grad_shield(j,i) +C gradient po skalowaniu + & +(sh_frac_dist_grad(j)*VofOverlap +C gradient po costhet + & +scale_fac_dist*VSolvSphere/VSolvSphere_div/4.0d0* + &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( + & sinphi/sinthet*costhet*costhet_grad(j) + & +sinthet/sinphi*cosphi*cosphi_grad_long(j))) + & )*wshield +C grad_shield_side is Cbeta sidechain gradient + grad_shield_side(j,ishield_list(i),i)= + & (sh_frac_dist_grad(j)*-2.0d0 + & *VofOverlap + & -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0* + &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( + & sinphi/sinthet*costhet*costhet_grad(j) + & +sinthet/sinphi*cosphi*cosphi_grad_long(j))) + & )*wshield + + grad_shield_loc(j,ishield_list(i),i)= + & scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0* + &(1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*( + & sinthet/sinphi*cosphi*cosphi_grad_loc(j) + & )) + & *wshield + enddo + VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist + enddo + fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield) +C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i) +C write(2,*) "TU",rpp(1,1),short,long,buff_shield + enddo + return + end