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integer modecalc,iscode,indpdb,indback,indphi,iranconf,icheckgrad,
- & inprint,i2ndstr,mucadyn,constr_dist,symetr,AFMlog,selfguide
+ & inprint,i2ndstr,mucadyn,constr_dist,symetr,AFMlog,selfguide,
+ & shield_mode
logical minim,refstr,pdbref,outpdb,outmol2,overlapsc,energy_dec,
& sideadd,lsecondary,read_cart,unres_pdb,
& vdisulf,searchsc,lmuca,dccart,extconf,out1file,
& icheckgrad,minim,i2ndstr,refstr,pdbref,outpdb,outmol2,iprint,
& overlapsc,energy_dec,sideadd,lsecondary,read_cart,unres_pdb
& ,vdisulf,searchsc,lmuca,dccart,mucadyn,extconf,out1file,
- & selfguide,AFMlog,
+ & selfguide,AFMlog,shield_mode,
& constr_dist,gnorm_check,gradout,split_ene,with_theta_constr,
& symetr
C... minim = .true. means DO minimization.
--- /dev/null
+ double precision VSolvSphere,VSolvSphere_div,long_r_sidechain,
+ & short_r_sidechain,fac_shield
+ integer ishield_list,shield_list
+ common /shield/ VSolvSphere,VSolvSphere_div,
+ & long_r_sidechain(ntyp),
+ & short_r_sidechain(ntyp),fac_shield(maxres),
+ & ishield_list(maxres),shield_list(maxres)
+
+
C the shielding factor is set this factor is describing how each
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
+ write (iout,*) "shield_mode",shield_mode
if (shield_mode.gt.0) then
call set_shield_fac
endif
include 'COMMON.FFIELD'
include 'COMMON.TIME1'
include 'COMMON.SPLITELE'
+ 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),
eesij=(el1+el2)
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
+ ees=ees+eesij*fac_shield(i)*fac_shield(j)
+ else
ees=ees+eesij
+ endif
evdw1=evdw1+evdwij*sss
cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
C print *,'AFM',Eafmforce,totTafm*velAFMconst,dist
return
end
+C-----------------------------------------------------------
+C first for shielding is setting of function of side-chains
+ 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/
+
+C the vector between center of side_chain and peptide group
+ double precision pep_side(3),long,side_calf(3),
+ &pept_group(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
+ 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(k+nres,j)-(c(i,j)+c(i+1,j))/2.0d0
+C and vector conecting the side-chain with its proper calfa
+ side_calf(j)=c(k+nres,j)-c(k,j)
+ pept_group(j)=c(i,j)-c(i+1,j)
+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)
+C now sscale fraction
+ sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield
+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)=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*(scale_fac_dist-scale_fac_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)
+ 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+short**2/dist_pep_side**2)
+C now costhet_grad
+ costhet_fac=costhet**3*short**2*(-0.5)/dist_pep_side
+ 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
+ fac_alfa_sin=1.0-(pep_side0pept_group/
+ & (dist_pep_side*dist_side_calf))**2
+ fac_alfa_sin=dsqrt(fac_alfa_sin)
+ rkprim=fac_alfa_sin*(long-short)+short
+ cosphi=1.0d0/dsqrt(1+rkprim**2/dist_pep_side**2)
+ VofOverlap=VSolvSphere/2.0d0*(1.0-costhet)*(1.0-cosphi)
+ & /VSolvSphere_div
+ VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
+C if ((cosphi.le.0.0).or.(costhet.le.0.0)) write(iout,*) "ERROR",
+C & cosphi,costhet
+C now should be fac_side_grad(k) which will be gradient of factor k which also
+C affect the gradient of peptide group i fac_pept_grad(i) and i+1
+ write(2,*) "myvolume",VofOverlap,VSolvSphere_div,VolumeTotal
+ enddo
+C write(2,*) "TOTAL VOLUME",i,VolumeTotal
+C the scaling factor of the shielding effect
+ fac_shield(i)=VolumeTotal*div77_81+div4_81
+ write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i)
+ enddo
+ return
+ end
include 'COMMON.SBRIDGE'
include 'COMMON.MD'
