I have recompiled everything, but why the cpptraj version is not the latest?
Will it affect the analysis I am going to perform (combining trajectories,
clustering, H-bond, SASA and some other analysis)?
Thank you.
On Mon, Mar 25, 2013 at 3:33 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Yes, you need to recompile everything.
>
> --
> Jason M. Swails
> Quantum Theory Project
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Mar 25, 2013, at 1:43 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > Dear Dr. Jason and Amber people,
> > Thanks a lot for helping me figure about that small (silly) directory
> name
> > error. After fixing that it seems to have worked fine as shown below and
> > patch level is also 35 and 14 for AmberTools and Amber respectively now.
> I
> > hope whatever files patch_amber.py has moved, is what was expected,
> please
> > suggest if you find something wrong there.
> >
> > About setting mirrors: As we had discussed earlier
> > here<http://archive.ambermd.org/201301/0451.html>,
> > I tried many ways but my proxy settings won't let me go online while
> using
> > patch_amber.py and gives error "No internet access!". Thus I have to
> follow
> > this path.
> >
> > The make install & make test steps gave a few warnings, but have
> completed
> > successfully as seen in the bottom of this message.
> >
> > Out of curiosity: whenever a new patch becomes available for AmberTools,
> is
> > it necessary for us to reconfigure/recompile Amber along with AmberTools
> > and vise-versa?
> > Thanks a lot.
> >
> > linux-rfml:/usr/local/newamber/amber12 # vim patch_amber.py
> > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree
> > Determining patches to download for AmberTools12
> > Downloading bugfix.14
> > Downloading bugfix.15
> > Downloading bugfix.16
> > Downloading bugfix.17
> > Downloading bugfix.18
> > Downloading bugfix.19
> > Downloading bugfix.20
> > Downloading bugfix.21
> > Downloading bugfix.22
> > Downloading bugfix.23
> > Downloading bugfix.24
> > Downloading bugfix.25
> > Downloading bugfix.26
> > Downloading bugfix.27
> > Downloading bugfix.28
> > Downloading bugfix.29
> > Downloading bugfix.30
> > Downloading bugfix.31
> > Downloading bugfix.32
> > Downloading bugfix.33
> > Downloading bugfix.34
> > Downloading bugfix.35
> >
> > Determining patches to download for Amber12
> > Amber12 is up to date. Nothing to download
> >
> > Applying AmberTools12 patches
> > Moving bugfix.14 to AmberTools_Applied_Patches
> > Moving bugfix.15 to AmberTools_Applied_Patches
> > Creating file
> >
> /usr/local/newamber/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
> > Creating file
> > /usr/local/newamber/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.h
> > Moving bugfix.16 to AmberTools_Applied_Patches
> > Moving bugfix.17 to AmberTools_Applied_Patches
> > Moving bugfix.18 to AmberTools_Applied_Patches
> > Moving bugfix.19 to AmberTools_Applied_Patches
> > Moving bugfix.20 to AmberTools_Applied_Patches
> > Moving bugfix.21 to AmberTools_Applied_Patches
> > This patch patches patch_amber.py. I will quit after this patch so the
> rest
> > may be applied with the updated version.
