Dear Amber users:
I am new to amber, starting now with version 16.
I have just compiled amber16 and I can't find the chamber program, which I would like to use so that I can run a simulation in amber16 using the charmm36 force field. The amber16 manual discusses the chamber program, so I presume it is still the recommended way to proceed in this case.
$ which chamber|wc -l
0
$ ls /scratch/cneale/exe/AMBER/amber16/bin
acdoctor charmmgen ffgbsa make_crd_hg mdout_analyzer.py nc-config paramfit process_minout.perl sander sviol xaLeap
addles charmmlipid2amber.py fftw-wisdom makeDIST_RST minab nccopy parmcal PropPDB sander.LES sviol2 xleap
add_pdb ChBox fftw-wisdom-to-conf match mmE ncdump parmchk protonator saxs_md teLeap xparmed
AddToBox CheckMD fix_new_inpcrd_vel match_atomname mm_pbsa_nabnmode ncgen parmchk2 pymdpbsa saxs_rism tinker_to_amber yacc
am1bcc cphstats frcmod2xml matextract mm_pbsa.pl ncgen3 parmed pytleap senergy tleap
ambmask cpinutil.py func matgen MMPBSA.py nef_to_RST pbsa reduce sequenceAligner transform
ambpdb cpptraj gbnsr6 matmerge mmpbsa_py_energy new2oldparm pdb4amber residuegen sgldinfo.sh translate
antechamber database hcp_getpdb matmul mmpbsa_py_nabnmode new_crd_to_dyn pdbSearcher resp sgldwt.sh tss_init
ante-MMPBSA.py elsize hybrid MCPB mm_pbsa_statistics.pl new_to_old_crd PdbSearcher.py respgen softcore_setup.py tss_main
atomtype espgen IPMach.py MCPB.py molsurf nf-config pmemd rism1d sqm tss_next
bondtype espgen.py lmanal mdgx MTKppConstants nfe-umbrella-slice prep2xml rism3d.orave stats ucpp
capActiveSite fantasian makeANG_RST mdnab nab nmode prepgen rism3d.snglpnt stdLib2Sdf UnitCell
CartHess2FC.py FEW.pl makeCHIR_RST mdout2pymbar.pl nab2c OptC4.py process_mdout.perl rism3d.thermo superimposer volslice
$ ls /scratch/cneale/exe/AMBER/amber16/AmberTools/bin/
acdoctor charmmgen ffgbsa make_crd_hg mdout_analyzer.py nc-config paramfit process_minout.perl sander sviol xaLeap
addles charmmlipid2amber.py fftw-wisdom makeDIST_RST minab nccopy parmcal PropPDB sander.LES sviol2 xleap
add_pdb ChBox fftw-wisdom-to-conf match mmE ncdump parmchk protonator saxs_md teLeap xparmed
AddToBox CheckMD fix_new_inpcrd_vel match_atomname mm_pbsa_nabnmode ncgen parmchk2 pymdpbsa saxs_rism tinker_to_amber yacc
am1bcc cphstats frcmod2xml matextract mm_pbsa.pl ncgen3 parmed pytleap senergy tleap
ambmask cpinutil.py func matgen MMPBSA.py nef_to_RST pbsa reduce sequenceAligner transform
ambpdb cpptraj gbnsr6 matmerge mmpbsa_py_energy new2oldparm pdb4amber residuegen sgldinfo.sh translate
antechamber database hcp_getpdb matmul mmpbsa_py_nabnmode new_crd_to_dyn pdbSearcher resp sgldwt.sh tss_init
ante-MMPBSA.py elsize hybrid MCPB mm_pbsa_statistics.pl new_to_old_crd PdbSearcher.py respgen softcore_setup.py tss_main
atomtype espgen IPMach.py MCPB.py molsurf nf-config pmemd rism1d sqm tss_next
bondtype espgen.py lmanal mdgx MTKppConstants nfe-umbrella-slice prep2xml rism3d.orave stats ucpp
capActiveSite fantasian makeANG_RST mdnab nab nmode prepgen rism3d.snglpnt stdLib2Sdf UnitCell
CartHess2FC.py FEW.pl makeCHIR_RST mdout2pymbar.pl nab2c OptC4.py process_mdout.perl rism3d.thermo superimposer volslice
I compiled like this (after successfully running update_amber --update):
make clean
./configure gnu
source /scratch/cneale/exe/AMBER/amber16/amber.sh
make install -j 2
I don't see any error messages (or any messages at all) during compilation about the chamber program.
$ grep chamber output.serial
(cd antechamber && make install )
make[2]: Entering directory `/scratch/cneale/exe/AMBER/amber16/AmberTools/src/antechamber'
gcc -c -fPIC -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -o antechamber.o antechamber.c
gcc -fPIC -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN antechamber.o \
-L/scratch/cneale/exe/AMBER/amber16/lib -lcifparse -lm -o /scratch/cneale/exe/AMBER/amber16/bin/antechamber
make[2]: Leaving directory `/scratch/cneale/exe/AMBER/amber16/AmberTools/src/antechamber'
copying parmed/amber/_chamberparm.py -> build/lib.linux-x86_64-2.7/parmed/amber
copying build/lib.linux-x86_64-2.7/parmed/amber/_chamberparm.py -> /scratch/cneale/exe/AMBER/amber16/lib/python2.7/site-packages/parmed/amber
byte-compiling /scratch/cneale/exe/AMBER/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py to _chamberparm.pyc
Thank you for your help,
Chris.
PS: chamber-related manual page 246-248 content is duplicated on page 248-250
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Received on Fri Nov 04 2016 - 09:30:02 PDT
