++<<<<<<< HEAD
+*.[oa]
+*~
+*.swp
+*.[eo][0-9][0-9][0-9][0-9]*
++=======
+ # ignore compiled stuff
+ *.[oa]
+
+ # ignore texteditors
+ *.swp
+ *~
+
+
+ # ignore build dir
+ build/
+
+ # ignored dirs form adasko
+ gradcheck/
+ mapcheck/
+ run/
+ sympcheck/
+
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
1L2Y
++<<<<<<< HEAD
+SEED=-3059743 REFSTR PDBREF MINIMIZE
+
++=======
+ SEED=-3059743 PDBREF ENE
+ maxmin=1000
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
*
* Array dimensions for level-based conformation comparison program:
*
++<<<<<<< HEAD
++=======
+ * Max. number of conformations in the data set.
+ *
+ integer maxconf
+ PARAMETER (MAXCONF=maxstr_proc)
+ *
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
* Max. number levels of comparison
*
integer maxlevel
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'sizesclu.dat'
- include "DIMENSIONS.COMPAR"
+ c include "DIMENSIONS.COMPAR"
parameter (accur=1.0d-10)
include 'COMMON.GEO'
include 'COMMON.VAR'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'sizesclu.dat'
- include "DIMENSIONS.COMPAR"
+ c include "DIMENSIONS.COMPAR"
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'sizesclu.dat'
- include "DIMENSIONS.COMPAR"
+ c include "DIMENSIONS.COMPAR"
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'sizesclu.dat'
- include "DIMENSIONS.COMPAR"
+ c include "DIMENSIONS.COMPAR"
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'sizesclu.dat'
- include "DIMENSIONS.COMPAR"
+ c include "DIMENSIONS.COMPAR"
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
dimension ggg(3)
ehpb=0.0D0
-cd print *,'edis: nhpb=',nhpb,' fbr=',fbr
-cd print *,'link_start=',link_start,' link_end=',link_end
+cd write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
+cd write(iout,*)'link_start=',link_start,' link_end=',link_end
if (link_end.eq.0) return
do i=link_start,link_end
C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
iii=ii
jjj=jj
endif
+c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
+c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
+cd write (iout,*) "eij",eij
+ else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "beta nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
else
C Calculate the distance between the two points and its difference from the
C target distance.
- dd=dist(ii,jj)
- rdis=dd-dhpb(i)
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
- waga=forcon(i)
+ waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "alpha reg",dd,waga*rdis*rdis
C
C Evaluate gradient.
C
- fac=waga*rdis/dd
+ fac=waga*rdis/dd
+ endif
cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
cd & ' waga=',waga,' fac=',fac
- do j=1,3
- ggg(j)=fac*(c(j,jj)-c(j,ii))
- enddo
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
C If this is a SC-SC distance, we need to calculate the contributions to the
C Cartesian gradient in the SC vectors (ghpbx).
- if (iii.lt.ii) then
+ if (iii.lt.ii) then
do j=1,3
ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
enddo
- endif
- do j=iii,jjj-1
+ endif
do k=1,3
- ghpbc(k,j)=ghpbc(k,j)+ggg(k)
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
enddo
- enddo
endif
enddo
ehpb=0.5D0*ehpb
do i=1,ndih_constr
itori=idih_constr(i)
phii=phi(itori)
- difi=phii-phi0(i)
+ difi=pinorm(phii-phi0(i))
if (difi.gt.drange(i)) then
difi=difi-drange(i)
edihcnstr=edihcnstr+0.25d0*ftors*difi**4
edihcnstr=edihcnstr+0.25d0*ftors*difi**4
gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
endif
-! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
-! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
+c write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
+c & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
enddo
-! write (iout,*) 'edihcnstr',edihcnstr
+ write (iout,*) 'edihcnstr',edihcnstr
return
end
c------------------------------------------------------------------------------
enddo
! 6/20/98 - dihedral angle constraints
edihcnstr=0.0d0
+c write (iout,*) "Dihedral angle restraint energy"
do i=1,ndih_constr
- print *,"i",i
itori=idih_constr(i)
phii=phi(itori)
- difi=phii-phi0(i)
+ difi=pinorm(phii-phi0(i))
+c write (iout,'(2i5,4f8.3,2e14.5)') i,itori,rad2deg*phii,
+c & rad2deg*difi,rad2deg*phi0(i),rad2deg*drange(i)
if (difi.gt.drange(i)) then
difi=difi-drange(i)
edihcnstr=edihcnstr+0.25d0*ftors*difi**4
gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+c write (iout,*) 0.25d0*ftors*difi**4
else if (difi.lt.-drange(i)) then
difi=difi+drange(i)
edihcnstr=edihcnstr+0.25d0*ftors*difi**4
gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+c write (iout,*) 0.25d0*ftors*difi**4
endif
-! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
-! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
enddo
-! write (iout,*) 'edihcnstr',edihcnstr
+c write (iout,*) 'edihcnstr',edihcnstr
return
end
c----------------------------------------------------------------------------
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ /j\
- C / \ / \
- C /| o | | o |\
- C \ j|/k\| / \ |/k\|l /
- C \ / \ / \ / \ /
- C o o o o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ /j\ C
+ C / \ / \ C
+ C /| o | | o |\ C
+ C \ j|/k\| / \ |/k\|l / C
+ C \ / \ / \ / \ / C
+ C o o o o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
itk=itortyp(itype(k))
s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C \ /l\ /j\ /
- C \ / \ / \ /
- C o| o | | o |o
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C \ /l\ /j\ / C
+ C \ / \ / \ / C
+ C o| o | | o |o C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
C AL 7/4/01 s1 would occur in the sixth-order moment,
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C j|/k\| / |/k\|l /
- C / \ / / \ /
- C / o / o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C j|/k\| / |/k\|l / C
+ C / \ / / \ / C
+ C / o / o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
& auxvec1(2),auxmat1(2,2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o \ o \
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o \ o \ C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
& r0d(ntyp,2),rpp(2,2),epp(2,2),elpp6(2,2),elpp3(2,2),
& eps_scp(20,2),rscp(20,2),eps_orig(ntyp,ntyp)
c 12/5/03 modified 09/18/03 Bond stretching parameters.
++<<<<<<< HEAD
+ double precision vbldp0,vbldsc0,akp,aksc,abond0
+ integer nbondterm
+ common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
+ & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),nbondterm(ntyp)
++=======
+ double precision vbldp0,vbldsc0,akp,aksc,abond0,distchainmax
+ integer nbondterm
+ common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
+ & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),
+ & distchainmax,nbondterm(ntyp)
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
double precision ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,dhpb,
++<<<<<<< HEAD
+ & dhpb1,forcon,weidis
+ integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end,
+ & ibecarb
+ common /sbridge/ ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,ns,nss,
+ & nfree,iss(maxss)
+ common /links/ dhpb(maxdim),dhpb1(maxdim),forcon(maxdim),
+ & ihpb(maxdim),jhpb(maxdim),ibecarb(maxdim),nhpb
++=======
+ & forcon,weidis
+ integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end
+ common /sbridge/ ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,ns,nss,
+ & nfree,iss(maxss)
+ common /links/ dhpb(maxdim),forcon(maxdim),ihpb(maxdim),
+ & jhpb(maxdim),nhpb
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
common /restraints/ weidis
common /links_split/ link_start,link_end
common/torsion/v0(maxtor,maxtor),v1(maxterm,maxtor,maxtor),
& v2(maxterm,maxtor,maxtor),vlor1(maxlor,maxtor,maxtor),
& vlor2(maxlor,maxtor,maxtor),vlor3(maxlor,maxtor,maxtor),
++<<<<<<< HEAD
+ & itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),nlor(maxtor,maxtor)
+ & ,nterm_old
++=======
+ & itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),
+ & nlor(maxtor,maxtor),nterm_old
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
C 6/23/01 - constants for double torsionals
double precision v1c,v1s,v2c,v2s
integer ntermd_1,ntermd_2
common /srutu/ icall
double precision energy(0:n_ene)
double precision energy_long(0:n_ene),energy_short(0:n_ene)
+ double precision varia(maxvar)
if (indpdb.eq.0) call chainbuild
time00=MPI_Wtime()
call chainbuild_cart
write (istat,'(a5,20a12)')"# ",
& (wname(print_order(i)),i=1,nprint_ene)
write (istat,'("# ",20(1pe12.4))')
- (weights(print_order(i)),i=1,nprint_ene)
+ & (weights(print_order(i)),i=1,nprint_ene)
if (refstr) then
write (istat,'(a5,20a12)')"# ",
& (ename(print_order(i)),i=1,nprint_ene),
- & ,"ETOT total","RMSD","nat.contact","nnt.contact"
+ & "ETOT total","RMSD","nat.contact","nnt.contact"
else
write (istat,'(a5,14a12)')"# ",
& (ename(print_order(i)),i=1,nprint_ene),"ETOT total"
-#-DCRYST_TOR
-# -DPROCOR
-# -DTSCSC
-#-DTIMING \
-# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-# -DMOMENT
-#-DPARVEC
-#-DPARINT -DPARINTDER
-
-#INSTALL_DIR = /users/local/mpi64/mpich-1.2.7p1/
-#INSTALL_DIR = /users/local/mpich2-1.3.1/
INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-#INSTALL_DIR = /users/software/mpich2.x86_64/
FC= ifort
- OPT = -O3 -ip -w
+ OPT = -g -ip -w -CB
FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include
C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
++<<<<<<< HEAD
+C 2 5 66
+ subroutine cinfo
+ include 'COMMON.IOUNITS'
+ write(iout,*)'++++ Compile info ++++'
+ write(iout,*)'Version 2.5 build 66'
+ write(iout,*)'compiled Thu Jun 14 06:40:11 2012'
+ write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
++=======
+ C 2 5 295
+ subroutine cinfo
+ include 'COMMON.IOUNITS'
+ write(iout,*)'++++ Compile info ++++'
+ write(iout,*)'Version 2.5 build 295'
+ write(iout,*)'compiled Mon Jun 18 05:08:20 2012'
+ write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
write(iout,*)'OS name: Linux '
write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
write(iout,*)'OS version:',
& ' #1 SMP Tue May 3 09:23:03 UTC 2011 '
write(iout,*)'flags:'
++<<<<<<< HEAD
+ write(iout,*)'FC = ifort'
+ write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include'
++=======
+ write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
+ write(iout,*)'FC= ifort'
+ write(iout,*)'OPT = -g -ip -w -CB '
+ write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...'
- write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include '
+ write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include'
write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...'
- write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...'
+ write(iout,*)'CC = cc'
+ write(iout,*)'CFLAGS = -DLINUX -DPGI -c'
+ write(iout,*)'OPT = -O3 -ip -w'
+ write(iout,*)'LIBS = -Lxdrf -lxdrf'
write(iout,*)'ARCH = LINUX'
write(iout,*)'PP = /lib/cpp -P'
write(iout,*)'object = unres.o arcos.o cartprint.o chainbuild...'
write(iout,*)'GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...'
- write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...'
+ write(iout,*)'GAB: BIN = ../../../bin/unres/MD/unres_ifort_si...'
write(iout,*)'E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...'
write(iout,*)'E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...'
write(iout,*)'++++ End of compile info ++++'
include 'mpif.h'
#endif
double precision gradbufc(3,maxres),gradbufx(3,maxres),
- & glocbuf(4*maxres),gradbufc_sum(3,maxres)
+ & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres)
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
include 'COMMON.MAXGRAD'
+ include 'COMMON.SCCOR'
#ifdef TIMING
#ifdef MPI
time01=MPI_Wtime()
& +wturn3*gel_loc_turn3(i)
& +wturn6*gel_loc_turn6(i)
& +wel_loc*gel_loc_loc(i)
- & +wsccor*gsccor_loc(i)
enddo
#ifdef DEBUG
write (iout,*) "gloc after adding corr"
do i=1,4*nres
glocbuf(i)=gloc(i,icg)
enddo
+ #define DEBUG
+ #ifdef DEBUG
+ write (iout,*) "gloc_sc before reduce"
+ do i=1,nres
+ do j=1,3
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+ #endif
+ #undef DEBUG
+ do i=1,nres
+ do j=1,3
+ gloc_scbuf(j,i)=gloc_sc(j,i,icg)
+ enddo
+ enddo
time00=MPI_Wtime()
call MPI_Barrier(FG_COMM,IERR)
time_barrier_g=time_barrier_g+MPI_Wtime()-time00
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
+ call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
time_reduce=time_reduce+MPI_Wtime()-time00
+ #define DEBUG
+ #ifdef DEBUG
+ write (iout,*) "gloc_sc after reduce"
+ do i=1,nres
+ do j=1,3
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+ #endif
+ #undef DEBUG
#ifdef DEBUG
write (iout,*) "gloc after reduce"
do i=1,4*nres
& 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
& 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
& 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
- & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6,
+ & 'EHPB= ',1pE16.6,' WEIGHT=',1pD16.6,
& ' (SS bridges & dist. cnstr.)'/
& 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
& 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
iii=ii
jjj=jj
endif
-cd write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj
+c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
+c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
cd write (iout,*) "eij",eij
+ else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "beta nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
else
C Calculate the distance between the two points and its difference from the
C target distance.
- dd=dist(ii,jj)
- rdis=dd-dhpb(i)
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
- waga=forcon(i)
+ waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "alpha reg",dd,waga*rdis*rdis
C
C Evaluate gradient.
