Please look at /home/vaibhav/Downloads/amber16/logs/test_at_serial/
2016-08-12_09-42-57.diff
if the failure is due to rounding, I think it's ok. Otherwise, please let
us know.
Hai
On Fri, Aug 12, 2016 at 3:43 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear All,
> I reran the ./config gnu command and this time it did patch all the update
> (so probably internet connection was the issue first time).
> Then I did "make install" and "make test", the test command gave the
> following output (3 comparisons failed).
> I think this is OK, is it? please suggest.
>
> My current interest is to generate AMBER like parameters for Pt-complexes
> and use these for docking and MD simulations.
> I am running GAMESS QM calculations, will use antechamber to extract dis,
> angle, dihedral and force constant parameters and will use a value of 1.87
> A for van der Waals radii of Pt.
>
> Please suggest on this also if possible. (if necessary I will post this as
> a new question)
>
> make test last few output lines
> ---------------------------
> Finished test suite for AmberTools at Fri Aug 12 12:54:55 IST 2016.
>
> make[2]: Leaving directory `/home/vaibhav/Downloads/
> amber16/AmberTools/test'
> 1861 file comparisons passed
> 3 file comparisons failed
> 0 tests experienced errors
> Test log file saved as
> /home/vaibhav/Downloads/amber16/logs/test_at_serial/
> 2016-08-12_09-42-57.log
> Test diffs file saved as
> /home/vaibhav/Downloads/amber16/logs/test_at_serial/
> 2016-08-12_09-42-57.diff
> make[1]: Leaving directory `/home/vaibhav/Downloads/
> amber16/AmberTools/test'
> ==============================================================
> /home/vaibhav/Downloads/amber16/src/Makefile not found.
> This is expected if you have not installed Amber16.
> ==============================================================
> [1]+ Done gedit .bashrc (wd: ~)
> (wd now: /home/vaibhav/Downloads/amber16)
>
>
> On Fri, Aug 12, 2016 at 10:41 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > .Vaibhav: it's likely that the updates were not successfully downloaded
> > (may be because your Python version is quite old (v2.6)).
> >
> > AMBER then offered to install python2.7 for you. However, you need to
> > explicit apply the update by yourself in this case
> >
> > Can you try
> >
> > *amber.python ./update_amber --update*
> >
> > *make install* # like Ross said
> >
> > (do not use "./update_amber" in your case since that script will look for
> > the old python2.6 existing in your env)
> >
> > Let us know if there is any issue.
> >
> > Hai
> >
> > On Fri, Aug 12, 2016 at 12:32 AM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> >
> > > Hi Vaibhav,
> > >
> > > I don't see anything highlighted in bold here but I also don't see any
> > > error. It is complaining that your don't have python installed but then
> > you
> > > say yes to download one which should fix it - does configure finish? If
> > yes
> > > you should then be good do type 'make'.
> > >
> > > All the best
> > > Ross
> > >
> > > > On Aug 11, 2016, at 8:44 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> > > wrote:
> > > >
> > > > Dear All,
> > > > I am trying to install AMBERTOOLS16 on my Linux PC.
> > > > While following the standard procedure I am getting the following
> > > message,
> > > > but I am not sure is it is an error (in bold) which might cause
> > problems
> > > > later.
> > > >
> > > > Is it that an update failed to patch?
> > > > Please suggest.
> > > > Thank you.
> > > >
> > > >
> > > > [root.localhost Downloads]# cd amber16/
> > > > [root.localhost amber16]# ls -arlt
> > > > total 44
> > > > -rwxrwxr-x. 1 501 games 1336 Apr 15 05:55 update_amber
> > > > -rw-rw-r--. 1 501 games 1452 Apr 15 17:57 README
> > > > -rwxrwxr-x. 1 501 games 2509 Apr 15 17:57 configure
> > > > drwxrwxr-x. 2 501 games 4096 Apr 15 17:57 updateutils
> > > > -rw-rw-r--. 1 501 games 3033 Apr 27 21:41 Makefile
> > > > drwxr-xr-x. 14 vaibhav vaibhav 4096 Aug 11 16:31 ..