> > Moving bugfix.22 to AmberTools_Applied_Patches
> > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree
> > Determining patches to download for AmberTools12
> > Downloading bugfix.23
> > Downloading bugfix.24
> > Downloading bugfix.25
> > Downloading bugfix.26
> > Downloading bugfix.27
> > Downloading bugfix.28
> > Downloading bugfix.29
> > Downloading bugfix.30
> > Downloading bugfix.31
> > Downloading bugfix.32
> > Downloading bugfix.33
> > Downloading bugfix.34
> > Downloading bugfix.35
> >
> > Determining patches to download for Amber12
> > Downloading bugfix.9.bz2_
> > Decompressing .patches/Amber_Unapplied_Patches/bugfix.9.bz2 with
> > /usr/bin/bunzip2
> > Downloading bugfix.10
> > Downloading bugfix.11
> > Downloading bugfix.12
> > Downloading bugfix.13
> > Downloading bugfix.14
> >
> > Applying AmberTools12 patches
> > Moving bugfix.23 to AmberTools_Applied_Patches
> > Moving bugfix.24 to AmberTools_Applied_Patches
> > Moving bugfix.25 to AmberTools_Applied_Patches
> > Moving bugfix.26 to AmberTools_Applied_Patches
> > Moving bugfix.27 to AmberTools_Applied_Patches
> > Moving bugfix.28 to AmberTools_Applied_Patches
> > Moving bugfix.29 to AmberTools_Applied_Patches
> > Moving bugfix.30 to AmberTools_Applied_Patches
> > Moving bugfix.31 to AmberTools_Applied_Patches
> > Moving bugfix.32 to AmberTools_Applied_Patches
> > Moving bugfix.33 to AmberTools_Applied_Patches
> > Moving bugfix.34 to AmberTools_Applied_Patches
> > Moving bugfix.35 to AmberTools_Applied_Patches
> > Applying Amber12 patches
> > Creating file /usr/local/newamber/amber12/src/pmemd/src/cuda/kCNF.h
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/src/pmemd/src/cuda/ptxmacros.h
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/Run.pme.amd1
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/Run.pme.amd2
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/Run.pme.amd3
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/dhfr.pdb
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/md12.x
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/amd/dhfr_pme/mdout.pme.amd1.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/amd/dhfr_pme/mdout.pme.amd2.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/amd/dhfr_pme/mdout.pme.amd3.save
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/dhfr_pme/prmtop
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/Run.ips.amd1
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/Run.ips.amd2
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/Run.ips.amd3
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/inpcrd
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/amd/gact_ips/mdout.ips.amd1.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/amd/gact_ips/mdout.ips.amd2.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/amd/gact_ips/mdout.ips.amd3.save
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/gact_ips/prmtop
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/Run.gb.amd1
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/Run.gb.amd2
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/Run.gb.amd3
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/md4.x
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/amd/rna_gb/mdout.gb.amd1.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/amd/rna_gb/mdout.gb.amd2.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/amd/rna_gb/mdout.gb.amd3.save
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/prmtop
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/amd/rna_gb/rna.pdb
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/4096wat/mdout.pure_wat.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/4096wat/mdout.vrand.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_npt_ntt1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nve.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt2.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdcrd.pure_wat_oct_nvt_ntt3.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_npt_ntt1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nve.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt2.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/4096wat_oct/mdout.pure_wat_oct_nvt_ntt3.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/Run.pme.amd1
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/Run.pme.amd2
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/Run.pme.amd3
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/dhfr.pdb
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/md12.x
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd2.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/mdout.pme.amd3.GPU_SPFP
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/dhfr_pme/prmtop
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/Run.ips.amd1
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/Run.ips.amd2
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/Run.ips.amd3
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/gact_ips/inpcrd
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd2.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/amd/gact_ips/mdout.ips.amd3.GPU_SPFP
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/gact_ips/prmtop
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/cuda/amd/rna_gb/Run.gb.amd1
> > Changing mode to 755
> > Creating file
> /usr/local/newamber/amber12/test/cuda/amd/rna_gb/Run.gb.amd2
> > Changing mode to 755
> > Creating file
> /usr/local/newamber/amber12/test/cuda/amd/rna_gb/Run.gb.amd3
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/md4.x
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd2.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/amd/rna_gb/mdout.gb.amd3.GPU_SPFP
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/prmtop
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/cuda/amd/rna_gb/rna.pdb
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr/mdout.dhfr_charmm_md.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr/mdout.dhfr_charmm_min.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap/mdout.dhfr_charmm_md.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap/mdout.dhfr_charmm_min.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_md.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_md_NPT.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_min.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_md.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_cmap_pbc/mdout.dhfr_charmm_pbc_noshake_min.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_pbc/mdout.dhfr_charmm_pbc_noshake_md.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/chamber/dhfr_pbc/mdout.dhfr_charmm_pbc_noshake_min.GPU_SPFP
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.min.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.noshake.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2_ntt1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2_ntt1_ntr1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntb2_ntt3.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/dhfr/mdout.dhfr.ntr1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/gb_ala3/igb1_ntc1_min.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest0_ntt0_igb1_ntc1_coldstart.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest0_ntt0_igb1_ntc1_hotstart.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc1.mdcrd.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc1.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc1.rst.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc2.mdcrd.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb1_ntc2.rst.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb2_ntc1.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb2_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc1.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_alpb.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_ntr1.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_rgbmax.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb5_ntc2_saltcon.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb7_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt0_igb8_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt1_igb1_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt2_igb1_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/gb_ala3/irest1_ntt3_igb1_ntc2.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/cuda/ips/mdout.ips.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/ips/mdout.ips_ntt3.GPU_SPFP