C
- fac=waga*rdis/dd
+ fac=waga*rdis/dd
+ endif
cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
cd & ' waga=',waga,' fac=',fac
- do j=1,3
- ggg(j)=fac*(c(j,jj)-c(j,ii))
- enddo
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
C If this is a SC-SC distance, we need to calculate the contributions to the
C Cartesian gradient in the SC vectors (ghpbx).
- if (iii.lt.ii) then
+ if (iii.lt.ii) then
do j=1,3
ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
enddo
- endif
+ endif
cgrad do j=iii,jjj-1
cgrad do k=1,3
cgrad ghpbc(k,j)=ghpbc(k,j)+ggg(k)
cgrad enddo
cgrad enddo
- do k=1,3
- ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
- ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
- enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
endif
enddo
ehpb=0.5D0*ehpb
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
& (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
- c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
+ write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
enddo
! 6/20/98 - dihedral angle constraints
edihcnstr=0.0d0
else
difi=0.0
endif
+ c write (iout,*) "gloci", gloc(i-3,icg)
cd write (iout,'(2i5,4f8.3,2e14.5)') i,itori,rad2deg*phii,
cd & rad2deg*phi0(i), rad2deg*drange(i),
cd & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
- C Regular cosine and sine terms
do j=1,ntermd_1(itori,itori1,itori2)
v1cij=v1c(1,j,itori,itori1,itori2)
v1sij=v1s(1,j,itori,itori1,itori2)
enddo
gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*gloci1
gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*gloci2
+ c write (iout,*) "gloci", gloc(i-3,icg)
enddo
return
end
c lprn=.true.
c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
esccor=0.0D0
- do i=iphi_start,iphi_end
+ do i=itau_start,itau_end
esccor_ii=0.0D0
- itori=itype(i-2)
- itori1=itype(i-1)
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
phii=phi(i)
+ cccc Added 9 May 2012
+ cc Tauangle is torsional engle depending on the value of first digit
+ c(see comment below)
+ cc Omicron is flat angle depending on the value of first digit
+ c(see comment below)
+
+
+ do intertyp=1,3 !intertyp
+ cc Added 09 May 2012 (Adasko)
+ cc Intertyp means interaction type of backbone mainchain correlation:
+ c 1 = SC...Ca...Ca...Ca
+ c 2 = Ca...Ca...Ca...SC
+ c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- do j=1,nterm_sccor
- v1ij=v1sccor(j,itori,itori1)
- v2ij=v2sccor(j,itori,itori1)
- cosphi=dcos(j*phii)
- sinphi=dsin(j*phii)
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
+ & (itype(i-1).eq.21)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.21)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.21)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21))
+ & cycle
+ do j=1,nterm_sccor(isccori,isccori1)
+ v1ij=v1sccor(j,intertyp,isccori,isccori1)
+ v2ij=v2sccor(j,intertyp,isccori,isccori1)
+ cosphi=dcos(j*tauangle(intertyp,i))
+ sinphi=dsin(j*tauangle(intertyp,i))
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+ gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
+ c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
+ c &gloc_sc(intertyp,i-3,icg)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6)
+ & (v1sccor(j,intertyp,itori,itori1),j=1,6)
+ & ,(v2sccor(j,intertyp,itori,itori1),j=1,6)
gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
+ enddo !intertyp
enddo
+ c do i=1,nres
+ c write (iout,*) "W@T@F", gloc_sc(1,i,icg),gloc(i,icg)
+ c enddo
return
end
c----------------------------------------------------------------------------
C Parallel Antiparallel
C
C o o
- C /l\ /j\
- C / \ / \
- C /| o | | o |\
+ C /l\ /j\
+ C / \ / \
+ C /| o | | o |\
C \ j|/k\| / \ |/k\|l /
C \ / \ / \ / \ /
C o o o o
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C \ /l\ /j\ /
- C \ / \ / \ /
- C o| o | | o |o
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C \ /l\ /j\ / C
+ C \ / \ / \ / C
+ C o| o | | o |o C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
C AL 7/4/01 s1 would occur in the sixth-order moment,
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C j|/k\| / |/k\|l /
- C / \ / / \ /
- C / o / o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C j|/k\| / |/k\|l / C
+ C / \ / / \ / C
+ C / o / o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
& auxvec1(2),auxmat1(2,2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o \ o \
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o \ o \ C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
&write (iout,'(a,i5,a)') "The following",nhpb-nss,
& " distance constraints have been imposed"
do i=nss+1,nhpb
- write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
+ write (iout,'(3i6,i2,3f10.5)') i-nss,ihpb(i),jhpb(i),
+ & ibecarb(i),dhpb(i),dhpb1(i),forcon(i)
enddo
#ifdef MPI
endif
call readi(controlcard,'MAXGEN',maxgen,10000)
call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
call readi(controlcard,"KDIAG",kdiag,0)
- call readi(controlcard,"RESCALE_MODE",rescale_mode,1)
+ call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
& write (iout,*) "RESCALE_MODE",rescale_mode
split_ene=index(controlcard,'SPLIT_ENE').gt.0
enddo
call contact(.true.,ncont_ref,icont_ref,co)
endif
-c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
- call flush(iout)
- if (constr_dist.gt.0) call read_dist_constr
-c write (iout,*) "After read_dist_constr nhpb",nhpb
- call hpb_partition
if(me.eq.king.or..not.out1file)
& write (iout,*) 'Contact order:',co
if (pdbref) then
enddo
endif
endif
+c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
+ if (constr_dist.gt.0) then
+ call read_dist_constr
+ call hpb_partition
+ endif
+c write (iout,*) "After read_dist_constr nhpb",nhpb
+c call flush(iout)
if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
& .and. modecalc.ne.8 .and. modecalc.ne.9 .and.
