X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fparmread.F;h=e96dfc3574236bc324dbef1e5227620bd2032000;hb=00ff2d632b212c4d4a388e8f7f5394763b65e3bb;hp=154fcf473db22952633ceaf14d5e62ba06cdfa4d;hpb=3e2116f1c3c9f9db1f8f34ea327e064df9345d67;p=unres.git diff --git a/source/unres/src_MD-M/parmread.F b/source/unres/src_MD-M/parmread.F index 154fcf4..e96dfc3 100644 --- a/source/unres/src_MD-M/parmread.F +++ b/source/unres/src_MD-M/parmread.F @@ -26,12 +26,14 @@ C 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 @@ -59,7 +61,7 @@ c Read the virtual-bond parameters, masses, and moments of inertia c and Stokes' radii of the peptide group and side chains c #ifdef CRYST_BOND - read (ibond,*) vbldp0,akp,mp,ip,pstok + read (ibond,*) vbldp0,vbldpdum,akp,mp,ip,pstok do i=1,ntyp nbondterm(i)=1 read (ibond,*) vbldsc0(1,i),aksc(1,i),msc(i),isc(i),restok(i) @@ -71,8 +73,9 @@ c endif enddo #else - read (ibond,*) junk,vbldp0,akp,rjunk,mp,ip,pstok + 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) @@ -97,6 +100,14 @@ c enddo enddo endif +C reading lipid parameters + write (iout,*) "iliptranpar",iliptranpar + call flush(iout) + read(iliptranpar,*) pepliptran + do i=1,ntyp + read(iliptranpar,*) liptranene(i) + enddo + close(iliptranpar) #ifdef CRYST_THETA C C Read the parameters of the probability distribution/energy expression @@ -210,6 +221,8 @@ C Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203 C read (ithep,*,err=111,end=111) nthetyp,ntheterm,ntheterm2, & ntheterm3,nsingle,ndouble + write (iout,*) "ithep",ithep + call flush(iout) nntheterm=max0(ntheterm,ntheterm2,ntheterm3) read (ithep,*,err=111,end=111) (ithetyp(i),i=1,ntyp1) do i=-ntyp1,-1 @@ -352,11 +365,12 @@ C Control printout of the coefficients of virtual-bond-angle potentials C if (lprint) then write (iout,'(//a)') 'Parameter of virtual-bond-angle potential' - do i=1,nthetyp+1 - do j=1,nthetyp+1 - do k=1,nthetyp+1 + do iblock=1,2 + do i=0,nthetyp + do j=-nthetyp,nthetyp + do k=-nthetyp,nthetyp write (iout,'(//4a)') - & 'Type ',onelett(i),onelett(j),onelett(k) + & 'Type ',toronelet(i),toronelet(j),toronelet(k) write (iout,'(//a,10x,a)') " l","a[l]" write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k,iblock) write (iout,'(i2,1pe15.5)') @@ -385,16 +399,19 @@ C enddo enddo enddo + enddo enddo call flush(iout) endif - write (2,*) "Start reading THETA_PDB" + write (2,*) "Start reading THETA_PDB",ithep_pdb do i=1,ntyp - read (ithep,*,err=111,end=111) a0thet(i),(athet(j,i,1,1),j=1,2), +c write (2,*) 'i=',i + read (ithep_pdb,*,err=111,end=111) + & a0thet(i),(athet(j,i,1,1),j=1,2), & (bthet(j,i,1,1),j=1,2) - read (ithep,*,err=111,end=111) (polthet(j,i),j=0,3) - read (ithep,*,err=111,end=111) (gthet(j,i),j=1,3) - read (ithep,*,err=111,end=111) theta0(i),sig0(i),sigc0(i) + read (ithep_pdb,*,err=111,end=111) (polthet(j,i),j=0,3) + read (ithep_pdb,*,err=111,end=111) (gthet(j,i),j=1,3) + read (ithep_pdb,*,err=111,end=111) theta0(i),sig0(i),sigc0(i) sigc0(i)=sigc0(i)**2 enddo do i=1,ntyp @@ -539,6 +556,7 @@ C C Read the parameters of the probability distribution/energy expression C of