Re: [AMBER] patching unsuccessful even after modifying patch_amber.py from Vaibhav Dixit on 2013-03-25 (Amber Archive Mar 2013)

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 25 Mar 2013 16:19:36 +0530

Dear Dr. Jan-Philip Gehrcke and amber people,
They system is somehow not able to use new (right) executable.
cd $AMBERHOME points to the right (newamber/amber12) directory.
But the command you suggested strangely gives output about old executable.
And the creation dates/time for newamber/amber12/bin files are latest
(today). I already have the following lines in my .bashrc which has been
sourced.

export PATH=$PATH\:$AMBERHOME/bin
export AMBERHOME=/usr/local/newamber/amber12
export PATH=$PATH:$AMBERHOME/exe
export PATH=$USERPATH:$PATH

What change I should make to use new executable? Should I delete all (old
and new installation) and reinstall/configure/compile again?

gm.linux-rfml:/usr/local/newamber/amber12/bin> ls -ahl $(command -v cpptraj)
*-rwxr-xr-x 1 root root 1.5M Jan 31 09:42 /usr/local/amber12/bin/cpptraj*
gm.linux-rfml:/usr/local/newamber/amber12/bin> cd $AMBERHOME
gm.linux-rfml:/usr/local/newamber/amber12/bin> ls
total 101708
drwxr-xr-x 14 gm 1000 4096 Mar 25 15:17 ..
-rwxr-xr-x 1 root root 286759 Mar 25 15:20 ncgen
-rwxr-xr-x 1 root root 246833 Mar 25 15:20 ncdump
-rwxr-xr-x 1 root root 1448415 Mar 25 15:21 fftw-wisdom
-rwxr-xr-x 1 root root 2267 Mar 25 15:21 fftw-wisdom-to-conf
-rwxr-xr-x 1 root root 32701 Mar 25 15:24 MTKppConstants
-rwxr-xr-x 1 root root 1498327 Mar 25 15:24 capActiveSite
-rwxr-xr-x 1 root root 1328187 Mar 25 15:24 frcmod2xml
-rwxr-xr-x 1 root root 1464824 Mar 25 15:24 func
-rwxr-xr-x 1 root root 1420876 Mar 25 15:24 hybrid
-rwxr-xr-x 1 root root 1536161 Mar 25 15:24 mmE
-rwxr-xr-x 1 root root 1459442 Mar 25 15:24 prep2xml
-rwxr-xr-x 1 root root 1515172 Mar 25 15:24 protonator
-rwxr-xr-x 1 root root 1650201 Mar 25 15:24 sequenceAligner
-rwxr-xr-x 1 root root 311215 Mar 25 15:24 stats
-rwxr-xr-x 1 root root 1536504 Mar 25 15:24 superimposer
-rwxr-xr-x 1 root root 1439304 Mar 25 15:24 stdLib2Sdf
-rwxr-xr-x 1 root root 1380319 Mar 25 15:24 pdbSearcher
-rwxr-xr-x 1 root root 1990585 Mar 25 15:24 MCPB
-rwxr-xr-x 1 root root 131984 Mar 25 15:24 ucpp
-rwxr-xr-x 1 root root 90762 Mar 25 15:24 yacc
-rwxr-xr-x 1 root root 119485 Mar 25 15:24 ambpdb
-rwxr-xr-x 1 root root 23090 Mar 25 15:24 elsize
-rwxr-xr-x 1 root root 112876 Mar 25 15:24 molsurf
-rwxr-xr-x 1 root root 78407 Mar 25 15:24 resp
-rwxr-xr-x 1 root root 33131 Mar 25 15:24 calcpka
-rwxr-xr-x 1 root root 15641 Mar 25 15:24 cpinutil.py
drwxr-xr-x 2 root root 4096 Mar 25 15:24 cpinutils
-rwxr-xr-x 1 root root 21868 Mar 25 15:24 softcore_setup.py
-rwxr-xr-x 1 root root 4498 Mar 25 15:24 process_minout.perl
-rwxr-xr-x 1 root root 6712 Mar 25 15:24 process_mdout.perl
-rwxr-xr-x 1 root root 2369 Mar 25 15:24 mdout2pymbar.pl
-rwxr-xr-x 1 root root 1387 Mar 25 15:24 sgldwt.sh