& modecalc.ne.10) then
call readi(minimcard,'MINFUN',minfun,maxmin)
call reada(minimcard,'TOLF',tolf,1.0D-2)
call reada(minimcard,'RTOLF',rtolf,1.0D-4)
+ print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
+ print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
+ print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
write (iout,'(/80(1h*)/20x,a/80(1h*))')
& 'Options in energy minimization:'
write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)')
open (isidep,file=sidename,status='old')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
- & readonly)
+ &action='read')
open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
C Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
- open (ibond,file=bondname,status='old',readonly)
+ open (ibond,file=bondname,status='old',action='read')
call getenv_loc('THETPAR',thetname)
- open (ithep,file=thetname,status='old',readonly)
+ open (ithep,file=thetname,status='old',action='read')
#ifndef CRYST_THETA
call getenv_loc('THETPARPDB',thetname_pdb)
print *,"thetname_pdb ",thetname_pdb
- open (ithep_pdb,file=thetname_pdb,status='old',readonly)
+ open (ithep_pdb,file=thetname_pdb,status='old',action='read')
print *,ithep_pdb," opened"
#endif
call getenv_loc('ROTPAR',rotname)
- open (irotam,file=rotname,status='old',readonly)
+ open (irotam,file=rotname,status='old',action='read')
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
- open (irotam_pdb,file=rotname_pdb,status='old',readonly)
+ open (irotam_pdb,file=rotname_pdb,status='old',action='read')
#endif
call getenv_loc('TORPAR',torname)
- open (itorp,file=torname,status='old',readonly)
+ open (itorp,file=torname,status='old',action='read')
call getenv_loc('TORDPAR',tordname)
- open (itordp,file=tordname,status='old',readonly)
+ open (itordp,file=tordname,status='old',action='read')
call getenv_loc('SCCORPAR',sccorname)
- open (isccor,file=sccorname,status='old',readonly)
+ open (isccor,file=sccorname,status='old',action='read')
call getenv_loc('FOURIER',fouriername)
- open (ifourier,file=fouriername,status='old',readonly)
+ open (ifourier,file=fouriername,status='old',action='read')
call getenv_loc('ELEPAR',elename)
- open (ielep,file=elename,status='old',readonly)
+ open (ielep,file=elename,status='old',action='read')
call getenv_loc('SIDEPAR',sidename)
- open (isidep,file=sidename,status='old',readonly)
+ open (isidep,file=sidename,status='old',action='read')
#endif
#ifndef OLDSCP
C
#elif (defined G77)
open (iscpp,file=scpname,status='old')
#else
- open (iscpp,file=scpname,status='old',readonly)
+ open (iscpp,file=scpname,status='old',action='read')
#endif
#endif
call getenv_loc('PATTERN',patname)
#elif (defined G77)
open (icbase,file=patname,status='old')
#else
- open (icbase,file=patname,status='old',readonly)
+ open (icbase,file=patname,status='old',action='read')
#endif
#ifdef MPI
C Open output file only for CG processes
#if defined(AIX) || defined(PGI)
if (me.eq.king .or. .not. out1file)
& open(iout,file=outname,status='unknown')
+ c#define DEBUG
#ifdef DEBUG
if (fg_rank.gt.0) then
write (liczba,'(i3.3)') myrank/nfgtasks
& status='unknown')
endif
#endif
+ c#undef DEBUG
if(me.eq.king) then
open(igeom,file=intname,status='unknown',position='append')
open(ipdb,file=pdbname,status='unknown')
#else
if (me.eq.king .or. .not.out1file)
& open(iout,file=outname,status='unknown')
+ c#define DEBUG
#ifdef DEBUG
if (fg_rank.gt.0) then
+ print "Processor",fg_rank," opening output file"
write (liczba,'(i3.3)') myrank/nfgtasks
write (ll,'(bz,i3.3)') fg_rank
open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
& status='unknown')
endif
#endif
+ c#undef DEBUG
if(me.eq.king) then
open(igeom,file=intname,status='unknown',access='append')
open(ipdb,file=pdbname,status='unknown')
c do i=1,npair_
c write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
c enddo
+ if (.not.refstr .and. nfrag.gt.0) then
+ write (iout,*)
+ & "ERROR: no reference structure to compute distance restraints"
+ write (iout,*)