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/cuda/jac/jac.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/large_solute_count/mdout.ntb2_ntt1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb7.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/Run.nmropt_1angle_gb
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/angle_gb_vs_t.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/angle/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/Run.dist_gb
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/dist_gb_vs_t.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/Run.distCOM_gb
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/distCOM_gb.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/distCOM_gb_vs_t.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/distance_COM/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/Run.jar_gb
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/dist_gb.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/dist_gb_vs_t.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance/mdout.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/Run.jar_gb
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/distCOM_gb.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/distCOM_gb_vs_t.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_distance_COM/mdout.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/Run.jar_torsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/jartorsion_gb.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/jartorsion_gb.dat.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/jar_torsion/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/myoglobin_gb.inpcrd
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/myoglobin_gb.prmtop
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/Run.nmropt_1_torsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/Run.nmropt_1tautp_gb
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/tautp/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/Run.nmropt_1temp_gb
> > Changing mode to 755
> > Creating file
> /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/gb/temp/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/Run.nmropt_1angle_pbc
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/angle_pbc_vs_t.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/angle/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/Run.dist_pbc
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/dist_pbc_vs_t.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/Run.distCOM_pbc
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/distCOM_pbc.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/distCOM_pbc_vs_t.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/distance_COM/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/Run.jar_pbc
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/dist_pbc.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/dist_pbc_vs_t.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance/mdout.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/Run.jar_pbc
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/distCOM_pbc.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/distCOM_pbc_vs_t.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/distCOM_pbc_vs_t.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/mdout.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_distance_COM/mdout.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/Run.jar_torsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/jartorsion_pbc.RST
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/jartorsion_pbc.dat.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/jar_torsion/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/myoglobin_pbc.inpcrd
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/myoglobin_pbc.prmtop
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/Run.nmropt_1_torsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/Run.nmropt_1tautp_pbc
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/tautp/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/Run.nmropt_1temp_pbc
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.CPU
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.GPU_DPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.GPU_SPDP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/nmropt/pme/temp/mdout.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/npt_ntr_ntt3_oct/mdout.ntp1.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nucleosome/nucleosome_md1_ntt1.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nucleosome/nucleosome_md2_ntt0.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/nucleosome/nucleosome_min.out.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_box_npt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_box_nvt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_oct_npt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/tip4pew/mdout.tip4pew_oct_nvt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_box_npt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_box_nvt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_oct_npt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/tip5p/mdout.tip5p_oct_nvt.GPU_SPFP
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/cuda/trpcage/trpcage_md.out.GPU_SPFP
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/nmropt/Makefile
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/2xangle/2xangle_gb_vs_t.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/2xangle/Run.nmropt_1_2xangle_gb
> > Changing mode to 755
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/gb/2xangle/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/angle/Run.nmropt_1angle_gb
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/angle/angle_gb_vs_t.save
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/nmropt/gb/angle/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/distance/Run.dist_gb
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/distance/dist_gb_vs_t.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/gb/distance/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/distance_COM/Run.distCOM_gb
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/distance_COM/distCOM_gb_vs_t.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/distance_COM/mdout.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/jar_comtorsion/Run.jar_comtorsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/jar_comtorsion/jartorsion_com_gb.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_comtorsion/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance/Run.jar_gb
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance/dist_gb_vs_t.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance_COM/Run.jar_gb
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/jar_distance_COM/distCOM_gb_vs_t.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_distance_COM/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod/Run.lcod_jar
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod_dist/Run.jar_lcod
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod_dist/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_lcod_dist/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_torsion/Run.jar_torsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/jar_torsion/jartorsion_gb.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/jar_torsion/mdout.save
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/nmropt/gb/lcod/Run.lcod
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/lcod/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/nmropt/gb/lcod/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/lcod_com/Run.lcod_com
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/lcod_com/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/gb/lcod_com/mdout.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/gb/myoglobin_gb.inpcrd
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/gb/myoglobin_gb.prmtop
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_2xtorsion/2xtorsion_gb.dat.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_2xtorsion/Run.nmropt_1_2xtorsion
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_2xtorsion/mdout.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_torsion/Run.nmropt_1_torsion
