X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fparmread.F;h=ae4d7100649e77a67a91f6cbbbd1a447c41b7bbc;hb=7308760ff07636ef6b1ee28d8c3a67a23c14b34b;hp=1102c8966bec88ddde2e02559c7797043383a0f0;hpb=d101c97dea752458d76055fdbae49c26fff03c1f;p=unres.git

diff --git a/source/unres/src_MD-M/parmread.F b/source/unres/src_MD-M/parmread.F
index 1102c89..ae4d710 100644
--- a/source/unres/src_MD-M/parmread.F
+++ b/source/unres/src_MD-M/parmread.F
@@ -26,6 +26,8 @@ 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"/
@@ -945,16 +947,16 @@ 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)
-        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)
+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)
-        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)
+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
@@ -1128,11 +1130,12 @@ C---------------------- GB or BP potential -----------------------------
 C now we start reading lipid
       do i=1,ntyp
        read (isidep,*,end=1161,err=1161)(epslip(i,j),j=i,ntyp)
-       print *,"WARNING!!"
-       do j=1,ntyp
-       epslip(i,j)=epslip(i,j)+0.05d0
-       enddo
+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
@@ -1333,6 +1336,25 @@ 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
@@ -1404,6 +1426,22 @@ 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