From 5ff7ad0bbfd2c60edf49b10b9f9e6f81ff42a1e2 Mon Sep 17 00:00:00 2001 From: Adam Kazimierz Sieradzan Date: Fri, 28 Jun 2013 14:12:54 -0400 Subject: [PATCH] Just few comments added to WHAM to clarify --- source/wham/src/energy_p_new.F | 8 ++++++++ source/wham/src/molread_zs.F | 4 ++++ source/wham/src/parmread.F | 2 +- source/wham/src/readrtns.F | 4 +++- 4 files changed, 16 insertions(+), 2 deletions(-) diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F index 9e0b2c5..d857079 100644 --- 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 --- 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 --- 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 --- 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 -- 1.7.9.5