C peptide group is shielded by side-chains
C the matrix - shield_fac(i) the i index describe the ith between i and i+1
C write (iout,*) "shield_mode",shield_mode
- if (shield_mode.gt.0) then
+ if (shield_mode.eq.1) then
call set_shield_fac
+ else if (shield_mode.eq.2) then
+ call set_shield_fac2
endif
c print *,"Processor",myrank," left VEC_AND_DERIV"
if (ipot.lt.6) then
C Calculate the virtual-bond-angle energy.
C
if (wang.gt.0d0) then
+ if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then
call ebend(ebe,ethetacnstr)
+ endif
+C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then
+ call ebend_kcc(ebe,ethetacnstr)
+ endif
else
ebe=0
ethetacnstr=0
C Calculate the virtual-bond torsional energy.
C
cd print *,'nterm=',nterm
+C print *,"tor",tor_mode
if (wtor.gt.0) then
+ if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then
call etor(etors,edihcnstr)
+ endif
+C etor kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then
+ call etor_kcc(etors,edihcnstr)
+ endif
else
etors=0
edihcnstr=0
C
C 6/23/01 Calculate double-torsional energy
C
- if (wtor_d.gt.0) then
+ if ((wtor_d.gt.0).and.((tor_mode.eq.0).or.(tor_mode.eq.2))) then
call etor_d(etors_d)
else
etors_d=0
return
end
#endif
+C----------------------------------------------------------------------------------
+C The rigorous attempt to derive energy function
+ subroutine etor_kcc(etors,edihcnstr)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ logical lprn
+ double precision thybt1(maxtermkcc),thybt2(maxtermkcc)
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (tor_mode.ne.2) then
+ etors=0.0D0
+ endif
+ do i=iphi_start,iphi_end
+C ANY TWO ARE DUMMY ATOMS in row CYCLE
+c if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or.
+c & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)) .or.
+c & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1))) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle
+ itori=itortyp_kcc(itype(i-2))
+ itori1=itortyp_kcc(itype(i-1))
+ phii=phi(i)
+ glocig=0.0D0
+ glocit1=0.0d0
+ glocit2=0.0d0
+ sumnonchebyshev=0.0d0
+ sumchebyshev=0.0d0
+C to avoid multiple devision by 2
+ theti22=0.5d0*theta(i)
+C theta 12 is the theta_1 /2
+C theta 22 is theta_2 /2
+ theti12=0.5d0*theta(i-1)
+C and appropriate sinus function
+ sinthet2=dsin(theta(i))
+ sinthet1=dsin(theta(i-1))
+ costhet1=dcos(theta(i-1))
+ costhet2=dcos(theta(i))
+C to speed up lets store its mutliplication
+ sint1t2=sinthet2*sinthet1
+C \sum_{i=1}^n (sin(theta_1) * sin(theta_2))^n * (c_n* cos(n*gamma)
+C +d_n*sin(n*gamma)) *
+C \sum_{i=1}^m (1+a_m*Tb_m(cos(theta_1 /2))+b_m*Tb_m(cos(theta_2 /2)))
+C we have two sum 1) Non-Chebyshev which is with n and gamma
+ do j=1,nterm_kcc(itori,itori1)
+
+ v1ij=v1_kcc(j,itori,itori1)
+ v2ij=v2_kcc(j,itori,itori1)
+C v1ij is c_n and d_n in euation above
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ sint1t2n=sint1t2**j
+ sumnonchebyshev=
+ & sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+ actval=sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+C etors=etors+sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+C if (energy_dec) etors_ii=etors_ii+
+C & v1ij*cosphi+v2ij*sinphi
+C glocig is the gradient local i site in gamma
+ glocig=j*(v2ij*cosphi-v1ij*sinphi)*sint1t2n
+C now gradient over theta_1
+ glocit1=actval/sinthet1*j*costhet1
+ glocit2=actval/sinthet2*j*costhet2
+
+C now the Czebyshev polinominal sum
+ do k=1,nterm_kcc_Tb(itori,itori1)
+ thybt1(k)=v1_chyb(k,j,itori,itori1)
+ thybt2(k)=v2_chyb(k,j,itori,itori1)
+C thybt1(k)=0.0
+C thybt2(k)=0.0
+ enddo
+ sumth1thyb=tschebyshev
+ & (1,nterm_kcc_Tb(itori,itori1),thybt1(1),dcos(theti12)**2)
+ gradthybt1=gradtschebyshev
+ & (0,nterm_kcc_Tb(itori,itori1)-1,thybt1(1),
+ & dcos(theti12)**2)
+ & *dcos(theti12)*(-dsin(theti12))
+ sumth2thyb=tschebyshev
+ & (1,nterm_kcc_Tb(itori,itori1),thybt2(1),dcos(theti22)**2)
+ gradthybt2=gradtschebyshev
+ & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),
+ & dcos(theti22)**2)
+ & *dcos(theti22)*(-dsin(theti22))
+C print *, sumth1thyb, gradthybt1, sumth2thyb, gradthybt2,
+C & gradtschebyshev
+C & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),
+C & dcos(theti22)**2),
+C & dsin(theti22)
+
+C now overal sumation