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_torsion/mdout.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/gb/nmropt_1_torsion/torsion_gb.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/tautp/Run.nmropt_1tautp_gb
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/nmropt/gb/tautp/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/gb/temp/Run.nmropt_1temp_gb
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/nmropt/gb/temp/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/2xangle/2xangle_pbc_vs_t.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/2xangle/Run.nmropt_1_2xangle_pbc
> > Changing mode to 755
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/pme/2xangle/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/angle/Run.nmropt_1angle_pbc
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/angle/angle_pbc_vs_t.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/pme/angle/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/distance/Run.dist_pbc
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/distance/dist_pbc_vs_t.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/distance/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/distance_COM/Run.distCOM_pbc
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/distance_COM/distCOM_pbc_vs_t.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/distance_COM/mdout.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/jar_comtorsion/Run.jar_comtorsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/jar_comtorsion/jartorsion_com_pbc.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_comtorsion/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance/Run.jar_pbc
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/jar_distance/dist_pbc_vs_t.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance_COM/Run.jar_pbc
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/jar_distance_COM/distCOM_pbc_vs_t.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_distance_COM/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod/Run.jar_lcod
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod_dist/Run.lcod_dist
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod_dist/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_lcod_dist/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_torsion/Run.jar_torsion
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/jar_torsion/jartorsion_pbc.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/jar_torsion/mdout.save
> > Changing mode to 644
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/pme/lcod/Run.lcod_pme
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/lcod/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file /usr/local/newamber/amber12/test/nmropt/pme/lcod/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/lcod_com/Run.lcod_com
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/lcod_com/lcod_vs_t.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/lcod_com/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/myoglobin_pbc.inpcrd
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/myoglobin_pbc.prmtop
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_2xtorsion/2xtorsion_pbc.dat.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_2xtorsion/Run.nmropt_1_2xtorsion
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_2xtorsion/mdout.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_torsion/Run.nmropt_1_torsion
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_torsion/mdout.save
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/nmropt/pme/nmropt_1_torsion/torsion_pbc.dat.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/tautp/Run.nmropt_1tautp_pbc
> > Changing mode to 755
> > Creating file
> /usr/local/newamber/amber12/test/nmropt/pme/tautp/mdout.save
> > Changing mode to 644
> > Creating file
> > /usr/local/newamber/amber12/test/nmropt/pme/temp/Run.nmropt_1temp_pbc
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/test/nmropt/pme/temp/mdout.save
> > Changing mode to 644
> > Moving bugfix.9 to Amber_Applied_Patches
> > Moving bugfix.10 to Amber_Applied_Patches
> > Moving bugfix.11 to Amber_Applied_Patches
> > Moving bugfix.12 to Amber_Applied_Patches
> > Moving bugfix.13 to Amber_Applied_Patches
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/cta_radix_rank.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/cta_radix_sort.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/downsweep/cta.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/downsweep/kernel.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/downsweep/kernel_policy.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/enactor.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/pass_policy.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/problem_instance.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/single/cta.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/single/kernel.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/single/kernel_policy.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/sort_utils.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/spine/cta.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/spine/kernel.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/spine/kernel_policy.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/tex_ref.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/upsweep/cta.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/upsweep/kernel.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/radix_sort/upsweep/kernel_policy.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/allocator.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/basic_utils.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/cta_work_distribution.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/cuda_properties.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/device_intrinsics.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/error_utils.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/load_tile.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/modified_load.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/modified_store.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/io/store_tile.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/kernel_props.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/multi_buffer.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/ns_umbrella.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/numeric_traits.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/operators.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/raking_grid.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/random_bits.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/reduction/cooperative_reduction.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/reduction/serial_reduce.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/reduction/warp_reduce.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/scan/cooperative_scan.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/scan/serial_scan.cuh
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/scan/warp_scan.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/spine.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/spinlock.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/srts_details.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/srts_grid.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/tex_vector.cuh
> > Changing mode to 755
> > Creating file
> > /usr/local/newamber/amber12/src/pmemd/src/cuda/B40C/util/vector_types.cuh
> > Changing mode to 755
> > Creating file /usr/local/newamber/amber12/src/pmemd/src/gbsa.F90
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/myoglobin/Run_md_myoglobin_igb8_gbsa
> > Changing mode to 755
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.CPU
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.GPU_DPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.GPU_SPDP
> > Changing mode to 644
> > Creating file
> >
> /usr/local/newamber/amber12/test/cuda/myoglobin/myoglobin_md_igb8_gbsa.out.GPU_SPFP
> > Changing mode to 644
> > Moving bugfix.14 to Amber_Applied_Patches
> > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree
> > Determining patches to download for AmberTools12
> > AmberTools12 is up to date. Nothing to download
> >
> > Determining patches to download for Amber12
> > Amber12 is up to date. Nothing to download
> >
> > linux-rfml:/usr/local/newamber/amber12 # ./configure gnu
> > Checking for updates...
