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Just few comments added to WHAM to clarify
author
Adam Kazimierz Sieradzan
<adasko@sun1.chem.univ.gda.pl>
Fri, 28 Jun 2013 18:12:54 +0000
(14:12 -0400)
committer
Adam Kazimierz Sieradzan
<adasko@sun1.chem.univ.gda.pl>
Fri, 28 Jun 2013 18:12:54 +0000
(14:12 -0400)
source/wham/src/energy_p_new.F
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source/wham/src/molread_zs.F
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source/wham/src/parmread.F
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source/wham/src/readrtns.F
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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)
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
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)
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'
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
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
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)
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.
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
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
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)
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)
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
call flush(iout)
return
end