AMBER Archive (2006)

Subject: Re: AMBER: Problem in compiling sander with MMTSB

From: luckyang_at_gmail.com
Date: Wed Feb 01 2006 - 21:26:55 CST

Dear Dr. Case,

I got the following message with the updated bugfix.all:

patching file src/leap/src/leap/unitio.c
patching file src/configure
patching file src/antechamber/pdb.c
patching file src/pbsa/pb_force.f
Hunk #1 succeeded at 3505 (offset -3 lines).
patching file src/configure
Hunk #1 succeeded at 728 (offset 13 lines).
patching file src/antechamber/am1bcc.c
patching file src/antechamber/antechamber.c
patching file src/antechamber/charge.c
patching file src/antechamber/ring.c
patching file src/antechamber/bondtype.C
patching file src/sander/findmask.f
patching file src/sander/getcor.f
patching file src/sander/mdread.f
patching file src/sander/sander.f
patching file src/antechamber/bondtype.C
patching file src/sander/dynlib.f
patching file dat/leap/cmd/leaprc.ff03
patching file src/lib/nxtsec.f
patching file src/sander/rdparm.f
patching file src/sander/dynlib.f
patching file src/sander/link_atoms.f
patching file src/sander/locmem.f
patching file src/sander/rdparm.f
patching file src/sander/runmd.f
patching file src/sander/sander.f
patching file src/divcon/dcartcl.f
patching file src/divcon/qm_mm.f
patching file src/divcon/rotatecl.f
patching file test/qmmm/standard/lysine.out.save
patching file test/qmmm/divcon/crambin.out.save
patching file src/sander/Makefile
patching file test/qmmm/divcon/crambin_md.out.save
patching file src/leap/src/leap/unit.c
patching file src/leap/src/leap/container.c
patching file src/leap/src/leap/commands.c
patching file src/leap/src/leap/chirality.c
patching file src/sander/parallel.f
patching file src/ptraj/ptraj.c
patching file src/lib/rgroup.f
patching file dat/leap/prep/all_amino03.in
patching file dat/leap/lib/all_amino03.lib
patching file dat/leap/parm/glycam04EP.dat
patching file src/sander/rdparm.f
patching file src/pbsa/rdparm.f
patching file src/anal/locmem.f
patching file src/sander/mdread.f
patching file src/ptraj/actions.c
patching file src/sander/runmd.f
patching file src/sander/locmem.f
patching file test/qmmm/divcon/crambin_md.out.save
patching file src/sander/rdparm.f
patching file dat/leap/parm/gaff.dat
patching file src/etc/ambpdb.f
patching file src/configure
patching file src/pmemd/src/nmr_calls.f90
patching file src/sander/runmd.f
patching file src/sander/ene.f
patching file src/sander/force.f
patching file src/antechamber/prepgen.c
patching file src/pmemd/src/nmr_calls.f90
patching file src/nmode/rgroup.f
patching file test/tgtmd/change_target.ntr/Run.tgtmd
Hunk #1 succeeded at 10 with fuzz 2.
patching file src/pmemd/src/pmemd_clib.c
patching file src/configure
patching file src/sander/forcecp.f
patching file src/leap/src/leap/atom.c
patching file src/leap/src/leap/commands.c
patching file src/leap/src/leap/helptext.text
patching file test/nonper/mdout.cap.save
patching file src/leap/src/leap/amber.c
patching file test/pb_pgb/mdout.pbpgb.save
patching file src/pmemd/src/ew_recip_cit.f90
patching file src/pmemd/src/ew_pairlist.f90
patching file src/pmemd/src/ew_direct_cit.f90
patching file src/sander/parallel.f
patching file src/sander/sander.f
patching file src/sander/nmrred.f
patching file src/pbsa/pb_force.f
patching file src/sander/ew_setup.f
patching file dat/leap/lib/solvents.lib
patching file src/sander/sander.f
patching file src/leap/src/leap/parmSet.c
patching file src/sander/runmd.f
patching file src/pmemd/src/prmtop_dat.f90
patching file src/sander/runmd.f
patching file src/pmemd/src/nextprmtop_section.f90
patching file src/pmemd/src/runmd_cit.f90
patching file src/sander/mmtsb_client.c
Hunk #1 FAILED at 180.
Hunk #2 FAILED at 195.
Hunk #3 FAILED at 301.
3 out of 3 hunks FAILED -- saving rejects to file patch_rejects

Do you know what's wrong with it? I applied the bugfix after unzip the
amber8.tgz

Thanks,

Lu Yang

On 2/1/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Wed, Feb 01, 2006, luckyang_at_gmail.com wrote:
> >
> > I added the bugfix 59 at the end of the bugfix.all and I got the
> following
> > when I patch it:
> >
> > patching file src/sander/mmtsb_client.c
> > Hunk #1 FAILED at 180.
> > Hunk #2 FAILED at 195.
> > Hunk #3 FAILED at 301.
> > 3 out of 3 hunks FAILED -- saving rejects to file patch_rejects. The
> > patch_rejects file is attached in this email.
>
> Try getting bugfix.all again from the web site. The paths in that file
> were incorrect for bugfix.59, but should be fixed now.
>
> ...dac
>
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