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Adam's corrections
author
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Fri, 22 May 2020 21:12:14 +0000
(23:12 +0200)
committer
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Fri, 22 May 2020 21:12:14 +0000
(23:12 +0200)
source/cluster/wham/src-HCD/energy_p_new.F
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source/unres/src-HCD-5D/MREMD.F
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source/unres/src-HCD-5D/readrtns_CSA.F
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source/wham/src-HCD/DIMENSIONS
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source/wham/src-HCD/energy_p_new.F
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source/wham/src-HCD/read_constr_homology.F
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source/wham/src-HCD/readpdb.F
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diff --git
a/source/cluster/wham/src-HCD/energy_p_new.F
b/source/cluster/wham/src-HCD/energy_p_new.F
index
27e944b
..
95898b4
100644
(file)
--- a/
source/cluster/wham/src-HCD/energy_p_new.F
+++ b/
source/cluster/wham/src-HCD/energy_p_new.F
@@
-10203,16
+10203,20
@@
c
enddo
c min_odl=minval(distancek)
enddo
c min_odl=minval(distancek)
- do kk=1,constr_homology
- if(l_homo(kk,ii)) then
- min_odl=distancek(kk)
- exit
- endif
- enddo
- do kk=1,constr_homology
- if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
+ if (nexl.gt.0) then
+ min_odl=0.0d0
+ else
+ do kk=1,constr_homology
+ if(l_homo(kk,ii)) then
+ min_odl=distancek(kk)
+ exit
+ endif
+ enddo
+ do kk=1,constr_homology
+ if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
& min_odl=distancek(kk)
& min_odl=distancek(kk)
- enddo
+ enddo
+ endif
c write (iout,* )"min_odl",min_odl
#ifdef DEBUG
write (iout,*) "ij dij",i,j,dij
c write (iout,* )"min_odl",min_odl
#ifdef DEBUG
write (iout,*) "ij dij",i,j,dij
diff --git
a/source/unres/src-HCD-5D/MREMD.F
b/source/unres/src-HCD-5D/MREMD.F
index
38db8a8
..
9191402
100644
(file)
--- a/
source/unres/src-HCD-5D/MREMD.F
+++ b/
source/unres/src-HCD-5D/MREMD.F
@@
-62,6
+62,7
@@
cold integer nup(0:maxprocs),ndown(0:maxprocs)
& ene_i_iex,xxx,tmp,econstr_temp_iex,econstr_temp_i
integer iran_num
double precision ran_number
& ene_i_iex,xxx,tmp,econstr_temp_iex,econstr_temp_i
integer iran_num
double precision ran_number
+ integer i_econstr/20/
cdeb imin_itime_old=0
ntwx_cache=0
cdeb imin_itime_old=0
ntwx_cache=0
@@
-186,8
+187,9
@@
cd write (*,*) me," After broadcast: file_exist",file_exist
do i=nnt,nct
if (itype(i).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i)))
& *dsqrt(gamsc(iabs(itype(i))))
do i=nnt,nct
if (itype(i).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i)))
& *dsqrt(gamsc(iabs(itype(i))))
- enddo
+ enddo
endif
endif
+
endif
if(me.eq.king) then
endif
if(me.eq.king) then
@@
-250,20
+252,20
@@
cd write (*,*) me," After broadcast: file_exist",file_exist
write (iout,'(a6,i4,a1,100i4)') "ndowna",il,":",
& (ndowna(i,il),i=1,ndowna(0,il))
enddo
write (iout,'(a6,i4,a1,100i4)') "ndowna",il,":",
& (ndowna(i,il),i=1,ndowna(0,il))
enddo
+
stdfp=dsqrt(2*Rb*t_bath/d_time)
do i=1,ntyp
stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
enddo
if (lang.gt.0 .and. .not.surfarea) then
stdfp=dsqrt(2*Rb*t_bath/d_time)
do i=1,ntyp
stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
enddo
if (lang.gt.0 .and. .not.surfarea) then
- do i=nnt,nct-1
- stdforcp(i)=stdfp*dsqrt(gamp)
- enddo
+ do i=nnt,nct-1