-rwxr-xr-x 1 root root 1794 Mar 25 15:24 sgldinfo.sh
-rwxr-xr-x 1 root root 134627 Mar 25 15:24 charmmlipid2amber.x
-rwxr-xr-x 1 root root 250494 Mar 25 15:24 chamber
-rwxr-xr-x 1 root root 2735137 Mar 25 15:25 pbsa
-rwxr-xr-x 1 root root 100490 Mar 25 15:25 am1bcc
-rwxr-xr-x 1 root root 219195 Mar 25 15:25 acdoctor
-rwxr-xr-x 1 root root 257468 Mar 25 15:25 antechamber
-rwxr-xr-x 1 root root 159060 Mar 25 15:25 atomtype
-rwxr-xr-x 1 root root 132972 Mar 25 15:25 bondtype
-rwxr-xr-x 1 root root 157255 Mar 25 15:25 charmmgen
-rwxr-xr-x 1 root root 32961 Mar 25 15:25 database
-rwxr-xr-x 1 root root 19280 Mar 25 15:25 espgen
-rwxr-xr-x 1 root root 31604 Mar 25 15:25 parmcal
-rwxr-xr-x 1 root root 165449 Mar 25 15:25 parmchk
-rwxr-xr-x 1 root root 144562 Mar 25 15:25 prepgen
-rwxr-xr-x 1 root root 73910 Mar 25 15:25 residuegen
-rwxr-xr-x 1 root root 103375 Mar 25 15:25 respgen
-rwxr-xr-x 1 root root 119894 Mar 25 15:25 translate
-rwxr-xr-x 1 root root 28263 Mar 25 15:25 top2mol2
-rwxr-xr-x 1 root root 1372976 Mar 25 15:25 sqm
-rwxr-xr-x 1 root root 1336406 Mar 25 15:25 rdparm
-rwxr-xr-x 1 root root 1336406 Mar 25 15:25 ptraj
-rwxr-xr-x 1 root root 1527793 Mar 25 15:26 cpptraj
-rwxr-xr-x 1 root root 594667 Mar 25 15:26 reduce
-rwxr-xr-x 1 root root 341 Mar 25 15:26 tleap
-rwxr-xr-x 1 root root 816980 Mar 25 15:26 teLeap
-rwxr-xr-x 1 root root 1497149 Mar 25 15:26 xaLeap
-rwxr-xr-x 1 root root 406 Mar 25 15:26 xleap
-rwxr-xr-x 1 root root 14078 Mar 25 15:27 hcp_getpdb
-rwxr-xr-x 1 root root 625748 Mar 25 15:27 rism1d
-rwxr-xr-x 1 root root 18638 Mar 25 15:27 nab
-rwxr-xr-x 1 root root 169033 Mar 25 15:27 nab2c
-rwxr-xr-x 1 root root 321 Mar 25 15:27 lmodprmtop
-rwxr-xr-x 1 root root 19498 Mar 25 15:27 matextract
-rwxr-xr-x 1 root root 3519129 Mar 25 15:27 matgen
-rwxr-xr-x 1 root root 3493434 Mar 25 15:27 matmerge
-rwxr-xr-x 1 root root 3493266 Mar 25 15:27 matmul
-rwxr-xr-x 1 root root 3510347 Mar 25 15:27 transform
-rwxr-xr-x 1 root root 3523279 Mar 25 15:27 tss_init
-rwxr-xr-x 1 root root 3553725 Mar 25 15:27 tss_main
-rwxr-xr-x 1 root root 3523490 Mar 25 15:27 tss_next
-rwxr-xr-x 1 root root 3748479 Mar 25 15:27 rism3d.snglpnt
-rwxr-xr-x 1 root root 2271633 Mar 25 15:27 mdgx
-rwxr-xr-x 1 root root 53552 Mar 25 15:27 AddToBox
-rwxr-xr-x 1 root root 14050 Mar 25 15:27 ChBox
-rwxr-xr-x 1 root root 65926 Mar 25 15:27 CheckMD
-rwxr-xr-x 1 root root 40798 Mar 25 15:27 PropPDB
-rwxr-xr-x 1 root root 32241 Mar 25 15:27 UnitCell
-rwxr-xr-x 1 root root 45451 Mar 25 15:27 add_xray
-rwxr-xr-x 1 root root 46031 Mar 25 15:27 add_pdb
-rwxr-xr-x 1 root root 7007 Mar 25 15:27 parmed.py
-rwxr-xr-x 1 root root 2916 Mar 25 15:27 xparmed.py
-rwxr-xr-x 1 root root 6469 Mar 25 15:27 ante-MMPBSA.py
-rwxr-xr-x 1 root root 28291 Mar 25 15:27 MMPBSA.py
-rwxr-xr-x 1 root root 4057328 Mar 25 15:27 mmpbsa_py_nabnmode
-rwxr-xr-x 1 root root 3739994 Mar 25 15:27 mmpbsa_py_energy
