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single chain correction of dihedral homology restraints phi(i+3)
author
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Wed, 8 Jun 2016 12:01:29 +0000
(14:01 +0200)
committer
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Wed, 8 Jun 2016 12:01:29 +0000
(14:01 +0200)
source/cluster/wham/src/energy_p_new.F
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source/cluster/wham/src/initialize_p.F
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source/cluster/wham/src/readrtns.F
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source/unres/src_MD/energy_p_new_barrier.F
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source/unres/src_MD/initialize_p.F
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source/unres/src_MD/readrtns.F
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source/wham/src/energy_p_new.F
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source/wham/src/initialize_p.F
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source/wham/src/molread_zs.F
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diff --git
a/source/cluster/wham/src/energy_p_new.F
b/source/cluster/wham/src/energy_p_new.F
index
3b1c095
..
7ee0e64
100644
(file)
--- a/
source/cluster/wham/src/energy_p_new.F
+++ b/
source/cluster/wham/src/energy_p_new.F
@@
-3312,7
+3312,7
@@
c write (iout,*) idihconstr_start_homo,idihconstr_end_homo
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
- betai = phi(i+3)
+ betai = phi(i)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
diff --git
a/source/cluster/wham/src/initialize_p.F
b/source/cluster/wham/src/initialize_p.F
index
3fe87fc
..
e8eac93
100644
(file)
--- a/
source/cluster/wham/src/initialize_p.F
+++ b/
source/cluster/wham/src/initialize_p.F
@@
-590,10
+590,10
@@
c include 'COMMON.SETUP'
& " lim_dih",lim_dih
#ifdef MPL
call int_bounds(lim_odl,link_start_homo,link_end_homo)
& " lim_dih",lim_dih
#ifdef MPL
call int_bounds(lim_odl,link_start_homo,link_end_homo)
- call int_bounds(lim_dih-nnt+1,idihconstr_start_homo,
+ call int_bounds(lim_dih,idihconstr_start_homo,
& idihconstr_end_homo)
& idihconstr_end_homo)
- idihconstr_start_homo=idihconstr_start_homo+nnt-1
- idihconstr_end_homo=idihconstr_end_homo+nnt-1
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
@@
-604,8
+604,8
@@
c include 'COMMON.SETUP'
#else
link_start_homo=1
link_end_homo=lim_odl
#else
link_start_homo=1
link_end_homo=lim_odl
- idihconstr_start_homo=nnt
- idihconstr_end_homo=lim_dih
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+3
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
diff --git
a/source/cluster/wham/src/readrtns.F
b/source/cluster/wham/src/readrtns.F
index
16fdbeb
..
34692c5
100644
(file)
--- a/
source/cluster/wham/src/readrtns.F
+++ b/
source/cluster/wham/src/readrtns.F
@@
-917,6
+917,7
@@
c====-------------------------------------------------------------------
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
include 'COMMON.HOMRESTR'
c
c For new homol impl
include 'COMMON.HOMRESTR'
c
c For new homol impl
@@
-995,11
+996,6
@@
cd call flush(iout)
lim_odl=0
lim_dih=0
c
lim_odl=0
lim_dih=0
c
-c New
-c
- lim_theta=0
- lim_xx=0
-c
c Reading HM global scores (prob not required)
c
do i = nnt,nct
c Reading HM global scores (prob not required)
c
do i = nnt,nct
@@
-1094,7
+1090,7
@@
c
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
open (ientin,file=tpl_k_rescore,status='old')
if (nnt.gt.1) rescore(k,1)=0.0d0
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
open (ientin,file=tpl_k_rescore,status='old')
if (nnt.gt.1) rescore(k,1)=0.0d0
- do irec=nnt,maxdim ! loop for reading res sim
+ do irec=nnt,nct ! loop for reading res sim
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
& idomain_tmp
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
& idomain_tmp
@@
-1102,6
+1098,9
@@
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
idomain(k,i_tmp)=idomain_tmp
rescore(k,i_tmp)=rescore_tmp
rescore2(k,i_tmp)=rescore2_tmp
idomain(k,i_tmp)=idomain_tmp
rescore(k,i_tmp)=rescore_tmp
rescore2(k,i_tmp)=rescore2_tmp
+ write(iout,'(a7,i5,2f10.5,i5)') "rescore",
+ & i_tmp,rescore2_tmp,rescore_tmp,
+ & idomain_tmp
else
idomain(k,irec)=1
read (ientin,*,end=1401) rescore_tmp
else
idomain(k,irec)=1
read (ientin,*,end=1401) rescore_tmp
@@
-1201,7
+1200,8
@@
c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
c Instead of res sim other local measure of b/b str reliability possible
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
c Instead of res sim other local measure of b/b str reliability possible
- sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
enddo
lim_dih=nct-nnt-2
c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
enddo
lim_dih=nct-nnt-2
@@
-1233,14
+1233,14
@@
c read (ientin,*) sigma_theta(k,i) ! 1st variant
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& rescore(k,i-2))/3.0
c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& rescore(k,i-2))/3.0
c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
- sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
- lim_theta=nct-nnt-1
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
@@
-1267,14
+1267,14
@@
c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
sigma_d(k,i)=rescore(k,i) ! right expression ?