> > > > drwxr-xr-x. 6 root root 4096 Aug 11 16:33 AmberTools
> > > > drwxrwxr-x. 143 501 games 4096 Aug 11 16:33 test
> > > > drwxr-xr-x. 13 root root 4096 Aug 11 16:33 dat
> > > > drwxr-xr-x. 2 root root 4096 Aug 11 16:33 doc
> > > > drwxr-xr-x. 7 root root 4096 Aug 11 16:33 .
> > > > [root.localhost amber16]# export AMBERHOME=`pwd`
> > > > [root.localhost amber16]# ./configure gnu
> > > > Checking for updates...
> > > > Checking for available patches online. This may take a few seconds...
> > > > Checking for available patches online. This may take a few seconds...
> > > > Traceback (most recent call last):
> > > > File "./update_amber", line 23, in <module>
> > > > app.mainloop()
> > > > File "/home/vaibhav/Downloads/amber16/updateutils/main.py", line
> 479,
> > > in
> > > > mainloop
> > > > self.check_updates()
> > > > File "/home/vaibhav/Downloads/amber16/updateutils/main.py", line
> 171,
> > > in
> > > > check_updates
> > > > self.verbose) + '\n')
> > > > File "/home/vaibhav/Downloads/amber16/updateutils/repos.py", line
> > 184,
> > > in
> > > > patch_details
> > > > self.fill_list()
> > > > File "/home/vaibhav/Downloads/amber16/updateutils/downloader.py",
> > line
> > > > 104, in new_fcn
> > > > return fcn(*args, **kwargs)
> > > > File "/home/vaibhav/Downloads/amber16/updateutils/repos.py", line
> > 204,
> > > in
> > > > fill_list
> > > > p = urlopen(url)
> > > > File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen
> > > > return _opener.open(url, data, timeout)
> > > > File "/usr/lib64/python2.6/urllib2.py", line 391, in open
> > > > response = self._open(req, data)
> > > > File "/usr/lib64/python2.6/urllib2.py", line 409, in _open
> > > > '_open', req)
> > > > File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
> > > > result = func(*args)
> > > > File "/usr/lib64/python2.6/urllib2.py", line 1190, in http_open
> > > > return self.do_open(httplib.HTTPConnection, req)
> > > >
> > > >
> > > >
> > > > * File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open
> > > raise
> > > > URLError(err)urllib2.URLError: <urlopen error timed out>Check for
> > updates
> > > > failed.*
> > > > require Python version 2.7 or >= 3.4
> > > >
> > > > No compatible Python installation found. I can download one from
> > > Continuum
> > > > via Miniconda with all prerequisites. This will only need to be done
> > > once.
> > > > This may take several minutes and will require Internet access.
> > > > (You can also install missing packages by yourself)
> > > >
> > > > Should I do that? [y/n] y
> > > > Downloading an Amber-compatible Python version 2.7 via Miniconda
> > > > and installing it. This may take several minutes.
> > > >
> > > > ============================================================
> > > > ====================
> > > > This script will download and install a version of Python compatible
> > > > with every component of AmberTools and install all required and
> > optional
> > > > prerequisites. The Python distribution is downloaded for your
> operating
> > > > system from Miniconda.
> > > >
> > > > Downloading Python 2.7 Miniconda
> > > > Detected Linux kernel. Downloading the Linux installer
> > > > Downloading the latest Miniconda distribution
> > > > Detected 64-bit Linux
> > > > --2016-08-11 16:34:32-- https://repo.continuum.io/
> > > > miniconda/Miniconda-latest-Linux-x86_64.sh
> > > > Resolving repo.continuum.io... 54.225.68.13, 50.16.198.140,
> > > 54.225.146.221,
> > > > ...
> > > > Connecting to repo.continuum.io|54.225.68.13|:443... connected.