+ stdforcp(i)=stdfp*dsqrt(gamp)
+ enddo
do i=nnt,nct
if (itype(i).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i)))
& *dsqrt(gamsc(iabs(itype(i))))
do i=nnt,nct
if (itype(i).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i)))
& *dsqrt(gamsc(iabs(itype(i))))
- enddo
- endif
-
+ enddo
+ endif
ELSE IF (.not.(rest.and.file_exist)) THEN
do il=1,remd_m(1)
ifirst(il)=il
ELSE IF (.not.(rest.and.file_exist)) THEN
do il=1,remd_m(1)
ifirst(il)=il
@@
-319,7
+321,7
@@
cd print *,'ttt',me,remd_tlist,(remd_t(i),i=1,nrep)
iset=i2set(me)
if(me.eq.king.or..not.out1file)
& write(iout,*) me,"iset=",iset,"t_bath=",t_bath
iset=i2set(me)
if(me.eq.king.or..not.out1file)
& write(iout,*) me,"iset=",iset,"t_bath=",t_bath
- call flush(iout)
+c call flush(iout)
endif
c
stdfp=dsqrt(2*Rb*t_bath/d_time)
endif
c
stdfp=dsqrt(2*Rb*t_bath/d_time)
@@
-721,7
+723,7
@@
ctime call flush(iout)
write(iout,*) "MIN ii_write=",ii_write
endif
endif
write(iout,*) "MIN ii_write=",ii_write
endif
endif
- call flush(iout)
+c call flush(iout)
endif
if (synflag) then
c Update the time safety limiy
endif
if (synflag) then
c Update the time safety limiy
@@
-855,7
+857,7
@@
cd end
time05=MPI_WTIME()
if (me.eq.king .or. .not. out1file) then
write(iout,*) 'REMD writing traj time=',time05-time04
time05=MPI_WTIME()
if (me.eq.king .or. .not. out1file) then
write(iout,*) 'REMD writing traj time=',time05-time04
- call flush(iout)
+c call flush(iout)
endif
endif
@@
-1089,12
+1091,12
@@
cd write(iout,*) "i_dir=",i_dir
iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1)
c 9/1/17 AL: Correction; otherwise the restraint energies are mis-assigned
c on failed replica exchange attempt
iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1)
c 9/1/17 AL: Correction; otherwise the restraint energies are mis-assigned
c on failed replica exchange attempt
- econstr_temp_i=remd_ene(20,i)
- econstr_temp_iex=remd_ene(20,iex)
+ econstr_temp_i=remd_ene(i_econstr,i)
+ econstr_temp_iex=remd_ene(i_econstr,iex)
c 9/11/17 AL: Adaptive sampling (temperature dependent restraints potentials)
if (adaptive) then
c 9/11/17 AL: Adaptive sampling (temperature dependent restraints potentials)
if (adaptive) then
- remd_ene(20,i)=remd_ene(n_ene+5,i)
- remd_ene(20,iex)=remd_ene(n_ene+6,iex)
+ remd_ene(i_econstr,i)=remd_ene(n_ene+5,i)
+ remd_ene(i_econstr,iex)=remd_ene(n_ene+6,iex)
endif
elseif(i_dir.eq.2 .and. mset(i_iset+1).gt.0)then
endif
elseif(i_dir.eq.2 .and. mset(i_iset+1).gt.0)then
@@
-1103,10
+1105,10
@@
c 9/11/17 AL: Adaptive sampling (temperature dependent restraints potentials)
i_iset1=i_iset+1
i_mset1=iran_num(1,mset(i_iset1))
iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1)
i_iset1=i_iset+1
i_mset1=iran_num(1,mset(i_iset1))
iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1)
- econstr_temp_i=remd_ene(20,i)
- econstr_temp_iex=remd_ene(20,iex)
- remd_ene(20,i)=remd_ene(n_ene+3,i)
- remd_ene(20,iex)=remd_ene(n_ene+4,iex)
+ econstr_temp_i=remd_ene(i_econstr,i)
+ econstr_temp_iex=remd_ene(i_econstr,iex)
+ remd_ene(i_econstr,i)=remd_ene(n_ene+3,i)
+ remd_ene(i_econstr,iex)=remd_ene(n_ene+4,iex)
elseif(remd_m(i_temp+1).gt.0.and.mset(i_iset+1).gt.0)then
elseif(remd_m(i_temp+1).gt.0.and.mset(i_iset+1).gt.0)then
@@
-1115,14
+1117,14
@@
c 9/11/17 AL: Adaptive sampling (temperature dependent restraints potentials)
i_iset1=i_iset+1
i_mset1=iran_num(1,mset(i_iset1))
iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1)
i_iset1=i_iset+1