c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
sigma_d(k,i)=rescore(k,i) ! right expression ?
- sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
c read (ientin,*) sigma_d(k,i) ! 1st variant
if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
enddo
c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
c read (ientin,*) sigma_d(k,i) ! 1st variant
if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
enddo
- lim_xx=nct-nnt+1
endif
enddo
c
endif
enddo
c
@@
-1323,17
+1323,19
@@
cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i),
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*dih(ki,i),
& rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "Virtual-bond angle restraints from templates"
& rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "Virtual-bond angle restraints from templates"
- do i=nnt+2,lim_theta
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*thetatpl(ki,i),
& rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "SC restraints from templates"
& rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "SC restraints from templates"
- do i=nnt,lim_xx
+ do i=nnt,nct
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
diff --git
a/source/unres/src_MD/energy_p_new_barrier.F
b/source/unres/src_MD/energy_p_new_barrier.F
index
a91710d
..
115cb57
100644
(file)
--- a/
source/unres/src_MD/energy_p_new_barrier.F
+++ b/
source/unres/src_MD/energy_p_new_barrier.F
@@
-6234,7
+6234,7
@@
c write (iout,*) idihconstr_start_homo,idihconstr_end_homo
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
- betai = phi(i+3)
+ betai = phi(i)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
diff --git
a/source/unres/src_MD/initialize_p.F
b/source/unres/src_MD/initialize_p.F
index
369e6bc
..
53a90bf
100644
(file)
--- a/
source/unres/src_MD/initialize_p.F
+++ b/
source/unres/src_MD/initialize_p.F
@@
-1415,10
+1415,10
@@
cd & " lim_dih",lim_dih
#ifdef MPI
if (me.eq.king .or. .not. out1file) write (iout,*) "MPI"
call int_bounds(lim_odl,link_start_homo,link_end_homo)
#ifdef MPI
if (me.eq.king .or. .not. out1file) write (iout,*) "MPI"
call int_bounds(lim_odl,link_start_homo,link_end_homo)
- call int_bounds(lim_dih-nnt+1,idihconstr_start_homo,
+ call int_bounds(lim_dih,idihconstr_start_homo,
& idihconstr_end_homo)
& idihconstr_end_homo)
- idihconstr_start_homo=idihconstr_start_homo+nnt-1
- idihconstr_end_homo=idihconstr_end_homo+nnt-1
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
@@
-1430,8
+1430,8
@@
cd & " lim_dih",lim_dih
write (iout,*) "Not MPI"
link_start_homo=1
link_end_homo=lim_odl
write (iout,*) "Not MPI"
link_start_homo=1
link_end_homo=lim_odl
- idihconstr_start_homo=nnt
- idihconstr_end_homo=lim_dih
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+3
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
diff --git
a/source/unres/src_MD/readrtns.F
b/source/unres/src_MD/readrtns.F
index
0b6f1ae
..
