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
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Received on Fri Aug 12 2016 - 01:00:02 PDT