the side chains. C + write (2,*) "Start reading ROTAM_PDB" do i=1,ntyp read (irotam_pdb,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i) if (i.eq.10) then @@ -577,6 +595,7 @@ C endif enddo close (irotam_pdb) + write (2,*) "End reading ROTAM_PDB" #endif close(irotam) @@ -648,8 +667,9 @@ c &v2(k,-i,-j,iblock),v2(k,i,j,iblock) close (itorp) if (lprint) then write (iout,'(/a/)') 'Torsional constants:' - do i=1,ntortyp - do j=1,ntortyp + do iblock=1,2 + do i=0,ntortyp-1 + do j=-ntortyp+1,ntortyp-1 write (iout,*) 'ityp',i,' jtyp',j write (iout,*) 'Fourier constants' do k=1,nterm(i,j,iblock) @@ -663,6 +683,7 @@ c &v2(k,-i,-j,iblock),v2(k,i,j,iblock) enddo enddo enddo + enddo endif C @@ -762,6 +783,80 @@ C Martix of D parameters for two dimesional fourier series enddo endif #endif +C read Czybyshev torsional parameters + read (itorkcc,*,end=121,err=121) nkcctyp + read (itorkcc,*,end=121,err=121) (itortyp_kcc(i),i=1,ntyp) + do i=-ntyp,-1 + itortyp_kcc(i)=-itortyp_kcc(-i) + enddo + do i=0,nkcctyp + do j=0,nkcctyp +C first we read the cos and sin gamma parameters + read (itorkcc,*,end=121,err=121) + & nterm_kcc(j,i),nterm_kcc_Tb(j,i) +C read (itorkcc,*,end=121,err=121) nterm_kcc_Tb(j,i) + do k=1,nterm_kcc(j,i) + do l=1,nterm_kcc_Tb(j,i) + read (itorkcc,*,end=121,err=121) v11_chyb(l,k,j,i) + enddo + do l=1,nterm_kcc_Tb(j,i) + read (itorkcc,*,end=121,err=121) v21_chyb(l,k,j,i) + enddo + do l=1,nterm_kcc_Tb(j,i) + read (itorkcc,*,end=121,err=121) v12_chyb(l,k,j,i) + enddo + do l=1,nterm_kcc_Tb(j,i) + read (itorkcc,*,end=121,err=121) v22_chyb(l,k,j,i) + enddo + read (itorkcc,*,end=121,err=121) v1_kcc(k,j,i) + read (itorkcc,*,end=121,err=121) v2_kcc(k,j,i) + enddo + enddo + enddo + if (lprint) then +c Print valence-torsional parameters + write (iout,'(a)') + & "Parameters of the valence-torsional potentials" + do i=0,nkcctyp + do j=0,nkcctyp + write (iout,'(3a)') "Type ",toronelet(i),toronelet(j) + write (iout,'(2a20,a15)') "v_kcc","v1_chyb","v2_chyb" + do k=1,nterm_kcc(j,i) + write (iout,'(i5,f15.10,i5,2f15.10)') + & k,v1_kcc(k,j,i),1,v11_chyb(1,k,j,i),v21_chyb(1,k,j,i) + do l=2,nterm_kcc_Tb(j,i) + write (iout,'(20x,i5,2f15.10)') + & l,v11_chyb(l,k,j,i),v21_chyb(l,k,j,i) + enddo + write (iout,'(i5,f15.10,i5,2f15.10)') + & k,v2_kcc(k,j,i),1,v12_chyb(1,k,j,i),v22_chyb(1,k,j,i) + do l=2,nterm_kcc_Tb(j,i) + write (iout,'(20x,i5,2f15.10)') + & l,v12_chyb(l,k,j,i),v22_chyb(l,k,j,i) + enddo + write (iout,'(a)') + enddo + enddo + enddo + endif +C here will be the apropriate recalibrating for D-aminoacid +C read (ithetkcc,*,end=121,err=121) nkcctyp + do i=0,nkcctyp + read (ithetkcc,*,end=121,err=121) nbend_kcc_Tb(i) + do j=1,nbend_kcc_Tb(i) + read (ithetkcc,*,end=121,err=121) v1bend_chyb(j,i) + enddo + enddo + if (lprint) then + write (iout,'(a)') + & "Parameters of the valence-only potentials" + do i=0,nkcctyp + write (iout,'(2a)') "Type ",toronelet(i) + do k=1,nbend_kcc_Tb(i) + write(iout,'(i5,f15.10)') k,v1bend_chyb(k,i) + enddo + enddo + endif C Read of Side-chain backbone correlation parameters C Modified 11 May 2012 by Adasko CCC @@ -869,7 +964,7 @@ cc maxinter is maximum interaction sites v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/ &(1+vlor3sccor(k,i,j)**2) enddo - v0sccor(i,j,iblock)=v0ijsccor + v0sccor(l,i,j)=v0ijsccor enddo enddo enddo @@ -878,6 +973,7 @@ cc maxinter is maximum interaction sites #endif if (lprint) then write (iout,'(/a/)') 'Torsional constants:' + do l=1,maxinter do i=1,nsccortyp do j=1,nsccortyp write (iout,*) 'ityp',i,' jtyp',j @@ -892,6 +988,7 @@ cc maxinter is maximum interaction sites enddo enddo enddo + enddo endif C @@ -903,97 +1000,139 @@ C write (iout,*) "Coefficients of the cumulants" endif read (ifourier,*) nloctyp +#ifdef NEWCORR + read (ifourier,*,end=115,err=115) (itype2loc(i),i=1,ntyp) + read (ifourier,*,end=115,err=115) (iloctyp(i),i=0,nloctyp-1) + itype2loc(ntyp1)=nloctyp + iloctyp(nloctyp)=ntyp1 +#else + do i=1,ntyp1 + itype2loc(i)=itortyp(i) + enddo + iloctyp(0)=10 + iloctyp(1)=9 + iloctyp(2)=20 + iloctyp(3)=ntyp1 +#endif + do i=1,ntyp1 + itype2loc(-i)=-itype2loc(i) + enddo + do i=1,nloctyp + iloctyp(-i)=-iloctyp(i) + enddo + write (iout,*) "itype2loc",(itype2loc(i),i=1,ntyp1) + write (iout,*) "nloctyp",nloctyp, + & " iloctyp",(iloctyp(i),i=0,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) +cc B1tilde(1,i) = b(3,i) +cc B1tilde(2,i) =-b(5,i) +C B1tilde(1,-i) =-b(3,i) +C B1tilde(2,-i) =b(5,i) +cc b1tilde(1,i)=0.0d0 +cc b1tilde(2,i)=0.0d0 +cc B2(1,i) = b(2,i) +cc 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 @@ -1011,10 +1150,11 @@ c ee(2,1,i)=ee(1,2,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 @@ -1061,7 +1201,7 @@ C & ', 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:' @@ -1073,7 +1213,7 @@ C----------------------- 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:' @@ -1087,12 +1227,21 @@ C----------------------- 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 @@ -1111,7 +1260,7 @@ C For the GB potential convert sigma'**2 into chi' 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 @@ -1131,6 +1280,7 @@ C Calculate the "working" parameters of SC interactions. 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 @@ -1159,10 +1309,17 @@ C Calculate the "working" parameters of SC interactions. 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 @@ -1195,7 +1352,7 @@ c augm(i,j)=0.5D0**(2*expon)*aa(i,j) 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 @@ -1252,7 +1409,7 @@ c lprint=.false. 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 @@ -1263,13 +1420,13 @@ c Constants of the disulfide-bond potential determined based on the RHF/6-31G** 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 @@ -1277,14 +1434,33 @@ c v1ss=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 @@ -1299,11 +1475,15 @@ c v3ss=0.0d0 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." goto 999 119 write (iout,*) "Error reading SCCOR parameters" + go to 999 + 121 write (iout,*) "Error in Czybyshev parameters" 999 continue #ifdef MPI call MPI_Finalize(Ierror) @@ -1354,6 +1534,22 @@ c-HP- if(ierror.ne.0) stop '--error returned by pxfgetenv--' #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