b51386c
100644
(file)
--- a/
source/unres/src_MD/readrtns.F
+++ b/
source/unres/src_MD/readrtns.F
@@
-2721,6
+2721,7
@@
c-------------------------------------------------------------------------------
include 'COMMON.MD'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
include 'COMMON.MD'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
c
c For new homol impl
c
c
c For new homol impl
c
@@
-2794,11
+2795,6
@@
cd call flush(iout)
lim_odl=0
lim_dih=0
c
lim_odl=0
lim_dih=0
c
-c New
-c
- lim_theta=0
- lim_xx=0
-c
write(iout,*) 'nnt=',nnt,'nct=',nct
c
do i = nnt,nct
write(iout,*) 'nnt=',nnt,'nct=',nct
c
do i = nnt,nct
@@
-2862,7
+2858,7
@@
c
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
open (ientin,file=tpl_k_rescore,status='old')
if (nnt.gt.1) rescore(k,1)=0.0d0
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
open (ientin,file=tpl_k_rescore,status='old')
if (nnt.gt.1) rescore(k,1)=0.0d0
- do irec=nnt,maxdim ! loop for reading res sim
+ do irec=nnt,nct ! loop for reading res sim
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
& idomain_tmp
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
& idomain_tmp
@@
-2870,6
+2866,9
@@
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
idomain(k,i_tmp)=idomain_tmp
rescore(k,i_tmp)=rescore_tmp
rescore2(k,i_tmp)=rescore2_tmp
idomain(k,i_tmp)=idomain_tmp
rescore(k,i_tmp)=rescore_tmp
rescore2(k,i_tmp)=rescore2_tmp
+ write(iout,'(a7,i5,2f10.5,i5)') "rescore",
+ & i_tmp,rescore2_tmp,rescore_tmp,
+ & idomain_tmp
else
idomain(k,irec)=1
read (ientin,*,end=1401) rescore_tmp
else
idomain(k,irec)=1
read (ientin,*,end=1401) rescore_tmp
@@
-2969,7
+2968,8
@@
c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
c Instead of res sim other local measure of b/b str reliability possible
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
c Instead of res sim other local measure of b/b str reliability possible
- sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
enddo
lim_dih=nct-nnt-2
c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
enddo
lim_dih=nct-nnt-2
@@
-3001,14
+3001,14
@@
c read (ientin,*) sigma_theta(k,i) ! 1st variant
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& rescore(k,i-2))/3.0
c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& rescore(k,i-2))/3.0
c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
- sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
- lim_theta=nct-nnt-1
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
@@
-3035,14
+3035,14
@@
c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
sigma_d(k,i)=rescore(k,i) ! right expression ?
c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
sigma_d(k,i)=rescore(k,i) ! right expression ?
- sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
c read (ientin,*) sigma_d(k,i) ! 1st variant
if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
enddo
c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
c read (ientin,*) sigma_d(k,i) ! 1st variant
if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
enddo
- lim_xx=nct-nnt+1
endif
enddo
c
endif
enddo
c
@@
-3091,17
+3091,19
@@
cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i),
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*dih(ki,i),
& rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "Virtual-bond angle restraints from templates"
& rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "Virtual-bond angle restraints from templates"
- do i=nnt+2,lim_theta
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*thetatpl(ki,i),
& rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "SC restraints from templates"
& rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "SC restraints from templates"
- do i=nnt,lim_xx
+ do i=nnt,nct
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
diff --git
a/source/wham/src/energy_p_new.F
b/source/wham/src/energy_p_new.F
index
13267da
..
cf4b2e2
100644
(file)
--- a/
source/wham/src/energy_p_new.F
+++ b/
source/wham/src/energy_p_new.F
@@
-3386,7
+3386,7
@@
c write (iout,*) idihconstr_start_homo,idihconstr_end_homo
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
- betai = phi(i+3)
+ betai = phi(i)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
diff --git
a/source/wham/src/initialize_p.F
b/source/wham/src/initialize_p.F
index
c1c1950
..
