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"/
logical lprint,LaTeX
dimension blower(3,3,maxlob)
- dimension b(13)
+C dimension b(13)
character*3 lancuch,ucase
C
C For printing parameters after they are read set the following in the UNRES
#else
read (ibond,*) junk,vbldp0,vbldpdum,akp,rjunk,mp,ip,pstok
do i=1,ntyp
+ print *,i
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),
& j=1,nbondterm(i)),msc(i),isc(i),restok(i)
dsc(i) = vbldsc0(1,i)
write (iout,*) "Coefficients of the cumulants"
endif
read (ifourier,*) nloctyp
+
do i=0,nloctyp-1
read (ifourier,*,end=115,err=115)
- read (ifourier,*,end=115,err=115) (b(ii),ii=1,13)
+ read (ifourier,*,end=115,err=115) (b(ii,i),ii=1,13)
+#ifdef NEWCORR
+ read (ifourier,*,end=115,err=115) (bnew1(ii,1,i),ii=1,3)
+ read (ifourier,*,end=115,err=115) (bnew2(ii,1,i),ii=1,3)
+ read (ifourier,*,end=115,err=115) (bnew1(ii,2,i),ii=1,1)
+ read (ifourier,*,end=115,err=115) (bnew2(ii,2,i),ii=1,1)
+ read (ifourier,*,end=115,err=115) (eenew(ii,i),ii=1,1)
+#endif
if (lprint) then
write (iout,*) 'Type',i
- write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii),ii=1,13)
+ write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
endif
- B1(1,i) = b(3)
- B1(2,i) = b(5)
- B1(1,-i) = b(3)
- B1(2,-i) = -b(5)
+c B1(1,i) = b(3)
+c B1(2,i) = b(5)
+c B1(1,-i) = b(3)
+c B1(2,-i) = -b(5)
c b1(1,i)=0.0d0
c b1(2,i)=0.0d0
- B1tilde(1,i) = b(3)
- B1tilde(2,i) =-b(5)
- B1tilde(1,-i) =-b(3)
- B1tilde(2,-i) =b(5)
+c B1tilde(1,i) = b(3)
+c B1tilde(2,i) =-b(5)
+c B1tilde(1,-i) =-b(3)
+c B1tilde(2,-i) =b(5)
c b1tilde(1,i)=0.0d0
c 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)
+c B2(1,i) = b(2)
+c B2(2,i) = b(4)
+c B2(1,-i) =b(2)
+c B2(2,-i) =-b(4)
+ B1tilde(1,i) = b(3,i)
+ B1tilde(2,i) =-b(5,i)
+C B1tilde(1,-i) =-b(3,i)
+C B1tilde(2,-i) =b(5,i)
+ b1tilde(1,i)=0.0d0
+ b1tilde(2,i)=0.0d0
+ B2(1,i) = b(2,i)
+ B2(2,i) = b(4,i)
+C B2(1,-i) =b(2,i)
+C B2(2,-i) =-b(4,i)
c b2(1,i)=0.0d0
c b2(2,i)=0.0d0
- CC(1,1,i)= b(7)
- CC(2,2,i)=-b(7)
- CC(2,1,i)= b(9)
- CC(1,2,i)= b(9)
- CC(1,1,-i)= b(7)
- CC(2,2,-i)=-b(7)
- CC(2,1,-i)=-b(9)
- CC(1,2,-i)=-b(9)
+ CC(1,1,i)= b(7,i)
+ CC(2,2,i)=-b(7,i)
+ CC(2,1,i)= b(9,i)
+ CC(1,2,i)= b(9,i)
+ CC(1,1,-i)= b(7,i)
+ CC(2,2,-i)=-b(7,i)
+ CC(2,1,-i)=-b(9,i)