> > AmberTools12 is up to date
> > Amber12 is up to date
> >
> > Searching for python2... Found python2.7: /usr/bin/python2.7
> >
> > Obtaining the gnu suite version:
> > gcc -v
> > The version is 4.6.2
> >
> > Testing the gcc compiler:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> > OK
> >
> > Testing the gfortran compiler:
> > gfortran -O0 -o testp testp.f
> > OK
> >
> > Testing mixed C/Fortran compilation:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> > testp.c
> > gfortran -O0 -c -o testp.f.o testp.f
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
> > testp.f.o -lgfortran -w
> > OK
> >
> > Testing pointer size:
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
> > test_pointer_size.c
> > Detected 32 bit operating system.
> >
> > Testing flex: OK
> >
> > Configuring NetCDF (may be time-consuming)...
> >
> > NetCDF configure succeeded.
> >
> > Checking for zlib: OK
> >
> > Checking for libbz2: OK
> >
> > Configuring fftw-3.3 (may be time-consuming)...
> >
> > fftw-3.3 configure succeeded.
> >
> > Configuring XBLAS (may be time-consuming)...
> >
> > XBLAS configure succeeded.
> >
> > Configuring MTK++ (may be time-consuming)...
> >
> > MTK++-0.2.0 configure succeeded.
> >
> > The configuration file, config.h, was successfully created.
> >
> > The next step is to type 'make install'
> >
> > Cleaning the src directories. This may take a few moments.
> > Configure complete.
> > linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --patch-level
> > Latest patch applied to AmberTools12: 35
> > Latest patch applied to Amber12: 14
> >
> > linux-rfml:/usr/local/newamber/amber12 # make install
> > make[3]: Leaving directory
> > `/usr/local/newamber/amber12/src/pmemd.amoeba/src'
> > Installation of pmemd.amoeba complete
> > make[2]: Leaving directory `/usr/local/newamber/amber12/src/pmemd.amoeba'
> >
> > Installation of Amber12 (serial) is complete at Mon Mar 25 15:29:40 IST
> > 2013.
> >
> > make[1]: Leaving directory `/usr/local/newamber/amber12/src'
> > linux-rfml:/usr/local/newamber/amber12 # make test
> > ........
> > make[2]: Leaving directory `/usr/local/newamber/amber12/test'
> > 524 file comparisons passed
> > 36 file comparisons failed
> > 26 tests experienced errors
> > Test log file saved as
> >
> /usr/local/newamber/amber12/logs/test_amber_serial/2013-03-25_15-59-30.log
> > Test diffs file saved as
> >
> /usr/local/newamber/amber12/logs/test_amber_serial/2013-03-25_15-59-30.diff
> > make[1]: Leaving directory `/usr/local/newamber/amber12/test'
> >
> > Summary of AmberTools serial tests:
> >
> > 604 file comparisons passed
> > 6 file comparisons failed
> > 0 tests experienced errors
> > Test log file saved as
> > /usr/local/newamber/amber12/logs/test_at_serial/2013-03-25_15-32-02.log
> > Test diffs file saved as
> > /usr/local/newamber/amber12/logs/test_at_serial/2013-03-25_15-32-02.diff
> >
> >
> >
> > On Mon, Mar 25, 2013 at 5:49 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> Please disregard my last suggestion. I found your problem.
> >>
> >> On Sun, Mar 24, 2013 at 8:17 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >>> wrote:
> >>
> >>>
> >>> linux-rfml:/usr/local/newamber/amber12 # ls
> >>> ../../bugfixes/AmberTools12/12.0/
> >>
> >> You are storing the bug fixes for AmberTools 12 in
> >> /usr/local/bugfixes/AmberTools12/12.0/ but you are looking for them in
> >> /usr/local/bugfixes/AmberTools/12.0/ (notice the extra 12 in the first
> >> version). Therefore, patch_amber.py finds no patches for AmberTools 12
> and
> >> patches nothing. And bugfixes for Amber 9 and above cannot be
> >> applied/found until bugfix.22 from AmberTools has been applied.
> >>
> >> So change the directory name from AmberTools12 to AmberTools and
> everything
> >> should work.
> >>
> >> The question remains though, why set up mirrors instead of allowing
> >> patch_amber.py to download the files directly?
> >>
> >> All the best,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D.
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408, +91-7709129400.
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 25 2013 - 03:30:04 PDT