11bf4ab
100644
(file)
--- a/
source/wham/src/initialize_p.F
+++ b/
source/wham/src/initialize_p.F
@@
-596,10
+596,10
@@
c include 'COMMON.SETUP'
& " lim_dih",lim_dih
#ifdef MPL
call int_bounds(lim_odl,link_start_homo,link_end_homo)
& " lim_dih",lim_dih
#ifdef MPL
call int_bounds(lim_odl,link_start_homo,link_end_homo)
- call int_bounds(lim_dih-nnt+1,idihconstr_start_homo,
+ call int_bounds(lim_dih,idihconstr_start_homo,
& idihconstr_end_homo)
& idihconstr_end_homo)
- idihconstr_start_homo=idihconstr_start_homo+nnt-1
- idihconstr_end_homo=idihconstr_end_homo+nnt-1
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
@@
-610,8
+610,8
@@
c include 'COMMON.SETUP'
#else
link_start_homo=1
link_end_homo=lim_odl
#else
link_start_homo=1
link_end_homo=lim_odl
- idihconstr_start_homo=nnt
- idihconstr_end_homo=lim_dih
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+3
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
diff --git
a/source/wham/src/molread_zs.F
b/source/wham/src/molread_zs.F
index
b11e3fb
..
579d85a
100644
(file)
--- a/
source/wham/src/molread_zs.F
+++ b/
source/wham/src/molread_zs.F
@@
-508,6
+508,7
@@
c====-------------------------------------------------------------------
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
include 'COMMON.HOMRESTR'
c
c For new homol impl
include 'COMMON.HOMRESTR'
c
c For new homol impl
@@
-663,7
+664,7
@@
c
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
open (ientin,file=tpl_k_rescore,status='old')
if (nnt.gt.1) rescore(k,1)=0.0d0
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
open (ientin,file=tpl_k_rescore,status='old')
if (nnt.gt.1) rescore(k,1)=0.0d0
- do irec=nnt,maxdim ! loop for reading res sim
+ do irec=nnt,nct ! loop for reading res sim
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
& idomain_tmp
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
& idomain_tmp
@@
-671,6
+672,9
@@
c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
idomain(k,i_tmp)=idomain_tmp
rescore(k,i_tmp)=rescore_tmp
rescore2(k,i_tmp)=rescore2_tmp
idomain(k,i_tmp)=idomain_tmp
rescore(k,i_tmp)=rescore_tmp
rescore2(k,i_tmp)=rescore2_tmp
+ write(iout,'(a7,i5,2f10.5,i5)') "rescore",
+ & i_tmp,rescore2_tmp,rescore_tmp,
+ & idomain_tmp
else
idomain(k,irec)=1
read (ientin,*,end=1401) rescore_tmp
else
idomain(k,irec)=1
read (ientin,*,end=1401) rescore_tmp
@@
-770,7
+774,8
@@
c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
c Instead of res sim other local measure of b/b str reliability possible
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
c Instead of res sim other local measure of b/b str reliability possible
- sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ if (sigma_dih(k,i).ne.0)
+ & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
enddo
lim_dih=nct-nnt-2
c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
enddo
lim_dih=nct-nnt-2
@@
-802,14
+807,14
@@
c read (ientin,*) sigma_theta(k,i) ! 1st variant
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& rescore(k,i-2))/3.0
c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& rescore(k,i-2))/3.0
c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
- sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
+ if (sigma_theta(k,i).ne.0)
+ & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
c rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
- lim_theta=nct-nnt-1
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
@@
-836,14
+841,13
@@
c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
sigma_d(k,i)=rescore(k,i) ! right expression ?
c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
sigma_d(k,i)=rescore(k,i) ! right expression ?
- sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
+ if (sigma_d(k,i).ne.0)
+ & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
c read (ientin,*) sigma_d(k,i) ! 1st variant
c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
c read (ientin,*) sigma_d(k,i) ! 1st variant
- if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
enddo
enddo
- lim_xx=nct-nnt+1
endif
enddo
c
endif
enddo
c
@@
-892,17
+896,19
@@
cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i),
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*dih(ki,i),
& rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "Virtual-bond angle restraints from templates"
& rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "Virtual-bond angle restraints from templates"
- do i=nnt+2,lim_theta
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
+ & (rad2deg*thetatpl(ki,i),
& rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "SC restraints from templates"
& rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
enddo
write (iout,*) "SC restraints from templates"
- do i=nnt,lim_xx
+ do i=nnt,nct
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)