+ CC(1,2,-i)=-b(9,i)
c CC(1,1,i)=0.0d0
c CC(2,2,i)=0.0d0
c CC(2,1,i)=0.0d0
c CC(1,2,i)=0.0d0
- Ctilde(1,1,i)=b(7)
- Ctilde(1,2,i)=b(9)
- Ctilde(2,1,i)=-b(9)
- Ctilde(2,2,i)=b(7)
- Ctilde(1,1,-i)=b(7)
- Ctilde(1,2,-i)=-b(9)
- Ctilde(2,1,-i)=b(9)
- Ctilde(2,2,-i)=b(7)
+ Ctilde(1,1,i)=b(7,i)
+ Ctilde(1,2,i)=b(9,i)
+ Ctilde(2,1,i)=-b(9,i)
+ Ctilde(2,2,i)=b(7,i)
+ Ctilde(1,1,-i)=b(7,i)
+ Ctilde(1,2,-i)=-b(9,i)
+ Ctilde(2,1,-i)=b(9,i)
+ Ctilde(2,2,-i)=b(7,i)
c Ctilde(1,1,i)=0.0d0
c Ctilde(1,2,i)=0.0d0
c Ctilde(2,1,i)=0.0d0
c Ctilde(2,2,i)=0.0d0
- DD(1,1,i)= b(6)
- DD(2,2,i)=-b(6)
- DD(2,1,i)= b(8)
- DD(1,2,i)= b(8)
- DD(1,1,-i)= b(6)
- DD(2,2,-i)=-b(6)
- DD(2,1,-i)=-b(8)
- DD(1,2,-i)=-b(8)
+ DD(1,1,i)= b(6,i)
+ DD(2,2,i)=-b(6,i)
+ DD(2,1,i)= b(8,i)
+ DD(1,2,i)= b(8,i)
+ DD(1,1,-i)= b(6,i)
+ DD(2,2,-i)=-b(6,i)
+ DD(2,1,-i)=-b(8,i)
+ DD(1,2,-i)=-b(8,i)
c DD(1,1,i)=0.0d0
c DD(2,2,i)=0.0d0
c DD(2,1,i)=0.0d0
c DD(1,2,i)=0.0d0
- Dtilde(1,1,i)=b(6)
- Dtilde(1,2,i)=b(8)
- Dtilde(2,1,i)=-b(8)
- Dtilde(2,2,i)=b(6)
- Dtilde(1,1,-i)=b(6)
- Dtilde(1,2,-i)=-b(8)
- Dtilde(2,1,-i)=b(8)
- Dtilde(2,2,-i)=b(6)
+ Dtilde(1,1,i)=b(6,i)
+ Dtilde(1,2,i)=b(8,i)
+ Dtilde(2,1,i)=-b(8,i)
+ Dtilde(2,2,i)=b(6,i)
+ Dtilde(1,1,-i)=b(6,i)
+ Dtilde(1,2,-i)=-b(8,i)
+ Dtilde(2,1,-i)=b(8,i)
+ Dtilde(2,2,-i)=b(6,i)
c Dtilde(1,1,i)=0.0d0
c Dtilde(1,2,i)=0.0d0
c Dtilde(2,1,i)=0.0d0
c Dtilde(2,2,i)=0.0d0
- EE(1,1,i)= b(10)+b(11)
- EE(2,2,i)=-b(10)+b(11)
- EE(2,1,i)= b(12)-b(13)
- EE(1,2,i)= b(12)+b(13)
- EE(1,1,-i)= b(10)+b(11)
- EE(2,2,-i)=-b(10)+b(11)
- EE(2,1,-i)=-b(12)+b(13)
- EE(1,2,-i)=-b(12)-b(13)
-
+ EEold(1,1,i)= b(10,i)+b(11,i)
+ EEold(2,2,i)=-b(10,i)+b(11,i)
+ EEold(2,1,i)= b(12,i)-b(13,i)
+ EEold(1,2,i)= b(12,i)+b(13,i)
+ EEold(1,1,-i)= b(10,i)+b(11,i)
+ EEold(2,2,-i)=-b(10,i)+b(11,i)
+ EEold(2,1,-i)=-b(12,i)+b(13,i)
+ EEold(1,2,-i)=-b(12,i)-b(13,i)
+ write(iout,*) "TU DOCHODZE"
+ print *,"JESTEM"
c ee(1,1,i)=1.0d0
c ee(2,2,i)=1.0d0
c ee(2,1,i)=0.0d0
c ee(1,2,i)=0.0d0
c ee(2,1,i)=ee(1,2,i)
enddo
+c lprint=.true.
if (lprint) then
do i=1,nloctyp
write (iout,*) 'Type',i
enddo
write(iout,*) 'EE'
do j=1,2
- write (iout,'(2f10.5)') EE(j,1,i),EE(j,2,i)
+ write (iout,'(2f10.5)') EEold(j,1,i),EEold(j,2,i)
enddo
enddo
endif
+c lprint=.false.