+ & "Restraints must be specified explicitly (NDIST=number)"
+ stop
+ endif
+ if (nfrag.lt.2 .and. npair.gt.0) then
+ write (iout,*) "ERROR: Less than 2 fragments specified",
+ & " but distance restraints between pairs requested"
+ stop
+ endif
call flush(iout)
do i=1,nfrag_
if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
endif
enddo
do i=1,ndist_
- read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
+ read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+ & ibecarb(i),forcon(nhpb+1)
if (forcon(nhpb+1).gt.0.0d0) then
nhpb=nhpb+1
- dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+ if (ibecarb(i).gt.0) then
+ ihpb(i)=ihpb(i)+nres
+ jhpb(i)=jhpb(i)+nres
+ endif
+ if (dhpb(nhpb).eq.0.0d0)
+ & dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+ endif
+ enddo
#ifdef MPI
- if (.not.out1file .or. me.eq.king)
- & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
- & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
-#else
- write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
- & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+ if (.not.out1file .or. me.eq.king) then
#endif
- endif
+ do i=1,nhpb
+ write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
+ & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
enddo
call flush(iout)
+#ifdef MPI
+ endif
+#endif
return
end
c-------------------------------------------------------------------------------
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+
& wel_loc*gel_loc(j,i)+
& 0.5d0*(wscp*gvdwc_scpp(j,i)+
- & welec*gelc_long(j,i)
+ & welec*gelc_long(j,i)+
& wel_loc*gel_loc_long(j,i)+
& wcorr*gcorr_long(j,i)+
& wcorr5*gradcorr5_long(j,i)+
logical lprn
evdw=0.0D0
ccccc energy_dec=.false.
-c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+c write(iout,*) 'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
evdw_p=0.0D0
evdw_m=0.0D0
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ /j\
- C / \ / \
- C /| o | | o |\
- C \ j|/k\| / \ |/k\|l /
- C \ / \ / \ / \ /
- C o o o o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ /j\ C
+ C / \ / \ C
+ C /| o | | o |\ C
+ C \ j|/k\| / \ |/k\|l / C
+ C \ / \ / \ / \ / C
+ C o o o o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
itk=itortyp(itype(k))
s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C \ /l\ /j\ /
- C \ / \ / \ /
- C o| o | | o |o
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C \ /l\ /j\ / C
+ C \ / \ / \ / C
+ C o| o | | o |o C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
C AL 7/4/01 s1 would occur in the sixth-order moment,
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C j|/k\| / |/k\|l /
- C / \ / / \ /
- C / o / o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C j|/k\| / |/k\|l / C
+ C / \ / / \ / C
+ C / o / o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
& auxvec1(2),auxmat1(2,2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o \ o \
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o \ o \ C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'DIMENSIONS.ZSCOPT'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
dimension ggg(3)
ehpb=0.0D0
-cd print *,'edis: nhpb=',nhpb,' fbr=',fbr
-cd print *,'link_start=',link_start,' link_end=',link_end
+cd write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
+cd write(iout,*)'link_start=',link_start,' link_end=',link_end
if (link_end.eq.0) return
do i=link_start,link_end
C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
iii=ii
jjj=jj
endif
+c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
+c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
+cd write (iout,*) "eij",eij
+ else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "beta nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
else
C Calculate the distance between the two points and its difference from the
C target distance.
- dd=dist(ii,jj)
- rdis=dd-dhpb(i)
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
- waga=forcon(i)
+ waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "alpha reg",dd,waga*rdis*rdis
C
C Evaluate gradient.