i_mset1=iran_num(1,mset(i_iset1))
iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1)
- econstr_temp_i=remd_ene(20,i)
- econstr_temp_iex=remd_ene(20,iex)
+ econstr_temp_i=remd_ene(i_econstr,i)
+ econstr_temp_iex=remd_ene(i_econstr,iex)
if (adaptive) then
if (adaptive) then
- remd_ene(20,i)=remd_ene(n_ene+7,i)
- remd_ene(20,iex)=remd_ene(n_ene+8,iex)
+ remd_ene(i_econstr,i)=remd_ene(n_ene+7,i)
+ remd_ene(i_econstr,iex)=remd_ene(n_ene+8,iex)
else
else
- remd_ene(20,i)=remd_ene(n_ene+3,i)
- remd_ene(20,iex)=remd_ene(n_ene+4,iex)
+ remd_ene(i_econstr,i)=remd_ene(n_ene+3,i)
+ remd_ene(i_econstr,iex)=remd_ene(n_ene+4,iex)
endif
else
goto 444
endif
else
goto 444
@@
-1222,8
+1224,8
@@
cd write(iout,'(2i4,a6,2f12.5)') i,iex,' delta',delta,xxx
else
remd_ene(0,iex)=ene_iex_iex
remd_ene(0,i)=ene_i_i
else
remd_ene(0,iex)=ene_iex_iex
remd_ene(0,i)=ene_i_i
- remd_ene(20,iex)=econstr_temp_iex
- remd_ene(20,i)=econstr_temp_i
+ remd_ene(i_econstr,iex)=econstr_temp_iex
+ remd_ene(i_econstr,i)=econstr_temp_i
endif
cd do il=1,nset
endif
cd do il=1,nset
@@
-1259,7
+1261,7
@@
c-------------------------------------
enddo
endif
enddo
endif
- call flush(iout)
+c call flush(iout)
cd write (iout,'(a6,100i4)') "ifirst",
cd & (ifirst(i),i=1,remd_m(1))
cd write (iout,'(a6,100i4)') "ifirst",
cd & (ifirst(i),i=1,remd_m(1))
@@
-1305,7
+1307,6
@@
co & " rescaling weights with temperature",t_bath
do i=1,ntyp
stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
enddo
do i=1,ntyp
stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
enddo
-
c Compute the standard deviations of stochastic forces for Langevin dynamics
c if the friction coefficients do not depend on surface area
if (lang.gt.0 .and. .not.surfarea) then
c Compute the standard deviations of stochastic forces for Langevin dynamics
c if the friction coefficients do not depend on surface area
if (lang.gt.0 .and. .not.surfarea) then
@@
-1317,11
+1318,11
@@
c if the friction coefficients do not depend on surface area
& *dsqrt(gamsc(iabs(itype(i))))
enddo
endif
& *dsqrt(gamsc(iabs(itype(i))))
enddo
endif
-cde write(iout,*) 'REMD after',me,t_bath
+cde write(iout,*) 'REMD after',me,t_bath
time08=MPI_WTIME()
if (me.eq.king .or. .not. out1file) then
write(iout,*) 'REMD exchange time=',time08-time00
time08=MPI_WTIME()
if (me.eq.king .or. .not. out1file) then
write(iout,*) 'REMD exchange time=',time08-time00
- call flush(iout)
+c call flush(iout)
endif
endif
enddo
endif
endif
enddo
diff --git
a/source/unres/src-HCD-5D/readrtns_CSA.F
b/source/unres/src-HCD-5D/readrtns_CSA.F
index
c51e45e
..
16c0f37
100644
(file)
--- a/
source/unres/src-HCD-5D/readrtns_CSA.F
+++ b/
source/unres/src-HCD-5D/readrtns_CSA.F
@@
-2979,10
+2979,11
@@
c & sigma_odl_temp(maxres,maxres,max_template)
character*24 model_ki_dist, model_ki_angle
character*500 controlcard
integer ki,i,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec,
character*24 model_ki_dist, model_ki_angle
character*500 controlcard
integer ki,i,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec,
- & ik,iistart,iishift
+ & ik,iistart
integer ilen
external ilen
integer ilen
external ilen
- logical liiflag
+ logical liiflag,lfirst
+ integer i01,i10
c
c FP - Nov. 2014 Temporary specifications for new vars
c
c
c FP - Nov. 2014 Temporary specifications for new vars
c
@@
-3314,6
+3315,7
@@
c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct
if (waga_dist.ne.0.0d0) then
ii=0
liiflag=.true.
if (waga_dist.ne.0.0d0) then
ii=0
liiflag=.true.
