Just few comments added to WHAM to clarify

diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F
index 9e0b2c5..d857079 100644 (file)
--- a/source/wham/src/energy_p_new.F
+++ b/source/wham/src/energy_p_new.F
@@ -803,8 +803,16 @@ C
         do iint=1,nint_gr(i)
           do j=istart(i,iint),iend(i,iint)
 C in case of diagnostics    write (iout,*) "TU SZUKAJ",i,j,dyn_ss_mask(i),dyn_ss_mask(j)
+C /06/28/2013 Adasko: In case of dyn_ss - dynamic disulfide bond
+C formation no electrostatic interactions should be calculated. If it
+C would be allowed NaN would appear
             IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+C /06/28/2013 Adasko: dyn_ss_mask is logical statement wheather this Cys
+C residue can or cannot form disulfide bond. There is still bug allowing
+C Cys...Cys...Cys bond formation
               call dyn_ssbond_ene(i,j,evdwij)
+C /06/28/2013 Adasko: dyn_ssbond_ene is dynamic SS bond foration energy
+C function in ssMD.F
               evdw=evdw+evdwij
 c              if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
 c     &                        'evdw',i,j,evdwij,' ss'

diff --git a/source/wham/src/molread_zs.F b/source/wham/src/molread_zs.F
index a7166b7..6e0727f 100644 (file)
--- a/source/wham/src/molread_zs.F
+++ b/source/wham/src/molread_zs.F
@@ -205,7 +205,10 @@ C bridging residues.
       endif
       endif
       if (ns.gt.0.and.dyn_ss) then
+C /06/28/2013 Adasko:ns is number of Cysteins bonded also called half of
+C the bond
           do i=nss+1,nhpb
+C /06/28/2013 Adasko: nss number of full SS bonds
             ihpb(i-nss)=ihpb(i)
             jhpb(i-nss)=jhpb(i)
             forcon(i-nss)=forcon(i)
@@ -216,6 +219,7 @@ C bridging residues.
           call hpb_partition
           do i=1,ns
             dyn_ss_mask(iss(i))=.true.
+C /06/28/2013 Adasko: dyn_ss_mask which Cysteins can form disulfidebond
 c          write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU"
           enddo
       endif

diff --git a/source/wham/src/parmread.F b/source/wham/src/parmread.F
index 36730f5..435ee09 100644 (file)
--- a/source/wham/src/parmread.F
+++ b/source/wham/src/parmread.F
@@ -892,7 +892,7 @@ c           augm(i,j)=0.5D0**(2*expon)*aa(i,j)
         enddo
       enddo
 C
-C Define the SC-p interaction constants
+C Define the SC-p interaction constants and SS bond potentials
 C
       if (dyn_ss) then
         ss_depth=ebr/wsc-0.25*eps(1,1)

diff --git a/source/wham/src/readrtns.F b/source/wham/src/readrtns.F
index 3f03553..9fa6137 100644 (file)
--- a/source/wham/src/readrtns.F
+++ b/source/wham/src/readrtns.F
@@ -96,7 +96,9 @@
       refstr = index(controlcard,'REFSTR').gt.0
       pdbref = index(controlcard,'PDBREF').gt.0
       dyn_ss=(index(controlcard,'DYN_SS').gt.0)
-c      write (iout,*) "CHUJ Z PIZDA", dyn_ss
+C /06/28/2013 Adasko: dyn_ss is keyword allowing to break and create bond
+C disulfide bond. Note that in conterary to dynamics this in
+C CONTROLCARD. The bond are read in molread_zs.F 
       call flush(iout)
       return
       end