include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
character*1 t1,t2,t3
character*1 onelett(4) /"G","A","P","D"/
character*1 toronelet(-2:2) /"p","a","G","A","P"/
c B2(2,i) = b(4)
c B2(1,-i) =b(2)
c B2(2,-i) =-b(4)
- B1tilde(1,i) = b(3)
- B1tilde(2,i) =-b(5)
- B1tilde(1,-i) =-b(3)
- B1tilde(2,-i) =b(5)
+ B1tilde(1,i) = b(3,i)
+ B1tilde(2,i) =-b(5,i)
+ B1tilde(1,-i) =-b(3,i)
+ B1tilde(2,-i) =b(5,i)
b1tilde(1,i)=0.0d0
b1tilde(2,i)=0.0d0
- B2(1,i) = b(2)
- B2(2,i) = b(4)
- B2(1,-i) =b(2)
- B2(2,-i) =-b(4)
+ B2(1,i) = b(2,i)
+ B2(2,i) = b(4,i)
+ B2(1,-i) =b(2,i)
+ B2(2,-i) =-b(4,i)
c b2(1,i)=0.0d0
c b2(2,i)=0.0d0
C write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
C & ' v3ss:',v3ss
C endif
+C set the variables used for shielding effect
+C write (iout,*) "SHIELD MODE",shield_mode
+C if (shield_mode.gt.0) then
+C VSolvSphere the volume of solving sphere
+C 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
+C VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+C VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+C write (iout,*) VSolvSphere,VSolvSphere_div
+C long axis of side chain
+C do i=1,ntyp
+C long_r_sidechain(i)=vbldsc0(1,i)
+C short_r_sidechain(i)=sigma0(i)
+C enddo
+C lets set the buffor value
+C buff_shield=1.0d0
+C endif
return
111 write (iout,*) "Error reading bending energy parameters."
goto 999
#else
call getenv(var,val)
#endif
-
+C set the variables used for shielding effect
+C if (shield_mode.gt.0) then
+C VSolvSphere the volume of solving sphere
+C 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
+C VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+C VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+C long axis of side chain
+C do i=1,ntyp
+C long_r_sidechain(i)=vbldsc0(1,i)
+C short_r_sidechain(i)=sigma0(i)
+C enddo
+C lets set the buffor value
+C buff_shield=1.0d0
+C endif
return
end
include 'COMMON.INTERACT'
include 'COMMON.SETUP'
include 'COMMON.SPLITELE'
+ include 'COMMON.SHIELD'
COMMON /MACHSW/ KDIAG,ICORFL,IXDR
character*8 diagmeth(0:3) /'Library','EVVRSP','Givens','Jacobi'/
character*80 ucase
selfguide=(index(controlcard,'SELFGUIDE'))
print *,'AFMlog',AFMlog,selfguide,"KUPA"
call readi(controlcard,'IPRINT',iprint,0)
+C SHIELD keyword sets if the shielding effect of side-chains is used
+C 0 denots no shielding is used all peptide are equally despite the
+C solvent accesible area
+C 1 the newly introduced function
+C 2 reseved for further possible developement
+ call readi(controlcard,'SHIELD',shield_mode,0)
+C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "shield_mode",shield_mode
+C endif
call readi(controlcard,'MAXGEN',maxgen,10000)
call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
call readi(controlcard,"KDIAG",kdiag,0)
write(iout,*) "bordlipbot=",bordlipbot
write(iout,*) "bufliptop=",bufliptop
write(iout,*) "buflipbot=",buflipbot
-
-
+ write (iout,*) "SHIELD MODE",shield_mode
+ if (shield_mode.gt.0) then
+ pi=3.141592d0
+C VSolvSphere the volume of solving sphere
+C 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
+ 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)
+ enddo
+ endif
if (me.eq.king .or. .not.out1file )
& write (iout,*) "DISTCHAINMAX",distchainmax
c defined by atoms (i2), (i3), and (i4). The x axis is the axis from
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include "COMMON.CHAIN"
c this subroutine calculates unity vectors of a local reference system
c defined by atoms (i2), (i3), and (i4). the x axis is the axis from
c atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
logical fail
double precision e1(3),e2(3),e3(3)
double precision u(3),z(3)
- include 'COMMON.IOUNITS'
double precision coinc/1.0D-13/,align /1.0D-13/
c print *,'just initialize'
fail=.false.
projects / unres.git / commitdiff