> > > > HTTP request sent, awaiting response... 200 OK
> > > > Length: 27208383 (26M) [application/octet-stream]
> > > > Saving to: “miniconda.sh”
> > > >
> > > > 100%[=======================================================
> > > > ============================================================
> > ==========>]
> > > > 27,208,383 199K/s in 2m 14s
> > > >
> > > > 2016-08-11 16:36:48 (198 KB/s) - “miniconda.sh” saved
> > [27208383/27208383]
> > > >
> > > > Installing Miniconda Python.
> > > > PREFIX=/home/vaibhav/Downloads/amber16/miniconda
> > > > installing: _cache-0.0-py27_x0 ...
> > > > installing: python-2.7.11-0 ...
> > > > installing: conda-env-2.4.5-py27_0 ...
> > > > installing: openssl-1.0.2g-0 ...
> > > > installing: pycosat-0.6.1-py27_0 ...
> > > > installing: pyyaml-3.11-py27_1 ...
> > > > installing: readline-6.2-2 ...
> > > > installing: requests-2.9.1-py27_0 ...
> > > > installing: sqlite-3.9.2-0 ...
> > > > installing: tk-8.5.18-0 ...
> > > > installing: yaml-0.1.6-0 ...
> > > > installing: zlib-1.2.8-0 ...
> > > > installing: conda-4.0.5-py27_0 ...
> > > > installing: pycrypto-2.6.1-py27_0 ...
> > > > installing: pip-8.1.1-py27_1 ...
> > > > installing: wheel-0.29.0-py27_0 ...
> > > > installing: setuptools-20.3-py27_0 ...
> > > > Python 2.7.11 :: Continuum Analytics, Inc.
> > > > creating default environment...
> > > > installation finished.
> > > > Updating and installing required and optional packages...
> > > > Fetching package metadata: ....
> > > > Solving package specifications: .........
> > > >
> > > > Package plan for installation in environment /home/vaibhav/Downloads/
> > > > amber16/miniconda:
> > > >
> > > > The following packages will be downloaded:
> > > >
> > > > package | build
> > > > ---------------------------|-----------------
> > > > nomkl-1.0 | 0 402 B
> > > > sqlite-3.13.0 | 0 4.0 MB
> > > > python-2.7.12 | 1 12.1 MB
> > > > conda-env-2.5.1 | py27_0 26 KB
> > > > ruamel_yaml-0.11.14 | py27_0 352 KB
> > > > conda-4.1.11 | py27_0 201 KB
> > > > ------------------------------------------------------------
> > > > Total: 16.6 MB
> > > >
> > > > The following NEW packages will be INSTALLED:
> > > >
> > > > nomkl: 1.0-0
> > > > ruamel_yaml: 0.11.14-py27_0
> > > >
> > > > The following packages will be UPDATED:
> > > >
> > > > conda: 4.0.5-py27_0 --> 4.1.11-py27_0
> > > > conda-env: 2.4.5-py27_0 --> 2.5.1-py27_0
> > > > python: 2.7.11-0 --> 2.7.12-1
> > > > sqlite: 3.9.2-0 --> 3.13.0-0
> > > >
> > > > Fetching packages ...
> > > > nomkl-1.0-0.ta 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:00 351.71 kB/s
> > > > sqlite-3.13.0- 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:40 101.75 kB/s
> > > > python-2.7.12- 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:01:14 170.23 kB/s
> > > > conda-env-2.5. 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:00 63.07 kB/s
> > > > ruamel_yaml-0. 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:03 101.73 kB/s
> > > > conda-4.1.11-p 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:01 140.04 kB/s
> > > > Extracting packages ...
> > > > [ COMPLETE ]|############################
> > > > ############################################################
> > > > ##################################################| 100%
> > > > Unlinking packages ...
> > > > [ COMPLETE ]|############################
> > > > ############################################################
> > > > ##################################################| 100%
> > > > Linking packages ...