C
- fac=waga*rdis/dd
+ fac=waga*rdis/dd
+ endif
cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
cd & ' waga=',waga,' fac=',fac
- do j=1,3
- ggg(j)=fac*(c(j,jj)-c(j,ii))
- enddo
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
C If this is a SC-SC distance, we need to calculate the contributions to the
C Cartesian gradient in the SC vectors (ghpbx).
- if (iii.lt.ii) then
+ if (iii.lt.ii) then
do j=1,3
ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
enddo
- endif
- do j=iii,jjj-1
+ endif
do k=1,3
- ghpbc(k,j)=ghpbc(k,j)+ggg(k)
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
enddo
- enddo
endif
enddo
ehpb=0.5D0*ehpb
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ /j\
- C / \ / \
- C /| o | | o |\
- C \ j|/k\| / \ |/k\|l /
- C \ / \ / \ / \ /
- C o o o o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ /j\ C
+ C / \ / \ C
+ C /| o | | o |\ C
+ C \ j|/k\| / \ |/k\|l / C
+ C \ / \ / \ / \ / C
+ C o o o o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
itk=itortyp(itype(k))
s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C \ /l\ /j\ /
- C \ / \ / \ /
- C o| o | | o |o
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C \ /l\ /j\ / C
+ C \ / \ / \ / C
+ C o| o | | o |o C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
C AL 7/4/01 s1 would occur in the sixth-order moment,
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C j|/k\| / |/k\|l /
- C / \ / / \ /
- C / o / o
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C j|/k\| / |/k\|l / C
+ C / \ / / \ / C
+ C / o / o C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
& auxvec1(2),auxmat1(2,2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- C
- C Parallel Antiparallel
- C
- C o o
- C /l\ / \ /j\
- C / \ / \ / \
- C /| o |o o| o |\
- C \ j|/k\| \ |/k\|l
- C \ / \ \ / \
- C o \ o \
- C i i
- C
+ C C
+ C Parallel Antiparallel C
+ C C
+ C o o C
+ C /l\ / \ /j\ C
+ C / \ / \ / \ C
+ C /| o |o o| o |\ C
+ C \ j|/k\| \ |/k\|l C
+ C \ / \ \ / \ C
+ C o \ o \ C
+ C i i C
+ C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
character*3 sequenc(maxres)
character*50 tytul
character*8 onethree,cfreq,cntraj,citraj
+ character*3 licz
character*8 ucase
external ucase
- logical oneletter
+ logical oneletter, iblnk
integer rescode
external rescode
ifreq=1
- if (iargc().lt.3) then
+ if (iargc().lt.5) then
print '(2a)',
- & "Usage: xdrf2pdb-m one/three seqfile cxfile [freq] [pdbfile] ",
- & " [ntraj] [itraj]"
+ & "Usage: xdrf2pdb-m one/three seqfile cxfile ntraj itraj",
+ & " [pdbfile] [freq]"
stop
endif
call getarg(1,onethree)
10 continue
nres=i
i=0
- do while (.not.iblnk(sequenc(i+1)(1:1)))
+ c do while (.not.iblnk(sequenc(i+1)(1:1)))
+ do while (.not.(iblnk(sequenc(i+1)(1:1))==0) )
i=i+1
enddo
nres=i
11 continue
nres=i
i=0
- do while (.not.iblnk(sequenc(i+1)(1:1)))
+ c do while (.not.iblnk(sequenc(i+1)(1:1)))
+ do while (.not.(iblnk(sequenc(i+1)(1:1))==0))
i=i+1
enddo
nres=i
itype(i)=rescode(i,sequenc(i),0)
enddo
print *,nres
- print '(a3,1x)',(sequenc(i),i=1,nres)
+ print '(20(a3,1x))',(sequenc(i),i=1,nres)
endif
call getarg(3,arg)
iext = index(arg,'.cx') - 1
print *,"Error - not a cx file"
stop
endif
- if (iargc().gt.3) then
- call getarg(4,cfreq)
- read (cfreq,*) ifreq
- endif
- if (iargc().gt.4) then
- call getarg(5,pdbfile)
- else
- pdbfile=arg(:iext)//'.pdb'
- endif
+ call getarg(4,cntraj)
+ read (cntraj,*) ntraj
+ call getarg(5,citraj)
+ read (citraj,*) itraj
if (iargc().gt.5) then
- call getarg(6,cntraj)