+ lfirst=.true.
do i=nnt,nct-2
do j=i+2,nct
ii=ii+1
do i=nnt,nct-2
do j=i+2,nct
ii=ii+1
@@
-3321,34
+3323,35
@@
c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
c & .and. distal.le.dist2_cut ) then
c write (iout,*) "i",i," j",j," ii",ii
c call flush(iout)
c & .and. distal.le.dist2_cut ) then
c write (iout,*) "i",i," j",j," ii",ii
c call flush(iout)
- if (ii_in_use(ii).eq.0.and.liiflag) then
+ if (ii_in_use(ii).eq.0.and.liiflag.or.
+ & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then
liiflag=.false.
liiflag=.false.
- iistart=ii
+ i10=ii
+ if (lfirst) then
+ lfirst=.false.
+ iistart=ii
+ else
+ if(i10.eq.lim_odl) i10=i10+1
+ do ki=0,i10-i01-1
+ ires_homo(iistart+ki)=ires_homo(ki+i01)
+ jres_homo(iistart+ki)=jres_homo(ki+i01)
+ ii_in_use(iistart+ki)=ii_in_use(ki+i01)
+ do k=1,constr_homology
+ odl(k,iistart+ki)=odl(k,ki+i01)
+ sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01)
+ l_homo(k,iistart+ki)=l_homo(k,ki+i01)
+ enddo
+ enddo
+ iistart=iistart+i10-i01
+ endif
endif
endif
- if (ii_in_use(ii).ne.0.and..not.liiflag.or.
- & .not.liiflag.and.ii.eq.lim_odl) then
- if (ii.eq.lim_odl) then
- iishift=ii-iistart+1
- else
- iishift=ii-iistart
- endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag) then
+ i01=ii
liiflag=.true.
liiflag=.true.
- do ki=iistart,lim_odl-iishift
- ires_homo(ki)=ires_homo(ki+iishift)
- jres_homo(ki)=jres_homo(ki+iishift)
- ii_in_use(ki)=ii_in_use(ki+iishift)
- do k=1,constr_homology
- odl(k,ki)=odl(k,ki+iishift)
- sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
- l_homo(k,ki)=l_homo(k,ki+iishift)
- enddo
- enddo
- ii=ii-iishift
- lim_odl=lim_odl-iishift
-c endif
endif
enddo
enddo
endif
enddo
enddo
+ lim_odl=iistart-1
endif
c write (iout,*) "Removing distances completed"
c call flush(iout)
endif
c write (iout,*) "Removing distances completed"
c call flush(iout)
diff --git
a/source/wham/src-HCD/DIMENSIONS
b/source/wham/src-HCD/DIMENSIONS
index
4bc527f
..
4d690f3
100644
(file)
--- a/
source/wham/src-HCD/DIMENSIONS
+++ b/
source/wham/src-HCD/DIMENSIONS
@@
-24,7
+24,7
@@
c Max. number of chains
parameter (maxchain=6)
C Max number of symetries
integer maxsym,maxperm
parameter (maxchain=6)
C Max number of symetries
integer maxsym,maxperm
- parameter (maxsym=maxchain,maxperm=1200)
+ parameter (maxsym=maxchain,maxperm=720)
C Max. number of variables
integer maxvar
parameter (maxvar=4*maxres)
C Max. number of variables
integer maxvar
parameter (maxvar=4*maxres)
diff --git
a/source/wham/src-HCD/energy_p_new.F
b/source/wham/src-HCD/energy_p_new.F
index
bd69774
..