> > > > [ COMPLETE ]|############################
> > > > ############################################################
> > > > ##################################################| 100%
> > > > Fetching package metadata .......
> > > > Solving package specifications: ..........
> > > >
> > > > Package plan for installation in environment /home/vaibhav/Downloads/
> > > > amber16/miniconda:
> > > >
> > > > The following packages will be downloaded:
> > > >
> > > > package | build
> > > > ---------------------------|-----------------
> > > > libgfortran-3.0.0 | 1 281 KB
> > > > libsodium-1.0.10 | 0 1.2 MB
> > > > openblas-0.2.14 | 4 3.6 MB
> > > > zeromq-4.1.4 | 0 4.1 MB
> > > > backports-1.0 | py27_0 1 KB
> > > > backports_abc-0.4 | py27_0 5 KB
> > > > conda-env-2.5.2 | py27_0 26 KB
> > > > cython-0.24.1 | py27_0 5.3 MB
> > > > decorator-4.0.10 | py27_0 12 KB
> > > > functools32-3.2.3.2 | py27_0 15 KB
> > > > ipython_genutils-0.1.0 | py27_0 32 KB
> > > > markupsafe-0.23 | py27_2 31 KB
> > > > mistune-0.7.2 | py27_0 570 KB
> > > > numpy-1.11.1 | py27_nomkl_0 6.2 MB
> > > > path.py-8.2.1 | py27_0 45 KB
> > > > ptyprocess-0.5.1 | py27_0 19 KB
> > > > pygments-2.1.3 | py27_0 1.2 MB
> > > > pyzmq-15.4.0 | py27_0 705 KB
> > > > simplegeneric-0.8.1 | py27_1 7 KB
> > > > six-1.10.0 | py27_0 16 KB
> > > > wcwidth-0.1.7 | py27_0 21 KB
> > > > configparser-3.5.0 | py27_0 31 KB
> > > > get_terminal_size-1.0.0 | py27_0 4 KB
> > > > jinja2-2.8 | py27_1 264 KB
> > > > jsonschema-2.5.1 | py27_0 55 KB
> > > > pathlib2-2.1.0 | py27_0 26 KB
> > > > pexpect-4.0.1 | py27_0 63 KB
> > > > prompt_toolkit-1.0.3 | py27_0 295 KB
> > > > scipy-0.18.0 |np111py27_nomkl_0 31.0 MB
> > > > singledispatch-3.4.0.3 | py27_0 12 KB
> > > > ssl_match_hostname-3.4.0.2 | py27_1 6 KB
> > > > traitlets-4.2.2 | py27_0 108 KB
> > > > entrypoints-0.2.2 | py27_0 6 KB
> > > > jupyter_core-4.1.0 | py27_0 51 KB
> > > > pickleshare-0.7.3 | py27_0 8 KB
> > > > tornado-4.4.1 | py27_0 552 KB
> > > > ipython-5.0.0 | py27_0 933 KB
> > > > jupyter_client-4.3.0 | py27_0 96 KB
> > > > nbformat-4.0.1 | py27_0 112 KB
> > > > terminado-0.6 | py27_0 18 KB
> > > > ipykernel-4.3.1 | py27_0 117 KB
> > > > nbconvert-4.2.0 | py27_0 310 KB
> > > > notebook-4.2.2 | py27_0 5.0 MB
> > > > ------------------------------------------------------------
> > > > Total: 62.3 MB
> > > >
> > > > The following NEW packages will be INSTALLED:
> > > >
> > > > backports: 1.0-py27_0
> > > > backports_abc: 0.4-py27_0
> > > > configparser: 3.5.0-py27_0
> > > > cython: 0.24.1-py27_0
> > > > decorator: 4.0.10-py27_0
> > > > entrypoints: 0.2.2-py27_0
> > > > functools32: 3.2.3.2-py27_0
> > > > get_terminal_size: 1.0.0-py27_0
> > > > ipykernel: 4.3.1-py27_0
> > > > ipython: 5.0.0-py27_0
> > > > ipython_genutils: 0.1.0-py27_0
> > > > jinja2: 2.8-py27_1
> > > > jsonschema: 2.5.1-py27_0
> > > > jupyter_client: 4.3.0-py27_0
> > > > jupyter_core: 4.1.0-py27_0
> > > > libgfortran: 3.0.0-1