- read (cntraj,*) ntraj
+ call getarg(6,pdbfile)
else
- ntraj=1
+ write(licz,'(bz,i3.3)') itraj
+ pdbfile=arg(:iext)//'_'//licz//'.pdb'
endif
if (iargc().gt.6) then
- call getarg(7,citraj)
- read (citraj,*) itraj
- else
- itraj=1
+ call getarg(7,cfreq)
+ read (cfreq,*) ifreq
endif
- print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
+c print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
open(9,file=pdbfile)
nnt = 1
if (itype(1).eq.21) nnt = 2
FC=gfortran
-BINDIR = ../bin
+BINDIR = ../../../bin
#OPT = -fast
OPT =
FFLAGS = -c ${OPT}
- CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI -DSPLITELE -DPROCOR -DNEWUNRES
+ CPPFLAGS = -DNEWUNRES
M4 = m4
M4FILE = underscore.m4
character*8 onethree,cfreq
character*8 ucase
external ucase
++<<<<<<< HEAD
+ logical oneletter,iblnk
++=======
+ logical oneletter, iblnk
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
integer rescode
external rescode
nres=i
i=0
do while (.not.iblnk(sequenc(i+1)(1:1)))
+ c do while (.not.(iblnk(sequenc(i+1)(1:1)) == 0) )
i=i+1
enddo
nres=i
nres=i
i=0
do while (.not.iblnk(sequenc(i+1)(1:1)))
+ c do while (.not.(iblnk(sequenc(i+1)(1:1)) == 0) )
i=i+1
enddo
nres=i
character*3 sequenc(maxres)
character*50 tytul
character*8 onethree,cfreq,cntraj,citraj
+ character*3 licz
character*8 ucase
external ucase
++<<<<<<< HEAD
+ logical oneletter,iblnk
++=======
+ logical oneletter, iblnk
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
integer rescode
external rescode
ifreq=1
- if (iargc().lt.3) then
+ if (iargc().lt.5) then
print '(2a)',
- & "Usage: xdrf2pdb-m one/three seqfile cxfile [freq] [pdbfile] ",
- & " [ntraj] [itraj]"
+ & "Usage: xdrf2pdb-m one/three seqfile cxfile ntraj itraj",
+ & " [pdbfile] [freq]"
stop
endif
call getarg(1,onethree)
nres=i
i=0
do while (.not.iblnk(sequenc(i+1)(1:1)))
+ c do while (.not.(iblnk(sequenc(i+1)(1:1)) == 0))
i=i+1
enddo
nres=i
nres=i
i=0
do while (.not.iblnk(sequenc(i+1)(1:1)))
+ c do while (.not.(iblnk(sequenc(i+1)(1:1)) == 0))
i=i+1
enddo
nres=i
itype(i)=rescode(i,sequenc(i),0)
enddo
print *,nres
- print '(a3,1x)',(sequenc(i),i=1,nres)
+ print '(20(a3,1x))',(sequenc(i),i=1,nres)
endif
call getarg(3,arg)
iext = index(arg,'.cx') - 1
print *,"Error - not a cx file"
stop
endif
- if (iargc().gt.3) then
- call getarg(4,cfreq)
- read (cfreq,*) ifreq
- endif
- if (iargc().gt.4) then
- call getarg(5,pdbfile)
- else
- pdbfile=arg(:iext)//'.pdb'
- endif
+ call getarg(4,cntraj)
+ read (cntraj,*) ntraj
+ call getarg(5,citraj)
+ read (citraj,*) itraj
if (iargc().gt.5) then
- call getarg(6,cntraj)
- read (cntraj,*) ntraj
+ call getarg(6,pdbfile)
else
- ntraj=1
+ write(licz,'(bz,i3.3)') itraj
+ pdbfile=arg(:iext)//'_'//licz//'.pdb'
endif
if (iargc().gt.6) then
- call getarg(7,citraj)
- read (citraj,*) itraj
- else
- itraj=1
+ call getarg(7,cfreq)
+ read (cfreq,*) ifreq
endif
- print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
+c print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
open(9,file=pdbfile)
nnt = 1
if (itype(1).eq.21) nnt = 2
call xdrffloat(ixdrf, potE, iret)
call xdrffloat(ixdrf, uconst, iret)
call xdrffloat(ixdrf, t_bath, iret)
+ print *,"potE",potE," uconst",uconst," t_bath",t_bath
#ifdef NEWUNRES
call xdrffloat(ixdrf, uconst_back, iret)
#endif
+ print *,"uconst_back",uconst_back
call xdrfint(ixdrf, nss, iret)
do j=1,nss
call xdrfint(ixdrf, ihpb(j), iret)
prec=10000.0
isize=0
+ print *," call xdrf3coord"
call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
projects / unres.git / commitdiff