enddo
iti=itype(i)
di=dist(i,nres+i)
+C 10/03/12 Adam: Correction for zero SC-SC bond length
+ if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+ & di=dsc(itype(i))
vbld(i+nres)=di
if (itype(i).ne.10) then
vbld_inv(i+nres)=1.0d0/di
call contact(.false.,ncont_ref,icont_ref,co)
if (sideadd) then
+C Following 2 lines for diagnostics; comment out if not needed
+ write (iout,*) "Before sideadd"
+ call intout
if(me.eq.king.or..not.out1file)
& write(iout,*)'Adding sidechains'
maxsi=1000
endif
enddo
endif
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+ call chainbuild
+C Following 2 lines for diagnostics; comment out if not needed
+ write (iout,*) "After sideadd"
+ call intout
endif
if (indpdb.eq.0) then
enddo
iti=itype(i)
di=dist(i,nres+i)
+C 10/03/12 Adam: Correction for zero SC-SC bond length
+ if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+ & di=dsc(itype(i))
vbld(i+nres)=di
if (itype(i).ne.10) then
vbld_inv(i+nres)=1.0d0/di
call contact(.false.,ncont_ref,icont_ref,co)
if (sideadd) then
+C Following 2 lines for diagnostics; comment out if not needed
+ write (iout,*) "Before sideadd"
+ call intout
if(me.eq.king.or..not.out1file)
& write(iout,*)'Adding sidechains'
maxsi=1000
& i,' after ',nsi,' trials'
endif
enddo
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+ call chainbuild
endif
+C Following 2 lines for diagnostics; comment out if not needed
+ write (iout,*) "After sideadd"
+ call intout
endif
if (indpdb.eq.0) then
C Read sequence if not taken from the pdb file.
+++ /dev/null
-CPPFLAGS = -DPROCOR -DLINUX -DPGI -DISNAN \
- -DSPLITELE -DAMD64 -DLANG0 \
- -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DPROCOR
-
-FC= ifort -g
-
-OPT = -O3 -ip -w
-
-FFLAGS = -c ${OPT}
-FFLAGS1 = -c -w -g -d2 -CA -CB
-FFLAGS2 = -c -w -g -O0
-FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report
-
-
-BIN = ../../../bin/unres/MINIM/unres_Tc_procor_new_em64_min_sumsl_old.exe
-LIBS = -lpthread
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F.f
-.F.o:
- ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-.f.o:
- ${FC} ${FFLAGS} ${CPPFLAGS} $*.f
-
-
-object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \
- matmult.o readrtns_min.o parmread.o \
- pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
- cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
- gradient_p.o minimize_p.o sumsld.o \
- cored.o rmdd.o geomout_min.o readpdb.o \
- intcartderiv.o \
- MP.o printmat.o convert.o int_to_cart.o
-
-unres: ${object}
-# cc -o compinfo compinfo.c
-# ./compinfo | true
- ${FC} ${FFLAGS} cinfo.f
- ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
-
-
-clean:
- /bin/rm *.o
-
-chainbuild.o: chainbuild.F
- ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F
-
-matmult.o: matmult.f
- ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f
-
-parmread.o : parmread.F
- ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F
-
-intcor.o : intcor.f
- ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f
-
-cartder.o : cartder.F
- ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F
-
-readpdb.o : readpdb.F
- ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
-
-sumsld.o : sumsld.f
- ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f
-
-cored.o : cored.f
- ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f
-
-rmdd.o : rmdd.f
- ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f
-
-energy_p_new_barrier.o : energy_p_new_barrier.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F
-
-gradient_p.o : gradient_p.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F
-
-
-
-
+++ /dev/null
-CPPFLAGS = -DPROCOR -DLINUX -DG77 -DISNAN \
- -DSPLITELE -DAMD64 -DLANG0
-# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-#-DCRYST_TOR
-# -DPROCOR
-# -DTSCSC
-#-DTIMING \
-# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-# -DMOMENT
-#-DPARVEC
-#-DPARINT -DPARINTDER
-
-FC= gfortran
-
-OPT = -O
-
-FFLAGS = -c ${OPT}
-FFLAGS1 = -c -g -C
-FFLAGS2 = -c -g -O0
-FFLAGSE = -c -O3
-
-
-BIN = ../../../bin/unres/MIN/unres_min_gfortran.exe
-LIBS =
-#LIBS = -lpthread
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F
-.F.o:
- ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-
-object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \
- matmult.o readrtns_min.o parmread.o \
- pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
- cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
- gradient_p.o minimize_p.o sumsld.o \
- cored.o rmdd.o geomout_min.o readpdb.o \