C
C Read electrostatic-interaction parameters
& ', exponents are ',expon,2*expon
goto (10,20,30,30,40) ipot
C----------------------- LJ potential ---------------------------------
- 10 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ 10 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),
& (sigma0(i),i=1,ntyp)
if (lprint) then
write (iout,'(/a/)') 'Parameters of the LJ potential:'
endif
goto 50
C----------------------- LJK potential --------------------------------
- 20 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ 20 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),
& (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp)
if (lprint) then
write (iout,'(/a/)') 'Parameters of the LJK potential:'
goto 50
C---------------------- GB or BP potential -----------------------------
30 do i=1,ntyp
- read (isidep,*,end=116,err=116)(eps(i,j),j=i,ntyp)
+ read (isidep,*,end=117,err=117)(eps(i,j),j=i,ntyp)
enddo
read (isidep,*,end=116,err=116)(sigma0(i),i=1,ntyp)
read (isidep,*,end=116,err=116)(sigii(i),i=1,ntyp)
read (isidep,*,end=116,err=116)(chip(i),i=1,ntyp)
read (isidep,*,end=116,err=116)(alp(i),i=1,ntyp)
+C now we start reading lipid
+ do i=1,ntyp
+ read (isidep,*,end=1161,err=1161)(epslip(i,j),j=i,ntyp)
+C print *,"WARNING!!"
+C do j=1,ntyp
+C epslip(i,j)=epslip(i,j)+0.05d0
+C enddo
+ enddo
+ write(iout,*) epslip(1,1),"OK?"
C For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
endif
goto 50
C--------------------- GBV potential -----------------------------------
- 40 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ 40 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),
& (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp),(sigii(i),i=1,ntyp),
& (chip(i),i=1,ntyp),(alp(i),i=1,ntyp)
if (lprint) then
do i=2,ntyp
do j=1,i-1
eps(i,j)=eps(j,i)
+ epslip(i,j)=epslip(j,i)
enddo
enddo
do i=1,ntyp
epsij=eps(i,j)
sigeps=dsign(1.0D0,epsij)
epsij=dabs(epsij)
- aa(i,j)=epsij*rrij*rrij
- bb(i,j)=-sigeps*epsij*rrij
- aa(j,i)=aa(i,j)
- bb(j,i)=bb(i,j)
+ aa_aq(i,j)=epsij*rrij*rrij
+ bb_aq(i,j)=-sigeps*epsij*rrij
+ aa_aq(j,i)=aa_aq(i,j)
+ bb_aq(j,i)=bb_aq(i,j)
+ epsijlip=epslip(i,j)
+ sigeps=dsign(1.0D0,epsijlip)
+ epsijlip=dabs(epsijlip)
+ aa_lip(i,j)=epsijlip*rrij*rrij
+ bb_lip(i,j)=-sigeps*epsijlip*rrij
+ aa_lip(j,i)=aa_lip(i,j)
+ bb_lip(j,i)=bb_lip(i,j)
if (ipot.gt.2) then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
endif
if (lprint) then
write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))')
- & restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),
+ & restyp(i),restyp(j),aa_aq(i,j),bb_aq(i,j),augm(i,j),
& sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
endif
enddo
C
C Define the constants of the disulfide bridge
C
- ebr=-5.50D0
+C ebr=-12.00D0
c
c Old arbitrary potential - commented out.
c
c energy surface of diethyl disulfide.
c A. Liwo and U. Kozlowska, 11/24/03
c
- D0CM = 3.78d0
- AKCM = 15.1d0
- AKTH = 11.0d0
- AKCT = 12.0d0
- V1SS =-1.08d0
- V2SS = 7.61d0
- V3SS = 13.7d0
+C D0CM = 3.78d0
+C AKCM = 15.1d0
+C AKTH = 11.0d0
+C AKCT = 12.0d0
+C V1SS =-1.08d0
+C V2SS = 7.61d0
+C V3SS = 13.7d0
c akcm=0.0d0
c akth=0.0d0
c akct=0.0d0
c v2ss=0.0d0
c v3ss=0.0d0
- if(me.eq.king) then
- write (iout,'(/a)') "Disulfide bridge parameters:"
- write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
- write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
- write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
- write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
- & ' v3ss:',v3ss
- endif
+C if(me.eq.king) then
+C write (iout,'(/a)') "Disulfide bridge parameters:"
+C write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
+C write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
+C write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
+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
goto 999
116 write (iout,*) "Error reading electrostatic energy parameters."
goto 999
+ 1161 write (iout,*) "Error reading electrostatic energy parameters.Lip"
+ goto 999
117 write (iout,*) "Error reading side chain interaction parameters."
goto 999
118 write (iout,*) "Error reading SCp interaction parameters."
#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
projects / unres.git / blobdiff