Mr. Jason,
Thank you very much. I followed what you told. I set
environment variable http_proxy. Then give command
$./patch_amber.py --update-tree
Now, 21 bugfixes have been downloaded. Here, something "1 out of 1
hunk failed....." is showing. Ignoring it I wrote in command line as
given in
http://jswails.wikidot.com/installing-amber12-and-ambertools-12
,
$./configure gnu
bash: ./configure: No such file or directory
I am giving what I got after command $./patch_amber.py --update-tree.
Please have a look.
and let me know what I am doing wrong.
$./patch_amber.py --update-tree
Determining patches to download for AmberTools12
Downloading bugfix.1
Downloading bugfix.2
Downloading bugfix.3
Downloading bugfix.4
Downloading bugfix.5
Downloading bugfix.6
Downloading bugfix.7
Downloading bugfix.8
Downloading bugfix.9
Downloading bugfix.10
Downloading bugfix.11
Downloading bugfix.12
Downloading bugfix.13
Downloading bugfix.14
Downloading bugfix.15
Downloading bugfix.16
Downloading bugfix.17
Downloading bugfix.18
Downloading bugfix.19
Downloading bugfix.20
Downloading bugfix.21
Applying AmberTools12 patches
Creating file /home/sanjib/amber12/AmberTools/src/parmed/ParmedTools/exceptions.py
Creating file /home/sanjib/amber12/AmberTools/src/parmed/ParmedTools/gui/_guiactions.py
Creating file /home/sanjib/amber12/AmberTools/src/parmed/chemistry/amber/mask.py
Creating file /home/sanjib/amber12/AmberTools/src/parmed/chemistry/amber/readparm.py
Creating file /home/sanjib/amber12/AmberTools/src/parmed/chemistry/exceptions.py
Error or warning during patching process for
.patches/AmberTools_Unapplied_Patches/bugfix.1:
The text leading up to this was:
--------------------------
|********>Bugfix 1:
|Author: Jason Swails
|
|Date: Apr. 10, 2012
|
|Programs: ParmEd, xParmEd
Description: The Python mask parser didn't work for masks containing wildcards
| (*, ?, and =). This fixes that issue. It also adds a
| deleteDihedral action that can be used to remove
dihedrals so that,
| used with addDihedral, dihedral parameters can be changed (or just
| deleted)
|
|------------------------------------------------------------------------------
|
| AmberTools/src/parmed/ParmedTools/ParmedActions.py | 111 +++++++++++++++++++-
| AmberTools/src/parmed/ParmedTools/exceptions.py | 3 +
| .../src/parmed/ParmedTools/gui/_guiactions.py | 32 ++++++
| AmberTools/src/parmed/chemistry/amber/mask.py | 9 ++-
| AmberTools/src/parmed/chemistry/amber/readparm.py | 33 ++++++
| AmberTools/src/parmed/chemistry/exceptions.py | 3 +
| 6 files changed, 184 insertions(+), 7 deletions(-)
|
|diff --git AmberTools/src/parmed/ParmedTools/ParmedActions.py
AmberTools/src/parmed/ParmedTools/ParmedActions.py
|index 33e1e92..4dd905f 100644
|--- AmberTools/src/parmed/ParmedTools/ParmedActions.py
|+++ AmberTools/src/parmed/ParmedTools/ParmedActions.py
--------------------------
File to patch:
Skip this patch? [y]
6 out of 6 hunks ignored
1 out of 1 hunk FAILED -- saving rejects to file
AmberTools/src/parmed/ParmedTools/exceptions.py.rej
1 out of 1 hunk FAILED -- saving rejects to file
AmberTools/src/parmed/ParmedTools/gui/_guiactions.py.rej
2 out of 2 hunks FAILED -- saving rejects to file
AmberTools/src/parmed/chemistry/amber/mask.py.rej
1 out of 1 hunk FAILED -- saving rejects to file
AmberTools/src/parmed/chemistry/amber/readparm.py.rej
1 out of 1 hunk FAILED -- saving rejects to file
AmberTools/src/parmed/chemistry/exceptions.py.rej
Sanjib
On 8/30/12, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Aug 30, 2012 at 9:17 AM, Sanjib Paul <sanjib88paul.gmail.com>
> wrote:
>
>> Mr. Dac
>> I also downloaded AmberTools12(using the "download
>> AmberTools" link at http://ambermd.org) . It is AmberTools12.tar.bz2.
>> Then I proceed like following:
>> $tar xvjf AmberTools12.tar.bz2.
>> $cd amber12
>> $export AMBERHOME =/home/sanjib/
>> $./patch_amber.py --update-tree
>> Error: No internet access!
>>
>
> What this means is that patch_amber.py tried to contact
> http://ambermd.organd wasn't able to connect within 10 seconds. If
> you know it takes longer
> than that to contact ambermd.org, try:
>
> ./patch_amber.py --update-tree --timeout 20
>
> That will make patch_amber.py wait 20 seconds before giving up.
>
> Another possibility is that you have to connect to the internet via a proxy
> server -- do you know if this is the case? You can set the environment
> variable http_proxy like so:
>
> export http_proxy="http://username:password.proxyserver:port"
>
> In this case, substitute your user name, password, the proxy server
> address, and the port number (typically 800). I've done this, and it
> allows patch_amber.py to connect to ambermd.org and download updates.
>
> But I have internet access. In webpage
>> http://jswails.wikidot.com/installing-amber12-and-ambertools-12 I have
>> seen that patch_locs in patch_amber.py should be changed from
>>
>> patch_locs = ['http://ambermd.org/bugfixes/AmberTools/12.0/',
>> 'http://ambermd.org/bugfixes/12.0/']
>> to
>> patch_locs = ['file:///path/to/mirror/folder/',
>> 'file:///path/to/mirror/folder/']
>> Here I can't understand what should I do? Please help.
>>
>
> This is what you should do if you absolutely *cannot* get patch_amber.py to
> contact ambermd.org to download the bug fixes. (Talk to your network
> administrator for help). However, if it's absolutely impossible, what you
> should do is set up the following folders in your home directory:
>
> bugfixes/AmberTools/12.0
> bugfixes/12.0
>
> Then, download every bug fix for AmberTools 12 (from
> http://ambermd.org/bugfixesat.html) and put them in the
> bugfixes/AmberTools/12.0 directory. If you have Amber 12, do the same
> thing for Amber 12 (but put in the bugfixes/12.0 directory). After doing
> this, you need to change the patch_locs line in patch_amber.py like you
> mentioned above. For example, if your home directory is /home/sanjib, then
> those lines will become
>
> patch_locs = ['file:///home/sanjib/bugfixes/AmberTools/12.0/',
> 'file:///home/sanjib/bugfixes/12.0//']
>
> This will tell patch_amber.py to pull the files from your local filesystem
> instead of the internet. Note, you will also have to comment out the
> portion of the script that checks for internet access:
>
> # Make sure we have internet access, since we'll need it from now on
> try:
> amberhome = urlopen('http://ambermd.org')
> amberhome.close()
> del amberhome
> except IOError, err:
> if 'timed out' in str(err):
> print >> sys.stderr, \
> 'Error: Could not connect to http://ambermd.org in %.2f
> seconds' % (
> opt.timeout)
> else:
> print >> sys.stderr, 'Error: No internet access!'
> sys.exit(1)
>
> This starts around line 828. (To comment it out, put a # at the beginning
> of each line).
>
> HTH,
> 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
>
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Received on Thu Aug 30 2012 - 10:00:03 PDT
