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Peptide-Peptide interactions in the Liwo united residue model.

Peptide-Peptide interactions in the Liwo united residue model. Ref. A: Calculation of protein backbone geometry from α -carbon coordinates based on peptide-group dipole alignment, A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, and H.A. Scheraga, Protein Science 2, 1697-1714 (1993).

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Peptide-Peptide interactions in the Liwo united residue model.

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  1. Peptide-Peptide interactions in the Liwo united residue model. Ref. A: Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment, A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, and H.A. Scheraga, Protein Science 2, 1697-1714 (1993). Ref. B: Prediction of protein conformation on the basis of a search for compact structures: Test of avian pancreatic polypeptide, M.R. Pincus, R.J. Wawak, S. Rackovsky, and H.A. Scheraga, Protein Science 2, 1615-1731 (1993).

  2. Ref. A, Fig. 1.

  3. Subroutine of energy_p_new.F C-------------------------------------------------------------------------- subroutine eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4) . . ees=0.0D0 evdw1=0.0D0 eel_loc=0.0d0 eello_turn3=0.0d0 eello_turn4=0.0d0 ind=0 do i=1,nres num_cont_hb(i)=0 enddo do i=1,nres gel_loc_loc(i)=0.0d0 gcorr_loc(i)=0.0d0 enddo do i=iatel_s,iatel_e  The Calpha_i loop. dxi=dc(1,i)  dc = Ri+1-Ri dyi=dc(2,i) dzi=dc(3,i)

  4. dx_normi=dc_norm(1,i)  dc_norm is thee unit vector V which is ri+1- ri. dy_normi=dc_norm(2,i) dz_normi=dc_norm(3,i) xmedi=c(1,i)+0.5d0*dxi  The p-site ri+1/2(ri+1-ri) ymedi=c(2,i)+0.5d0*dyi zmedi=c(3,i)+0.5d0*dzi num_conti=0 c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) do j=ielstart(i),ielend(i)  The loop over calpha J ind=ind+1 iteli=itel(i) itelj=itel(j) if (j.eq.i+2 .and. itelj.eq.2) iteli=2 aaa=app(iteli,itelj)  The LJ constant for 1/r**12 bbb=bpp(iteli,itelj)  van der Waals for 1/r**6 C Diagnostics only!!! c aaa=0.0D0 c bbb=0.0D0 c ael6i=0.0D0 c ael3i=0.0D0 C End diagnostics ael6i=ael6(iteli,itelj)  The dipole electric constant for the 1/r**6 ael3i=ael3(iteli,itelj)  ditto for the 1/r**3

  5. dxj=dc(1,j) dyj=dc(2,j) dzj=dc(3,j) dx_normj=dc_norm(1,j) dy_normj=dc_norm(2,j) dz_normj=dc_norm(3,j) xj=c(1,j)+0.5D0*dxj-xmedi  x component of rij yj=c(2,j)+0.5D0*dyj-ymedi zj=c(3,j)+0.5D0*dzj-zmedi rij=xj*xj+yj*yj+zj*zj  |rij|^2 rrmij=1.0D0/rij rij=dsqrt(rij) rmij=1.0D0/rij r3ij=rrmij*rmij  1/r**3 r6ij=r3ij*r3ij  1/r**6 Next is cosalpha, cosbeta, cosgamma cosa=dx_normi*dx_normj+dy_normi*dy_normj+dz_normi*dz_normj cosb=(xj*dx_normi+yj*dy_normi+zj*dz_normi)*rmij cosg=(xj*dx_normj+yj*dy_normj+zj*dz_normj)*rmij fac=cosa-3.0D0*cosb*cosg ev1=aaa*r6ij*r6ij c 4/26/02 - AL scaling down 1,4 repulsive VDW interactions if (j.eq.i+2) ev1=scal_el*ev1

  6. ev2=bbb*r6ij fac3=ael6i*r6ij fac4=ael3i*r3ij evdwij=ev1+ev2 el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)) el2=fac4*fac eesij=el1+el2 C 12/26/95 - for the evaluation of multi-body H-bonding interactions THIS IS THE SCARY PART. ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg) ees=ees+eesij evdw1=evdw1+evdwij cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)') cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i, cd & 1.0D0/dsqrt(rrmij),evdwij,eesij, cd & xmedi,ymedi,zmedi,xj,yj,zj if (energy_dec) then write (iout,'(a6,2i,0pf7.3)') 'evdw1',i,j,evdwij write (iout,'(a6,2i,0pf7.3)') 'ees',i,j,eesij endif C C Calculate contributions to the Cartesian gradient.

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