> > > > libsodium: 1.0.10-0
> > > > markupsafe: 0.23-py27_2
> > > > mistune: 0.7.2-py27_0
> > > > nbconvert: 4.2.0-py27_0
> > > > nbformat: 4.0.1-py27_0
> > > > notebook: 4.2.2-py27_0
> > > > numpy: 1.11.1-py27_nomkl_0 [nomkl]
> > > > openblas: 0.2.14-4
> > > > path.py: 8.2.1-py27_0
> > > > pathlib2: 2.1.0-py27_0
> > > > pexpect: 4.0.1-py27_0
> > > > pickleshare: 0.7.3-py27_0
> > > > prompt_toolkit: 1.0.3-py27_0
> > > > ptyprocess: 0.5.1-py27_0
> > > > pygments: 2.1.3-py27_0
> > > > pyzmq: 15.4.0-py27_0
> > > > scipy: 0.18.0-np111py27_nomkl_0 [nomkl]
> > > > simplegeneric: 0.8.1-py27_1
> > > > singledispatch: 3.4.0.3-py27_0
> > > > six: 1.10.0-py27_0
> > > > ssl_match_hostname: 3.4.0.2-py27_1
> > > > terminado: 0.6-py27_0
> > > > tornado: 4.4.1-py27_0
> > > > traitlets: 4.2.2-py27_0
> > > > wcwidth: 0.1.7-py27_0
> > > > zeromq: 4.1.4-0
> > > >
> > > > The following packages will be UPDATED:
> > > >
> > > > conda-env: 2.5.1-py27_0 --> 2.5.2-py27_0
> > > >
> > > > Fetching packages ...
> > > > libgfortran-3. 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:03 93.87 kB/s
> > > > libsodium-1.0. 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:15 79.69 kB/s
> > > > openblas-0.2.1 100% |#############################
> > > > ############################################################
> > > > ##############################| Time: 0:00:23 161.98 kB/s
> > > >
> > > > --
> > > > With Regards.
> > > >
> > > > Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca,
> UK
> > > and
> > > > IISc, Bangalore)
> > > > Associate Professor,
> > > > Department of Pharmaceutical Chemistry,
> > > > School of Pharmacy & Technology Management,
> > > > SVKM's NMIMS,
> > > > Mukesh Patel Technology Park
> > > > Babulde, Bank of Tapi River,
> > > > Mumbai-Agra Road,
> > > > Shirpur, Dist. Dhule -425405
> > > > India.
> > > > Email: vaibhav.dixit.nmims.edu
> > > > www.nmims.edu
> > > >
> > > > http://pharmacy-shirpur.nmims.edu/faculty-and-research/
> > > > faculty/dr-vaibhav-dixit/
> > > >
> > > >
> > > > +91-7709129400.
> > > > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > > >
> > > > Please consider the environment before printing this e-mail
> > > > _______________________________________________
> > > > 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.
>
> Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK and
> IISc, Bangalore)
> Associate Professor,
> Department of Pharmaceutical Chemistry,
> School of Pharmacy & Technology Management,
> SVKM's NMIMS,
> Mukesh Patel Technology Park
> Babulde, Bank of Tapi River,
> Mumbai-Agra Road,
> Shirpur, Dist. Dhule -425405
> India.
> Email: vaibhav.dixit.nmims.edu
> www.nmims.edu
>
> http://pharmacy-shirpur.nmims.edu/faculty-and-research/
> faculty/dr-vaibhav-dixit/
>
>
> +91-7709129400.
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
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Received on Fri Aug 12 2016 - 07:00:02 PDT