-rwxr-xr-x 1 root root 3591523 Mar 25 15:27 ffgbsa
-rwxr-xr-x 1 root root 3514616 Mar 25 15:27 minab
-rwxr-xr-x 1 root root 3514739 Mar 25 15:27 mdnab
lrwxrwxrwx 1 root root 35 Mar 25 15:27 pytleap ->
../AmberTools/src/amberlite/pytleap
lrwxrwxrwx 1 root root 36 Mar 25 15:27 pymdpbsa ->
../AmberTools/src/amberlite/pymdpbsa
-rwxr-xr-x 1 root root 174101 Mar 25 15:27 paramfit
-rwxr-xr-x 1 root root 60242 Mar 25 15:27 new2oldparm
-rwxr-xr-x 1 root root 295654 Mar 25 15:27 addles
-rwxr-xr-x 1 root root 5566196 Mar 25 15:28 sander
-rwxr-xr-x 1 root root 5587381 Mar 25 15:28 sander.LES
-rwxr-xr-x 1 root root 88274 Mar 25 15:28 ambmask
-rwxr-xr-x 1 root root 40109 Mar 25 15:28 make_crd_hg
-rwxr-xr-x 1 root root 3831162 Mar 25 15:28 mm_pbsa_nabnmode
-rwxr-xr-x 1 root root 1117 Mar 25 15:28 mm_pbsa_statistics.pl
-rwxr-xr-x 1 root root 2256 Mar 25 15:28 mm_pbsa.pl
-rwxr-xr-x 1 root root 32899 Mar 25 15:28 makeDIST_RST
-rwxr-xr-x 1 root root 27649 Mar 25 15:28 makeANG_RST
-rwxr-xr-x 1 root root 5955 Mar 25 15:28 makeCHIR_RST
-rwxr-xr-x 1 root root 3253 Mar 25 15:28 makeDIP_RST.protein
-rwxr-xr-x 1 root root 9507 Mar 25 15:28 makeDIP_RST.dna
-rwxr-xr-x 1 root root 81169 Mar 25 15:29 fantasian
-rwxr-xr-x 1 root root 2049 Mar 25 15:29 sviol2
-rwxr-xr-x 1 root root 15475 Mar 25 15:29 sviol
-rwxr-xr-x 1 root root 8304 Mar 25 15:29 senergy
-rwxr-xr-x 1 root root 542422 Mar 25 15:29 nmode
-rwxr-xr-x 1 root root 1315117 Mar 25 15:29 pmemd
drwxr-xr-x 6 root root 4096 Mar 25 15:29 .
-rwxr-xr-x 1 root root 1402772 Mar 25 15:29 pmemd.amoeba
drwxr-xr-x 2 root root 4096 Mar 25 15:47 MMPBSA_mods
drwxr-xr-x 4 root root 4096 Mar 25 15:55 chemistry
drwxr-xr-x 3 root root 4096 Mar 25 15:55 ParmedTools

On Mon, Mar 25, 2013 at 4:02 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:

> Make sure that you really have compiled "everything" and that you are
> actually using the new executable.
>
> To that end, have a look in your build tree's bin directory (e.g.
> /path/to/amber12/bin) and check the file creation times. If the creation
> time of cpptraj corresponds to the compilation time, you can be sure
> that it has been rebuilt.
>
> Then, make sure that the environment variable AMBERHOME corresponds to
> your new build tree:
>
> export AMBERHOME=/path/to/amber12
>
> Then, prepend ${AMBERHOME}/bin to your PATH:
>
> export PATH=${AMBERHOME}/bin\:${PATH}
>
> Verify that the freshly built executables are in your PATH. Regarding
> cpptraj, you could check once again:
>
> $ ls -ahl $(command -v cpptraj)
> 2.7M -rwxr-x--- 1 user group 2.7M Mar 11 11:57
> /path/to/amber12/bin/cpptraj*
>
> HTH,
>
> Jan-Philip
>
>
> On 03/25/2013 11:17 AM, Vaibhav Dixit wrote:
> > 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
> >>
> >
> >
> >
>
>
> _______________________________________________
> 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 - 04:00:03 PDT