Please see the same question a week ago,
Quote from prof. David Case
"Chamber is now an action inside the parmed program. So, type "parmed"
to start the program, then type "help" or "help chamber" at the parmed prompt."
Thanks for your report about the manual.
Hai
> On Nov 4, 2016, at 12:25 PM, Neale, Christopher Andrew <cneale.lanl.gov> wrote:
>
> 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 - 10:00:02 PDT