- intcartderiv.o \
- MP.o printmat.o convert.o int_to_cart.o
-
-unres: ${object}
-# cc -o compinfo compinfo.c
-# ./compinfo | true
- ${FC} ${FFLAGS} cinfo.f
- ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
-
-
-clean:
- /bin/rm *.o *.il
-
-chainbuild.o: chainbuild.F
- ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F
-
-matmult.o: matmult.f
- ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f
-
-parmread.o : parmread.F
- ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F
-
-intcor.o : intcor.f
- ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f
-
-cartder.o : cartder.F
- ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F
-
-readpdb.o : readpdb.F
- ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
-
-sumsld.o : sumsld.f
- ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f
-
-cored.o : cored.f
- ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f
-
-rmdd.o : rmdd.f
- ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f
-
-energy_p_new_barrier.o : energy_p_new_barrier.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F
-
-gradient_p.o : gradient_p.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F
-
-
-
-
+++ /dev/null
-CPPFLAGS = -DPROCOR -DLINUX -DPGI -DISNAN \
- -DSPLITELE -DAMD64 -DLANG0
-# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-#-DCRYST_TOR
-# -DPROCOR
-# -DTSCSC
-#-DTIMING \
-# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
-# -DMOMENT
-#-DPARVEC
-#-DPARINT -DPARINTDER
-
-FC= ifort -g
-
-OPT = -O3 -ip -w
-
-FFLAGS = -c ${OPT}
-FFLAGS1 = -c -w -g -d2 -CA -CB
-FFLAGS2 = -c -w -g -O0
-FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report
-
-
-BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_92110_min_sumsl.exe
-LIBS = -lpthread
-
-ARCH = LINUX
-PP = /lib/cpp -P
-
-
-all: unres
-
-.SUFFIXES: .F
-.F.o:
- ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
-
-
-object = unres_min.o arcos.o cartprint.o chainbuild.o initialize_p.o \
- matmult.o readrtns_min.o parmread.o \
- pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
- cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
- gradient_p.o minimize_p.o sumsld.o \
- cored.o rmdd.o geomout_min.o readpdb.o \
- intcartderiv.o \
- MP.o printmat.o convert.o int_to_cart.o
-
-unres: ${object}
-# cc -o compinfo compinfo.c
-# ./compinfo | true
- ${FC} ${FFLAGS} cinfo.f
- ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
-
-
-clean:
- /bin/rm *.o *.il
-
-chainbuild.o: chainbuild.F
- ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F
-
-matmult.o: matmult.f
- ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f
-
-parmread.o : parmread.F
- ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F
-
-intcor.o : intcor.f
- ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f
-
-cartder.o : cartder.F
- ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F
-
-readpdb.o : readpdb.F
- ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
-
-sumsld.o : sumsld.f
- ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f
-
-cored.o : cored.f
- ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f
-
-rmdd.o : rmdd.f
- ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f
-
-energy_p_new_barrier.o : energy_p_new_barrier.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F
-
-gradient_p.o : gradient_p.F
- ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F
-
-
-
-
c common /przechowalnia/ v
icall = 1
-c print *,"liv",liv," lv",lv
+C Following 3 line for diagnostics; comment out if not needed
+ write(iout,*) "Enter MINIMIZE liv",liv," lv",lv
+ write (iout,*) "Coordinates before minimization"
+ call intout
call deflt(2,iv,liv,lv,v)
* 12 means fresh start, dont call deflt
iv(1)=12
enddo
iti=itype(i)
di=dist(i,nres+i)
+C 9/29/12 Adam: Correction for zero SC-SC bond length
+ if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+ & di=dsc(itype(i))
vbld(i+nres)=di
if (itype(i).ne.10) then
vbld_inv(i+nres)=1.0d0/di
c call contact(.false.,ncont_ref,icont_ref,co)
if (sideadd) then
+C Following 2 lines for diagnostics; comment out if not needed
+ write (iout,*) "Before sideadd"
+ call intout
if(me.eq.king.or..not.out1file)
& write(iout,*)'Adding sidechains'
maxsi=1000
& i,' after ',nsi,' trials'
endif
enddo
+C 9/29/12 Adam: Recalculate coordinates with new side chain positions
+ call chainbuild
endif
+C Following 2 lines for diagnostics; comment out if not needed
+ write (iout,*) "After sideadd"
+ call intout
endif
if (indpdb.eq.0) then
C Read sequence if not taken from the pdb file.