efba869
100644
(file)
--- a/
source/wham/src-HCD/energy_p_new.F
+++ b/
source/wham/src-HCD/energy_p_new.F
@@
-159,6
+159,7
@@
c write (iout,*) "Calling multibody_hbond"
call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
endif
#endif
call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
endif
#endif
+c write (iout,*) "nsaxs",nsaxs
c write (iout,*) "From Esaxs: Esaxs_constr",Esaxs_constr
if (nsaxs.gt.0 .and. saxs_mode.eq.0) then
call e_saxs(Esaxs_constr)
c write (iout,*) "From Esaxs: Esaxs_constr",Esaxs_constr
if (nsaxs.gt.0 .and. saxs_mode.eq.0) then
call e_saxs(Esaxs_constr)
@@
-4609,16
+4610,20
@@
c
enddo
c min_odl=minval(distancek)
enddo
c min_odl=minval(distancek)
- do kk=1,constr_homology
- if(l_homo(kk,ii)) then
- min_odl=distancek(kk)
- exit
- endif
- enddo
- do kk=1,constr_homology
- if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
+ if (nexl.gt.0) then
+ min_odl=0.0d0
+ else
+ do kk=1,constr_homology
+ if(l_homo(kk,ii)) then
+ min_odl=distancek(kk)
+ exit
+ endif
+ enddo
+ do kk=1,constr_homology
+ if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
& min_odl=distancek(kk)
& min_odl=distancek(kk)
- enddo
+ enddo
+ endif
c write (iout,* )"min_odl",min_odl
#ifdef DEBUG
write (iout,*) "ij dij",i,j,dij
c write (iout,* )"min_odl",min_odl
#ifdef DEBUG
write (iout,*) "ij dij",i,j,dij
diff --git
a/source/wham/src-HCD/read_constr_homology.F
b/source/wham/src-HCD/read_constr_homology.F
index
dece50f
..
0af2bdb
100644
(file)
--- a/
source/wham/src-HCD/read_constr_homology.F
+++ b/
source/wham/src-HCD/read_constr_homology.F
@@
-165,6
+165,7
@@
c call readpdb
write (iout,*) "read_constr_homology: after reading pdb file"
call flush(iout)
#endif
write (iout,*) "read_constr_homology: after reading pdb file"
call flush(iout)
#endif
+
c
c Distance restraints
c
c
c Distance restraints
c
@@
-553,14
+554,18
@@
c Distance restraints
c
c ... --> odl(k,ii)
C Copy the coordinates from reference coordinates (?)
c
c ... --> odl(k,ii)
C Copy the coordinates from reference coordinates (?)
+c write (iout,*) "k",k
do i=1,2*nres
do j=1,3
c(j,i)=chomo(j,i,k)
do i=1,2*nres
do j=1,3
c(j,i)=chomo(j,i,k)
-c write (iout,*) "c(",j,i,") =",c(j,i)
+c write (iout,*) "c(",j,i,") =",c(j,i)
enddo
enddo
enddo
enddo
+c call cartprint
+c write (iout,*) "read_klapaucjusz: calling int_from_cart"
call int_from_cart(.true.,.false.)
call sc_loc_geom(.false.)
call int_from_cart(.true.,.false.)
call sc_loc_geom(.false.)
+c write (iout,*) "en"
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
diff --git
a/source/wham/src-HCD/readpdb.F
b/source/wham/src-HCD/readpdb.F
index
83c63ab
..
55dcc04
100644
(file)
--- a/
source/wham/src-HCD/readpdb.F
+++ b/
source/wham/src-HCD/readpdb.F
@@
-27,10
+27,9
@@
C geometry.
ibeg=1
ishift1=0
sccalc=.false.
ibeg=1
ishift1=0
sccalc=.false.
- ires=0
do
read (ipdbin,'(a80)',end=10) card
do
read (ipdbin,'(a80)',end=10) card
-c write (iout,'(a)') card
+! write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
@@
-59,7
+58,7
@@
c write (iout,'(a)') card
iterter(ires_old)=1
ishift1=ishift1+1
ibeg=2
iterter(ires_old)=1
ishift1=ishift1+1
ibeg=2
- write (iout,*) "Chain ended",ires,ishift,ires_old
+! write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
@@
-120,7
+119,7
@@
c write (iout,*) "BEG ires",ires
! Start a new chain
ishift=-ires_old+ires-1 !!!!!
ishift1=ishift1-1 !!!!!
! Start a new chain
ishift=-ires_old+ires-1 !!!!!
ishift1=ishift1-1 !!!!!
- write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+! write (iout,*) "New chain started",ires,ishift,ishift1,"!"
ires=ires-ishift+ishift1
ires_old=ires
ibeg=0
ires=ires-ishift+ishift1
ires_old=ires
ibeg=0
@@
-326,7
+325,7
@@
c write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and.
& (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and.
& (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
- stop
+c stop
endif
vbld(i)=dist(i-1,i)
vbld_inv(i)=1.0d0/vbld(i)
endif
vbld(i)=dist(i-1,i)
vbld_inv(i)=1.0d0/vbld(i)