+ etors=etors+(1.0d0+sumth1thyb+sumth2thyb)*sumnonchebyshev
+C print *,"sumnon", sumnonchebyshev,sumth1thyb+sumth2thyb
+C derivative over gamma
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig
+ & *(1.0d0+sumth1thyb+sumth2thyb)
+C derivative over theta1
+ gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*
+ & (glocit1*(1.0d0+sumth1thyb+sumth2thyb)+
+ & sumnonchebyshev*gradthybt1)
+C now derivative over theta2
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*
+ & (glocit2*(1.0d0+sumth1thyb+sumth2thyb)+
+ & sumnonchebyshev*gradthybt2)
+ enddo
+ enddo
+
+C gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
+! 6/20/98 - dihedral angle constraints
+ if (tor_mode.ne.2) then
+ edihcnstr=0.0d0
+c do i=1,ndih_constr
+ do i=idihconstr_start,idihconstr_end
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=pinorm(phii-phi0(i))
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ 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(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ else
+ difi=0.0
+ endif
+ enddo
+ endif
+ return
+ end
+
+C The rigorous attempt to derive energy function
+ subroutine ebend_kcc(etheta,ethetacnstr)
+
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ logical lprn
+ double precision thybt1(maxtermkcc)
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (tormode.ne.2) etheta=0.0D0
+ do i=ithet_start,ithet_end
+c print *,i,itype(i-1),itype(i),itype(i-2)
+ if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
+ & .or.itype(i).eq.ntyp1) cycle
+ iti=itortyp_kcc(itype(i-1))
+ sinthet=dsin(theta(i)/2.0d0)
+ costhet=dcos(theta(i)/2.0d0)
+ do j=1,nbend_kcc_Tb(iti)
+ thybt1(j)=v1bend_chyb(j,iti)
+ enddo
+ sumth1thyb=tschebyshev
+ & (1,nbend_kcc_Tb(iti),thybt1(1),costhet)
+ ihelp=nbend_kcc_Tb(iti)-1
+ gradthybt1=gradtschebyshev
+ & (0,ihelp,thybt1(1),costhet)
+ etheta=etheta+sumth1thyb
+C print *,sumth1thyb,gradthybt1,sinthet*(-0.5d0)
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*
+ & gradthybt1*sinthet*(-0.5d0)
+ enddo
+ if (tormode.ne.2) then
+ ethetacnstr=0.0d0
+C print *,ithetaconstr_start,ithetaconstr_end,"TU"
+ do i=ithetaconstr_start,ithetaconstr_end
+ 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
+ if (energy_dec) then
+ write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc",
+ & i,itheta,rad2deg*thetiii,
+ & rad2deg*theta_constr0(i), rad2deg*theta_drange(i),
+ & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4,
+ & gloc(itheta+nphi-2,icg)
+ endif
+ enddo
+ endif
+ return
+ end
c------------------------------------------------------------------------------
subroutine eback_sc_corr(esccor)
c 7/21/2007 Correlations between the backbone-local and side-chain-local
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,
enddo
return
end
+C--------------------------------------------------------------------------
+ double precision function tschebyshev(m,n,x,y)
+ implicit none
+ include "DIMENSIONS"
+ integer i,m,n
+ double precision x(n),y,yy(0:maxvar),aux
+c Tschebyshev polynomial. Note that the first term is omitted
+c m=0: the constant term is included
+c m=1: the constant term is not included
+ yy(0)=1.0d0
+ yy(1)=y
+ do i=2,n
+ yy(i)=2*yy(1)*yy(i-1)-yy(i-2)
+ enddo
+ aux=0.0d0
+ do i=m,n
+ aux=aux+x(i)*yy(i)
+ enddo
+ tschebyshev=aux
+ return
+ end
+C--------------------------------------------------------------------------
+ double precision function gradtschebyshev(m,n,x,y)
+ implicit none
+ include "DIMENSIONS"
+ integer i,m,n
+ double precision x(n+1),y,yy(0:maxvar),aux
+c Tschebyshev polynomial. Note that the first term is omitted
+c m=0: the constant term is included
+c m=1: the constant term is not included
+ yy(0)=1.0d0
+ yy(1)=2.0d0*y
+ do i=2,n
+ yy(i)=2*y*yy(i-1)-yy(i-2)
+ enddo
+ aux=0.0d0
+ do i=m,n
+ aux=aux+x(i+1)*yy(i)*(i+1)
+C print *, x(i+1),yy(i),i
+ enddo
+ gradtschebyshev=aux
+ 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
+ & *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)))
+ & )*div77_81
+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)))
+ & )*div77_81
+
+ 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)
+ & ))
+ & *div77_81
+ 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
projects / unres.git / blobdiff